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Funded through the Australian Government’s Commonwealth Environment Research Facilities (CERF) program

21st Century Taxonomy: accelerating research and discovery of Australia’s biodiversity

Final Report – March 2011

Principal Researcher: Judy West

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Core Research Partners Key co-researchers

Australian National Herbarium (ANH) Centre for Plant Biodiversity Research CSIRO Plant Industry

Judy West, Jim Croft

Australian National Wildlife Collection (ANWC) CSIRO Ecosystem Sciences

Leo Joseph

Australian National Insect Collection (ANIC) CSIRO Ecosystem Sciences

John La Salle, David Yeates

Australian Biological Resources Study (ABRS)

Australian National University John Trueman

La Trobe University

Phil Suter

Primary Collaborators and Research Partners

• Curtin University • James Cook University • University of Adelaide • Melbourne University • University of New England • University of Queensland • University of Western Australia • Curtin University of Technology • Queensland Museum • South Australian Museum

• Western Australian Museum • Western Australian Herbarium • Department of Natural Resources, Mines

and Water, Queensland • Department of Primary Industries and

Fisheries, Queensland • Department of Primary Industries, Victoria • Department of Sustainability and

Environment, Victoria • Melbourne Water

CONTENTS

HIGHLIGHTS................................................................................................................................... 4

FINAL REPORT: JUNE 2007 TO MARCH 2011 .......................................................................... 6

Introduction ................................................................................................................. 6

A description and analysis of the progress of the Activity, including the Objectives achieved during the period to which the Report relates .............................................. 7

Achievements against Objectives ............................................................................... 9

A summary of the work undertaken in the Activity period & an analysis of the effectiveness of this work .......................................................................................... 11

MILESTONE 7 ...............................................................................................................................15

APPENDICES

ANTS: TAXONOMIC AND EVOLUTIONARY STUDIES OF A HYPERDIVERSE FAUNA.....19

TAXONOMY OF MAYFLIES AND AQUATIC INVERTEBRATES............................................25

AUSTRALIAN MANGROVE AND SALT MARSH SPECIES ....................................................31

BIODIVERSITY INFORMATION MANAGEMENT FRAMEWORK ...........................................36

AUSTRALIAN INSECT FAMILIES ON THE WEB .....................................................................49

COMMUNICATION AND KNOWLEDGE EXCHANGE..............................................................53

SMALL TERRESTRIAL VERTEBRATES: CLARIFYING TAXONOMIC STATUS .................61

SYSTEMATICS OF ENVIRONMENTAL WEEDS ......................................................................73

EMERGING PRIORITIES / DNA BARCODING FOR TAXONOMY ..........................................79

GENERALISED MOBILE FIELD DATA RECORDING APPLICATION FOR HAND-HELD DEVICE (PDA, SMARTPHONE, NETBOOK, ETC.) ..................................86

DEVELOPING A BENCHMARK INVERTEBRATE GROUP FOR BIODIVERSITY MODELLING......................................................................................................93

3D DIGITAL TYPE COLLECTION FOR AUSTRALIAN SMALL TERRESTRIAL VERTEBRATES...............................................................................................107

CONSERVING AUSTRALIA’S GENETIC DIVERSITY – A SUMMIT .....................................112

TRIN Final Report: June 2007 to March 2011 - 3 -

RAPID ASSESSMENT OF SPECIES BOUNDARIES OF POTENTIAL RARE AND THREATENED PLANT SPECIES.........................................................................101

Highlights Small Terrestrial Vertebrates: clarifying taxonomic status

• Integration of molecular and morphometric datasets reveal high levels of cryptic diversity. This demonstrates the need for a complete review of the Australian mammal and reptile faunas.

• The micro-CT scanner enabled major analytical advances with rapid progress now possible on morphometric and anatomical studies of the smallest and most problematic groups of Australian mammals.

• Transition project- The micro-CTscanner technology enabled the 3D collection of Australian type material from the Natural History Museum in London. This provides accessible legacy material essential for effective taxonomy on small mammals.

Biodiversity Information Management Framework

• Development of tools to improve functionality and delivery of online biodiversity information, such as taxon profile templates and the Linked Lab Book

• Provision of the collaboration platform in the form of the TRIN wiki provided the venue for collaborative projects and social interaction

• Transition- PDA initially developed for field and lab application for vertebrate data, has been enhanced for application to other groups, particularly insects and plants

Ants: Taxonomic and evolutionary studies of a hyperdiverse fauna

• PhD training resulting in two early career researchers with specialised knowledge and skills in taxonomic research of social insects

• The large meat ant group, Iridomyrmex, has been reviewed and a taxonomic treatment published in Zootaxa - this includes 30,000 specimens and images of all species.

Australian Insect Families on the Web

• The Insect Family Keys can be launched from the site What Bug Is That? • The identification tools have been widely tested by University student groups and are proven to be

user friendly. They are also freely available, allowing rapid identification of all insect groups. • The website has been made possible through the collation of a large number of insect images,

information and key data from a range of collaborators and covers the entire fauna of 640 insect families.

Taxonomy of Mayflies and Aquatic Invertebrates

• The identity of more than 50 species of mayflies have been clarified. This has increased the number of described species of Australian mayflies by 30%.

• The application of DNA barcoding techniques has improved the identification and delimitation of species. It has also led to the discovery of cryptic species and the association of adult and larval stages.

• The ECR trained in the project is now a employed by the Consortium for the Barcode Life in Canada Communication and Knowledge Exchange

• Development of a toolkit for product testing, such as identification keys, with users. The toolkit will be published in brief on the web and in the literature in more detail.

• Led the development of a brief outlining the key findings from the experiences and lessons learned in translating research into policy and practice by the CERF program and their knowledge brokers. The findings were delivered to CERF Secretariat to inform planning and implementation of knowledge brokering in NERP and future funded programs.

• Two field days held in Canberra and Cairns, organised for display, interaction and feedback from diverse range of users and research providers.

Systematics of Environmental Weeds

• The research methods have proven highly transferable to other weed problems, evidenced by the application of these methods to other WONS.

• The tools and protocols developed here are universally applicable and provide a rapid method for genetic profiling of other weeds with complex introduction histories.

Australian Mangrove Species • The Mangrove Wiki provides a framework for format and delivery of a comprehensive range of data,

and has potential to be applied to other ecosystems.


• Compilation of species lists, profiles and species interactions will assist the sustainable management of the Australian Mangrove and Saltmarsh Resource as a valuable multi-disciplinary resource that feeds into the Atlas of Living Australia.

DNA Barcoding for Taxonomy • The DNA libraries for a diverse range of organisms have been developed and are available for

comparative purposes in future identification issues • DNA barcoding of grasses identified an incursion of Mexican Feather Grass in Australia, resulting in

plant material being confiscated, and arresting further spread. Genetic Diversity Summit

• Transition - The development of a discussion paper for government and policy makers, with the longer term goal of strategies around conservation of genetic diversity being incorporated into government policy.

Benchmark invertebrate group

• Transition - The taxonomy, phylogenetic relationships and distributional databasing for native dung beetles was investigated. The resulting dataset has created a benchmark group for developing and testing biodiversity modelling methods. The dataset now includes over 100 species distributed across Australia and phylogenetic trees have been generated based on sequences from 300 individuals.

Rapid assessment of species delimitations

• Transition - The application of DNA barcoding and TRIN’s invasive species methodologies and protocols have enabled rapid assessment of genetic variation and taxonomy in an orchid group containing endangered species. Previously this research would have taken years to complete.


Final Report: June 2007 to March 2011

Introduction

Over the past 4 years, TRIN has researched issues around building taxonomic information for environmental benefits. Through exemplar groups it has addressed key gaps in taxonomic knowledge using the latest and best practice methodologies and techniques. TRIN has managed and delivered its research outcomes and biodiversity information using current industry standards and new and effective web-based technology. It has been able to achieve this through creating and maintaining a collaborative national approach aimed at reinvigorating Australian taxonomy.

Among TRIN’s most significant achievements is the professional development of early career researchers (ECRs), the enhancement of taxonomic processes and provision of on-line communication and information delivery mechanisms. This will lead to a greater capacity, and capability, to achieve efficient and effective taxonomic research.

TRIN’s research projects are complete and publications and journal articles have either been published or are pending publication. The application of resources and novel techniques and methodologies to these research areas has seen the successful growth of the taxonomic information base and it has realised impact in areas of research, policy and management.

A variety of outputs including scientific papers, applications for the web, identification tools, and reports to stakeholders and informatics enhancements have been produced. Most of TRIN’s products will be housed and maintained by their ‘owner’ institutions, with minor support remaining from the Biodiversity Informatics team who will manage the TRIN wiki and its component parts (e.g. the Mangrove wiki). TRIN’s products and outcomes are an important resource for endusers, and will continue to be widely and freely available.

The Knowledge Exchange project applied knowledge brokering techniques to better understand the endusers of taxonomic information and the issues involved in fulfilling their needs. A national consultation and product testing initiative has resulted in the development of practical recommendations to aid the generators of taxonomy knowledge in fulfilling users’ information needs. The recommendations and research findings will be written up and released over the next year as part of a continuing PhD project.

The Biodiversity Informatics team has worked closely with researchers and taxonomists to develop a taxonomic framework to deliver research directly to the web. Their work will continue beyond March 2011 in collaboration with the Atlas of Living Australia (ALA). The ALA has a vested interest in the Biodiversity Informatics’ Linked Lab Book, PDA and taxon profile projects, all of which will assist the ALA in the digitization, publication and sharing of online biodiversity data.


A description and analysis of the progress of the Activity, including the Objectives achieved during the period to which the Report relates

TRIN’s integrated portfolio of research and collaboration has resulted in the enhancement of the taxonomic process. TRIN research addressed groups that were either environmentally significant or iconic because they had either not been tackled before or had suffered from a lack of resources. As a consequence, TRIN has been able to close the knowledge gaps in these key taxonomic groups. For example, by using an iterative approach that combined traditional morphological investigations of museum specimens with the rapidly growing power of molecular approaches, the Small Terrestrial Vertebrates project was able to demonstrate previously unsuspected levels of diversity in groups of mammals, reptiles and amphibians. TRIN has developed a variety of tools and methodologies to accelerate the rate of description, documentation and understanding of Australian biodiversity. For example, the hand-held PDA application captures and manages zoological collection and survey data. That is the application enables entry of digital data in the field and subsequent downloading of this data into a specimen database from the field, increasing the operational efficiency and productivity of the collection process. TRIN applied best practice information management standards to deliver a framework for capturing, assembling, analysing and managing taxonomic information that can be easily used or adapted by other organisations such as the ALA. The ALA will incorporate a vast amount of TRIN’s data into its infrastructure, and will take on tools developed by the Biodiversity Informatics team. TRIN’s Knowledge Exchange (KE) project has been instrumental in understanding how to prepare and provide information in a form which meets end user needs. The KE project undertook an extensive study into discovering who the taxonomy information users are, what information they use, and how they use it. The study also considered which factors facilitate or impede practical application of taxonomic knowledge. The findings provide valuable insight into how best to provide information for users and in turn this will ensure more effective uptake. The training of ECRs has improved Australia’s capability in the field of taxonomy. It also provides a legacy to drive accelerated taxonomic research and delivery, as the ECRs will disseminate and apply their acquired skills in modern methods both nationally and internationally. Website The website will continue to function beyond the TRIN funding period. Relevant information will be migrated and stored on the TRIN wiki once the website ceases to function. The website has been TRIN’s port of call for upcoming events, publications and project updates. Steering Committee The Steering Committee met five times during the Activity Period and was instrumental in assisting the TRIN Management Team to identify key issues in the stakeholder arena and provide guidance to TRIN’s directions and priorities. The two SEWPaC members on the Committee provided effective contact within the Department, and were instrumental in the Genetic Diversity Summit receiving traction, and gaining a higher profile for the issues associated with conservation of genetic diversity. The Steering Committee: Professor Andy Beattie - Macquarie University (chair) Mr Gerard Early - SEWPaC Dr Charlie Zammit - SEWPaC Dr Tim Entwisle - Royal Botanic Gardens Sydney Professor Brendan Mackey - Fenner School, ANU Mr Donald Hobern – Atlas of Living Australia Mr Stephen Hunter – DAFF (retired 2009) Management Team The Management Team met monthly for most of the Activity Period. The members took responsibility for day to day management of the activities of the hub. It should be noted that from late 2009 the Principal Investigator for TRIN, Judy West, was seconded to Parks Australia Division of the Department of Sustainability, Environment, Water, Population and Communities


(SEWPaC). It was agreed by the CERF Secretariat that West continue to lead the hub and that no conflict of interest was involved, especially at this later stage of the hub activities. This has continued through to the endpoint of TRIN in March 2011. The Management Team:

• CSIRO Plant Industry/SEWPaC – Judy West • CPBR/CSIRO Plant Industry – Joe Miller (from 2010) • CSIRO Ecosystem Sciences; Australian National Insect Collection – David Yeates and John La

Salle CSIRO Ecosystem Sciences; Australian National Wildlife Collection – Leo Joseph • DEWHA/SEWPaC; Australian National Herbarium – Jim Croft • LaTrobe University – Phil Suter

Annual Research Forums TRIN held an Annual Research Forum in 2008, 2009 and 2010. The Annual Forums provided the opportunity for researchers and officers to exchange ideas in person, present project updates and to participate in the Network’s future planning. A media training session at the 2010 Annual Forum assisted researchers in preparing their key messages for the two TRIN Field Days, and provided useful tips on how to communicate science research. Communications The Knowledge Exchange project ensured a broad range of user communities were identified, scoped and considered. This formed the basis for targeting TRIN’s communication effort. TRIN engaged with users and stakeholders through:

• Biodiversity Forum • Posters • Website • Wiki • Seminars • Field Days • Summary documents • Vodcasts • Media Releases • Enquiries

The two Field Days (held in Canberra, August 2010 and Cairns, December 2010) were a highlight and provided two-way interaction between researchers, developers and scientists and the user community and target audience. The events were highly effective in disseminating TRIN’s achievements and outcomes and created awareness about the myriad of biodiversity products that are available and into which TRIN feeds. The first Field Day was well attended by Department members and initiated the staging of a second Field Day in Northern Australia. TRIN took a ‘no paper’ publications approach, with all communications conducted through online media and targeted to the extensive database of users generated through the knowledge exchange questionnaires and testing phases. Recruitment At least 57 researchers have been involved with TRIN activities, including four ECR’s employed to lead the taxonomic projects and 12 PhD students. Reporting This Final Report covers the entire TRIN Activity Period, providing summary information and outcomes for the duration of the research program. For each project area however, this report includes a project Final Report for the period June 2010 to March 2011.


Achievements against Objectives

A summary of some key project achievements relating to TRIN objectives is provided: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management. The revision of the ant genus Iridomyrmex includes details for some 30,000 specimens, tools for identification and images of all species. This is a comprehensive resource of one of the most widely occurring ant genera in Australia. Molecular dimensions to the project are being prepared for publication. The expansion of the PDA field data application to a greater range of organisms (beyond vertebrates), platforms (other mobile devices e.g. iPhones, iPads, Tablets, Smartphones), operating systems (beyond Windows Mobile OS), and data collection environments (lab as well as field) will greatly influence biological collecting processes beyond the TRIN network and will enhance data management and availability of information. The weeds work and data analysis provided a scientific basis for actions by weed managers and a new geographic focus for biocontrol discovery efforts. The first key to adult Australian Mayfly genera since the mid-1950s was updated in both dichotomous and electronic formats, and made available via the TRIN Wiki.

Accelerate the rate of description, documentation and understanding of Australian biodiversity, using an integrated approach for capturing, assembling, analysing and managing taxonomic information. The integration of mobile data capture technologies (PDA field data application) with collection management databases not only ensures accuracy, but also accelerates the rate of entry of taxonomic data into these databases, and thus their availability to taxonomy and other user-communities for analysis, research, policy-making etc. The use of DNA barcoding techniques has improved the ability to identify and delimit species, discover cryptic species, and associate adult and larval stages (for e.g. Australian Mayflies). A paper was published advocating integrating data for species delimitation. The use of electronic journals such as Zootaxa means descriptions have been published at a faster rate. Ensure seamless access to biodiversity data and taxonomic information by applying a best practice information management and delivery framework. The Australian Mangrove and Saltmarsh Resource is developing into a one-stop-shop for mangrove and saltmarsh information. The system allows for the capture of all information available on mangrove and saltmarsh biodiversity, including interactions between species. Information and images from the What Bug Is That? Insect Family Key website are input into BIOLINK, allowing them to be exposed on the web and used by the keys as needed, or other web based biodiversity outreach projects such as the Atlas of Living Australia.

Ensure information is provided in a form which meets end user needs, and ensure uptake of the product. The LUCID key to Australian rodents was tested in several contexts and refined to make it more effective and relevant to users, as were all other TRIN developed keys.


Weed information was delivered in collaboration with major end users and communications with Weeds of National Significance (WONS) coordinators ensured rapid uptake. Phylogeographic modelling requires both phylogenetic trees and databased spatial series of the species in a given group. Few groups satisfy both requirements and by progressing a benchmark invertebrate group (dung beetles) we serve their needs. Provide a legacy to drive accelerated taxonomic research and delivery. Effective, open source, free, generic mobile data capture technologies (e.g. PDA field data application) will facilitate a wider range of users and use-cases and produce a user-community actively involved in the enhancement and adaptation of the software for other research and data-capture purposes. The tools developed by the weeds project provide a universally applicable and rapid method for the genetic profiling of other weeds with complex introduction histories. The active education of end users in the capability that was developed encouraged the uptake of the work. The 3D digital type collection (of small vertebrates) represents a significant legacy; a collection of Australian type material in Australia, which would otherwise not have been possible, and which forms a significant component of our biological heritage. The Mangrove and Saltmarsh Resource framework for data format and delivery continues to be refined. The framework and methodology developed in this project has great potential to be used for other ecosystems. The TRIN Genetic Diversity Summit discussion paper highlights the need for genetic taxonomic work to identify and appropriately manage cryptic species and species complexes. The paper provides recommendations on how to incorporate genetic information into conservation decision making and planning; it is being finalised and will be available together with fact sheets for general comment by mid-2011.


A summary of the work undertaken in the Activity period & an analysis of the effectiveness of this work

A summary of work undertaken during June 2010- March 2011 is included in the attached Project Final Reports. A summary of the work undertaken for the entire Activity and its effectiveness is detailed below. TRIN established a vast network of collaborations that was instrumental in achieving faster research outputs. TRIN’s research partners realised benefit in being able to employ specialised staff and take on extra students to enhance their research efforts. Close linkages between TRIN researchers and TRIN stakeholders helped identify relevant issues and research questions, and facilitated a two-way dialogue with policy makers. The TRIN Genetic Diversity Summit was a direct result of engagement with SEWPaC members on the Steering Committee and other senior executives who realised the importance of genetic diversity and supported further investigation in the form of the Summit. The Summit brought together a broad range of participants with a primary interest in improving the management of Australia’s biodiversity. Participants were selected from State and Federal government agencies and Australian research institutions for their experience in conservation genetics, policy and biodiversity management. The aim of the summit was to highlight the importance of genetic information and the types of information it can provide, and to develop ways of incorporating this information into policy and decision making to improve biodiversity outcomes. TRIN developed tools or applied methods that assisted researchers in speeding up aspects of their work, particularly the process of gathering taxonomic information. Tools included the PDA field data application, DNA barcoding techniques (and the association of life stages) and the micro-CT scanner. TRIN developed a suite of new online identification keys (i.e. What Bug is That?, Mangroves, Small Vertebrates, Mayflies) using new technology. The keys were tested through a series of product testing workshops and feedback determined how they could be improved for the user. Identification tools will contribute to natural resource management and environmental impact studies by providing a means for accurate identification. This information, previously not available online, is now freely available on the web, as are the Insect Family Keys. The information generated by TRIN and its linkages with Botanic Gardens, Herbaria and Museums, has enhanced the various National collections and made significant contribution to the taxonomy knowledge base. TRIN’s legacy will remain through its products and data and has been leveraged through its extension to other areas of research (i.e. CERF transition projects, ABRS grant to further the benchmark invertebrate group work to apply to the Bush Blitz initiative and the continued support of the Biodiversity Informatics team by the ALA). TRIN’s legacy will also permeate through the training of ECRs and the direct support of six PhD students (ants 2, weeds 1, knowledge exchange 1, vertebrates 1, mayflies 1), as well as improving skills and expertise of numerous technical assistants. The effectiveness of some of the major contributions made by the TRIN research projects are noted below: Australian Ants The revision of Iridomyrmex resulted in detailed information for 30,000 specimens and images of all species. The revisional treatment is currently ‘in press’ with Zootaxa and will be released and made available to all interested parties. The project has developed the Iridomyrmex key and published valuable products in a shared space, including a vast number of new line illustrations to assist with accurate identifications a direct result of requests from users during the product testing phase. Specimens examined in the revision are now databased, providing additional resources for SEWPaC to use in the Australian National Heritage Assessment Tool. Molecular data on Iridomyrmex are also being readied for publication. Collaboration with specialists around Australia and the inclusion of two 2 PhD students working on Monomorium and Camponotus saw the creation of a highly effective team. One of the PhD students is now working in Romania and has taken the knowledge and skills of Camponotus, a worldwide genus, with her. The outcomes of Camponotus research will be released as a PhD thesis and via scientific journal papers. Mayflies The TRIN Activity period resulted in the reinvigoration of mayfly taxonomy in Australia. The number of known species of the Australian mayflies (Ephemeroptera) described and recognised increased by 30%, a major contribution when compared to all previous work. The dedicated commitment of mayfly researchers enabled this achievement and significantly sped up the publication of species descriptions. Also of note is the sorting of the entire Baetidae family for Australia (the most species rich mayfly family in the world). The mayflies


team held 3 taxonomic workshops and effectively disseminated its findings to a variety of stakeholders including water quality managers, catchment authorities and fly fishermen to name a few. The use of DNA barcoding techniques improved the ability to identify and delimit species, discover cryptic species, and associate adult and larval stages. The ECR trained in the project is now a employed by the Consortium for the Barcode Life in Canada. Knowledge Exchange The inclusion of knowledge brokering methodologies to the TRIN research program was a novel approach. While its findings are not in themselves unique, its method and approach were. The Knowledge Exchange project conducted a rigorous study into how users use taxonomic information by following a regimented qualitative and quantitative analysis process applying the latest guidelines in usability testing. As a result, TRIN will release practical recommendations to aid generators of taxonomy knowledge in fulfilling users’ information needs. It will also provide practical guidelines and realistic examples in an online toolkit for testing taxonomy products as a legacy for taxonomy. Weeds The weeds project showed that it is possible to use sequencing methods with effect in the policy arena. From very early on, powerful and useful information was being generated by the project. For example, research results within the Willows project provided managers with a way to prioritise trees for removal - removal of the top 20% of trees reduces seed production at an infested site by 50%. The work also gave particular weed issues scale, based on connectivity, i.e. there is no point controlling site A, if site B is connected to A. Both A and B should be controlled and often A and B occur in different States. This provided a science basis for a coordinated land management effort. The molecular methods applied in the early phase of the weeds project with Lantana were attained rapidly and were highly transferable to other weed problems. The ongoing success of the project was recognised by weed managers and weed scientists, who actively sought collaboration and in total the project addressed eight WONS. Small Terrestrial Vertebrates Over the course of the Activity Period, numerous molecular and morphometric datasets were integrated to reveal high levels of cryptic diversity in many different groups of vertebrates, including both ecologically generalized and highly specialized groups. Several new vertebrate species are now recognised and many described for the first time. The results demonstrate the need for a complete taxonomic review of the Australian mammal and reptile faunas. They affirm the vulnerability of the many aspects of biological science and environmental management that rest upon what is essentially false presumption for these groups of a solid taxonomic foundation. These techniques used also assisted in the provision of an accurate list of species that occurred in the Canberra region 200 years ago, which facilitated the choice of species for a reintroduction program in the Mulligan’s Flat region, and illustrates the project’s effective input into conservation management. The micro-CT scanner, purchased by CSIRO leveraged through CERF, was the cornerstone of the project’s approach to modernisation and provision of globally accessible morphometric taxonomy and legacy data sets. Through its use, rapid progress is now possible on morphometric and anatomical studies of the smallest, most problematic groups of Australian mammals. The Transition project funded two extended visits to overseas museums by early career researcher, Dr Fred Ford to scan type material of Australian mammals. The ongoing value of this resource for taxonomic research in Australia is immeasurable as ready access to digital type specimens by Australian researchers will negate the need for expensive travel and make integration of type material into taxonomic assessments straightforward. Biodiversity Informatics The Biodiversity Informatics project has provided new ways to deliver and compile taxonomic information, e.g. a Taxon Profile Toolkit which is a streamlined system for semantically enabled structured documents. Products have been developed as open source software, e.g. Wiki-based tools. And members of the team have engaged with national and international biodiversity information management projects to ensure information is provided using best practice methods and applying world recognised standards. The patent for the TRINPIN demonstrates development of innovative, modern solutions to accelerate the capture and delivery of taxonomic data. This innovation enables rapid access and identification of insect specimens held in biological collections world-wide. The expansion of the PDA application to a greater range of organisms (beyond vertebrates), platforms (other mobile devices e.g. iPhones, iPads, Tablets, Smartphones), operating systems (beyond Windows Mobile OS), and data collection environments (lab as well as field) shows the flexibility and relevance of the Biodiversity Informatics tools.


Insect Family Keys The Insect Family Keys project used currently accepted biodiversity informatics ‘best practice’ to convert the electronic keys of several insect orders to fit a web-based system. It also converted paper-based keys to electronic format, and developed new online keys. This is a global first collation of 640 insect families with single entry portal What Bug Is That? enabling identification of Australian insects to family level. This increased capability in insect taxonomy is assisting ecologists, border protection and University students, with tools on the site being used in the current ANU curriculum to teach insect systematics, and also by a University class in the United States. The keys are accessed widely with 2894 visitors to the site reported in the last month (Feb 1st –Mar 3rd, 2011). The site includes a number of approaches to entering the key process, from simple picture galleries for beginners to highly structured keys for more experienced users. These visitors came from over 70 countries or territories. It is a continual process to incorporate new keys onto the site as they become available. Emerging Priorities: DNA Barcoding The barcoding projects generated solid datasets from many diverse organisms including trees, grasses, fish, flies, fungi, termites, ants, beetles and butterflies. For example the focus on grasses has made a substantial impact on the available sequences that can be used to identify grasses. We were able to use DNA barcoding of grasses to identify an incursion of Mexican Feather Grass in Australia. This species is a weed of national significance and our results received considerable publicity and resulted in plant material confiscated by the Department of Primary Industries in Victoria being rapidly identified. Our team’s work was nominated for the DPI David McAlpine Science Award in October 2010. An important highlight is the successful bid by the TRIN Grass Barcoding group to bring the International Barcoding Conference to Australia (Adelaide) in December 2011. This meeting will provide an opportunity to showcase the successful TRIN barcoding projects on the international stage and will provide momentum for furthering this important work in Australia. Mangroves and Saltmarsh Species The Mangrove project and the Mangrove Wiki is a model community information resource. It was undertaken as an example of an ecosystem based resource for biodiversity information collation and delivery that is freely available on the web. The project will provide content to the ALA and includes information from a wide range of sources. The resource houses information on species that occur in a mangrove or saltmarsh ecosystem as well as ecological and human use information. Information can be easily added to and updated as it is based on a wiki platform. The Wiki is being used effectively by experts and enthusiasts to network and collaborate on the web. The amount and diversity of information coming together for mangrove and saltmarsh communities provides the potential for such a resource directory to assist policy development. Rapid assessment of species boundaries In testing the ability for molecular methods to rapidly assess species boundaries this project analysed significantly more (almost 600) than the 200 (Caladenia reticulata) plants it was projected to study. Data was generated using the methods developed through TRIN’s weeds project, which allowed the rapid assessment of genetic variation for a group of closely related species – a task that may take years of research based on morphology alone. Metrics can now be used to determine the extent of gene flow among populations and taxa within the Caladenia reticulata orchid complex. Information will be sent to relevant State and Commonwealth species listing agencies to assist in the threatened plants listing processes. Benchmark invertebrate group All specimens of the native dung beetle genus Lepanus Balthasar (held separately in three major collections) have been sorted and assigned to an improved informal taxonomy ahead of formal species descriptions to be made in the coming year. Over 10,000 geocoded database records have been generated that relate to all 100 species in the genus. The usefulness of older preserved material has been assessed, and a preliminary phylogeny has been generated using sequences obtained from 300 individuals. This data has been instrumental in developing the project to the point that it has been supported by the ABRS Bush Blitz program and has expanded the knowledge base of groups useful for geospatial modelling to include an invertebrate saprovore and an inhabitant of temperate forests. Rainforest Plants Identification and Information System (RFK) – now available on the web This is a long term project with a lifetime of over 40 years of continuous development and publication of five editions, noted for being the most comprehensive identification and information system for Australian tropical rainforest plants. TRIN has been involved in providing assistance with user needs analysis and a necessary


change in the software to ensure future viability and to enable web delivery, leading to significant changes in the look and operation of the system. The TRIN Knowledge Exchange project assisted during its development by running workshops to obtain feedback from users on the content, presentation, packaging and delivery. The workshops enabled recording of detailed and wide-ranging feedback on the new edition from a diverse range of participants, which led to various modifications and enhancements prior to release on the internet in December 2010. The TRIN Biodiversity Informatics project collaborated on the development of the system through processing of imagery, templates and software advice, as part of adapting existing electronic products for regional web applications. A companion product Australian Tropical Rainforest Orchids was also released online in December 2010. Issues While we have identified many achievements over the activity period and highlighted examples of effectiveness for TRIN, it has not been without some difficult issues. Our original aspiration to change the way taxonomists do business met with considerable inertia and was only partially achieved. The anticipated need to make the necessary cultural changes requires persistence and quiet persuasion over time. Even so, activities within TRIN, largely by example, have made significant contribution in this direction, and we have left a lasting legacy that will help to influence further progress in the taxonomic community. TRIN was not without the expected ‘end of research program’ issues. For example, it was necessary for ECRs to seek other employment while projects were still undergoing completion. Many were asking ‘what next?’ and it took prolonged discussion to ensure products and outputs had a home or ‘champion’. The TRIN wiki has played a strong role in facilitating communication between researchers nationally and internationally and has provided a sustainable home for orphan taxonomic and collection-based projects. It is likely the wiki will be taken on by the Atlas of Living Australia (ALA) to form the basis of their electronic communication system. The overlap of NERP changed the focus through 2010 with engagement from the Department at a lower level than in previous years.


MILESTONE 7 7.1 The Final Report is here provided to the Department. 7.2 Delivery of the remaining aspects of the Emerging Priorities Project being the following work:

a) the remainder of barcodes for each group The project has now successfully completed the DNA sequencing portion of the barcoding project. This project sequenced a diversity of organisms: trees, grasses, termites, fish, rust, ants, flies, beetles and butterflies. There were several subprojects that attempted a defined number of barcodes with replication of more than one sample per species and usually more than one gene per sample. Overall we were able to sample more species than we proposed in the original project. However it was not possible to sequence as many individuals per species in many cases. This primarily was due to difficulties of obtaining material appropriate for sequencing. The slight shortfall was offset by sequencing more species and in many cases, such as the grasses and trees, sequencing more genes. Overall the data generated in this CERF project contributes to the development of DNA libraries and is already being used in many ways, including barcode identification and evolutionary relationships among organisms. There is building momentum in Australia for DNA barcoding much of which emanated from this project.

b) the case studies: Invasive grass identification to limit incursion We were able to use DNA barcoding of grasses to identify an incursion of Mexican Feather Grass (Nassella tenuissima) in Australia. This species is a weed of national significance and the outcomes from the barcoding project enabled rapid identification and resulted in plant material being confiscated by the Department of Primary Industries in Victoria. Our team’s work received considerable publicity and was nominated for the DPI David McAlpine Science Award in October 2010. Biodiversity Analysis of Tropical Rainforest Floras We barcoded the vascular flora of over 200 0.1Ha plots (over 500 species) and used these data to improve estimates of plant diversity patterns in Australian tropical rainforests. Until now, analysis of biodiversity across entire floras has been limited to calculating taxonomic (e.g. species) richness. The barcode dataset we have compiled allows phylogenetic diversity – which measures evolutionary distinctiveness and is calculated by summing branch lengths on molecular phylogenies - to be determined for the first time. In preliminary analyses we have been able to determine the relationship between taxonomic diversity and phylogenetic diversity and have shown that for the well-known Wet Tropics flora they are tightly correlated (Fig 1). Mapping phylogenetic diversity and taxonomic diversity (as measured by genus richness) reinforces the close relationship between these two biodiversity metrics (Fig 2). These results confirm that taxonomic richness is a good proxy for phylogenetic diversity for the vascular flora of the Wet Tropics, and will enable more sophisticated biodiversity conservation planning in this World Heritage area. Whether these results can be generalised to other biomes remains to be tested. Analyses across all plants in a biome such as this are only possible with standardised data such as is offered by DNA barcoding approaches.


Fig 1. Approximately linear relationship between taxonomic richness (at genus level) and phylogenetic diversity in vascular plants demonstrated using data from nearly 200 plots across the Wet Tropics.

Fig. 2. Location of sampling plots and graphical comparison of phylogenetic diversity and taxonomic richness for vascular plants in the Wet Tropics.


APPENDICES –

Final Reports for individual projects

Project:

Ants: Taxonomic and Evolutionary Studies of a Hyperdiverse Fauna

Final Report

Ants: Taxonomic and Evolutionary Studies of a Hyperdiverse Fauna

FINAL REPORT

Context Information

Project Title Ants: Taxonomic and Evolutionary Studies of a Hyperdiverse Fauna

Duration of the entire project July 2007 to March 2011

Dates for which this progress report applies May 2010 to March 2011

Project Team Project Leader Dr Steven O. Shattuck

Host Organisation Australian National Insect Collection, CSIRO Sustainable Ecosystems

Project Team Member Role in

Project Organisation Expertise in

Project FTE

Dr Steven O. Shattuck

Project Leader

Australian National Insect Collection, CSIRO Sustainable Ecosystems

Ant systematist 0.2

Dr Alan Andersen Collaborator CSIRO Sustainable Ecosystems, Darwin

Ant ecologist 0.1

Prof. Andy Austin Collaborator University of Adelaide, Adelaide Invertebrate systematist

0.05

Dr Chris Burwell Collaborator Queensland Museum, Brisbane Invertebrate systematist

0.1

Prof. Jonathan Majer

Collaborator Curtin University of Technology, Perth

Ant ecologist 0.05

Dr Brian Heterick ECR Curtin University of Technology, Perth

Ant taxonomist 1.0

Ms Robyn Meier Technical Officer

CSIRO Sustainable Ecosystems Specimen processing and databasing

1.0

Ms Ellen Schlüns PhD student

James Cook University, Townsville

Camponotus phylogeny

1.0

Ms Kathryn Sparks PhD student

University of Adelaide, Adelaide Monomorium systematics

1.0

Ants: Taxonomic and Evolutionary Studies of a Hyperdiverse Fauna – Final Report: June 2007 to March 2011 - 19 -

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: As TRIN Ants wraps up we have focussed on completing projects to ensure we maximinse outputs and complete all milestones. The revision of Iridomyrmex has been completed and is currently in press with Zootaxa. We anticipate that it will appear in the next few weeks. At that time details for some 30,000 specimens and images of all species will be released and made available to all interested parties. Work on Camponotus has been completed and Ellen Schlüns is currently preparing her PhD thesis based on this research. It is anticipated that a series of papers will be produced over the coming year. Preliminary results of her work were presented at the IUSSI conference in Copenhagen in August, 2010 (see below). Work on Monomorium has been delayed. This is because Kate Sparks, the leader of these studies, has postponed her PhD program while taking a 6-month maternity leave of absence. She will thus complete her project towards the end of 2011 rather than near the beginning of the year as originally proposed. Kate presented a talk at the Copenhagen IUSSI meeting before beginning her leave. Finally, considerable progress has been made on the molecular studies of Iridomyrmex species although this work is ongoing. COI data has been collected from essentially all samples and two nuclear genes are currently being processed. It is anticipated that data collection will be completed over the next few months and a manuscript completed by the end of 2011. Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

A revision of the ant genus Calyptomyrmex has been published while the revision of Iridomyrmex is in press. Digital information from these studies is available in a range of formats to meet the needs of a broad range of user groups.

Accelerate the rate of description, documentation and understanding of Australian biodiversity, using an integrated approach for capturing, assembling, analysing and managing taxonomic information.

We continue to make incremental improvements in the processes used in taxonomic research. While we seek revolutionary change through investigations in remote microscopy and automated identification systems, these remain in the research domain and haven’t yet moved into production. Thus we continue to make evolutionary change while awaiting revolutionary change.

Ensure seamless access to biodiversity data and taxonomic information by applying a best practice information management and delivery framework.

All information generated by this project is being made electronically available using accepted international data-sharing standards. We are constantly monitoring changes in these standards and update our reporting procedures as required.

Ensure information is provided in a form which meets end user needs, and ensure uptake of the product.

See above item.


Provide a legacy to drive accelerated taxonomic research and delivery.

Training of ECRs. Greater understanding of some major ant groups in Australia has made information widely available.

Milestones Progress against outcomes and deliverables (outputs), including any milestones, for the period; activities to achieve these; associated completion dates. An explanation of any delays that have occurred, including the reasons for those delays and action proposed to take to address the delay and the expected effects (if any) the delay will have on the project (including subsequent Milestones and the overall completion of the project) (use milestones listed in the Work Plan):

Milestone Completion Date

Details – what did you achieve and what did you produce

14. Field work May 2010 All fieldwork has been completed.

15. Databasing specimens May 2010 All specimens involved in these studies have been databased and are available electronically.

16. Collection of phenotypic data (morphology) May 2010 Morphological studies have been completed.

17. Collection of genotypic data (molecular). May 2010

The collection of molecular data is complete for Camponotus and Monomorium and is ongoing for Iridomyrmex.

18. Development of taxon concepts (genera and species)

May 2010 Completed for Iridomyrmex, ongoing for Monomorium.

19. Preparation of datasets for taxon interactive keys

May 2010 Complete.

20. Analysis of data (parsimony, ML, Bayesian)

On-going Complete for Camponotus, ongoing for Iridomyrmex and Monomorium.

21. Development of phylogenetic hypotheses

On-going Complete for Camponotus, ongoing for Iridomyrmex and Monomorium.

22. Assembly of taxonomic descriptions May 2010 Complete for Iridomyrmex, ongoing for

Monomorium.

24. Preparation of manuscripts On-going Numerous manuscripts have been completed

while several are in preparation.

32. Annual taxonomic planning meeting May 2010 Done


Project Collaboration Progress in working with target areas of the Department of Environment, Water, Heritage and the Arts or other Commonwealth Government Departments or State agencies: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Linkages with Outcomes Progress in identifying/linking with target areas of the Department of Environment, Water, Heritage and the Arts or the Australian Government for project outcomes: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Issues Any issues associated with the project: There has been a delay in publishing the Iridomyrmex manuscript and key which is now In Press, and the PhD student working on Monomorium is on maternity leave which will delay release of that paper. Highlights Two highlights from the last period (May 10 to end): A total of 6 talks were given by staff associated with TRIN Ants at the International Union for the Study of Social Insect meeting in Copenhagen in August, 2010. Chris Burwell and Steve Shattuck were instructors on the Ant Course held at the Danum Valley Conservation Centre, Sabah, Malaysia, in August, 2010. This is an annual 2-week course with 37 students and 10 instructors. Both Chris and Steve gave several talks during the course. Steve Shattuck visited the Museum of Comparative Zoology (Harvard University) to image types of taxa not represented in Australian collections. This was a very successful visit with numerous images prepared.


Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: The following presentations were given at the IUSSI Conference in Copenhagen, August 2010. Australian monomorium ants: morphological plasticity or unfathomable diversity? Kathryn S. Sparks, Andrew D. Austin, Alan N. Andersen, Steve O. Shattuck, Stephen C. Donnellan

Evolution of nesting habitats and metapleural glands in ants Ellen A Schlüns, Simon KA Robson, Andrew D Austin, Ross H Crozier Regional processes as drivers of ant community structure Alan N. Andersen, Ricardo I. Campos Colony structure in three species of the ant genus myrmecia Zeng-Qiang Qian, Simon K. A. Robson, Ellen A. Schlüns, Helge Schlüns, Birgit C. Schlick-Steiner, Florian M. Steiner, Ross H. Crozier Problem solving in complex systems: collective chain formation and gap bridging in the weaver ant oecophylla smaragdina Simon Robson, Benjamin Kelly, Jose Halloy, Jean-Louis Deneubourg, Ross Crozier Evolution of immunity-related genes in myrmeciine ants Helge Schlüns, Y Ching Crozier, Ross H Crozier The following papers where published during the period of this report: Crozier, R.H., Newey, P.S., Schlüns, E.A., Robson, S.K.A. 2010. A masterpiece of evolution – Oecophylla weaver ants (Hymenoptera: Formicidae). Myrmecological News 13:57-71.

Dominiak, B.C., Worsley, P., Gillespie, P.S., Löcker, H., Kerr, M., Shattuck, S. 2010. Search for Red Imported Fire Ant Solenopsis invicta Buren in New South Wales from 2004-2006. Plant Protection Quarterly 25:15-18.

LaPolla, J.S., Brady, S.G., Shattuck, S. 2010. Designation of a neotype for Paratrechina currens Motschoulsky, 1863. Notulae Naturae 481:1-2.

LaPolla, J.S., Brady, S.G., Shattuck, S. 2010. Phylogeny and taxonomy of the Prenolepis genus-group of ants (Hymenoptera: Formicidae). Systematic Entomology 35:118-131.

Schlüns, E.A., Wegener, B.J., Robson, S.K.A. 2011. Genetic polyethism and nest building in the weaver ant Oecophylla smaragdina (FABRICIUS, 1775) (Hymenoptera: Formicidae). Myrmecological News 15:7-11.

Shattuck, S.O. 2010. Book review: HETERICK, B.E. 2009: A guide to the ants of south-western Australia. Myrmecological News 13:114.

Shattuck, S.O. 2011. Revision of the ant genus Calyptomyrmex (Hymenoptera: Formicidae) in South-east Asia and Oceania. Zootaxa 2743:1-26.


Project:


Final Report


FINAL REPORT

Context Information

Project Title Taxonomy of Mayflies and Aquatic Invertebrates Duration of the entire project July 2007 to March 2011


Project Team Project Leader Dr Phillip Suter

Host Organisation La Trobe University

Project Team Member Role in Project Organisation Expertise in Project FTE

Dr Phillip Suter Project Leader La Trobe University Aquatic Macroinvertebrate Taxonomist

0.2

Dr Jeff Webb ECR La Trobe University Aquatic Entomologist 1.0

Mr John Hawking PhD student La Trobe University Aquatic Entomologist 1.0

Julia Mynott Casual Technician

La Trobe University Technical Assistance 1.0

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work:

Collection of fresh material from northern Qld, Northern Territory, and alpine regions of New SouthWales and Victoria completed. Fresh material for nearly all species of Australian Baetidae, Coloburiscidae, and Nesamelitidae (Ephemeroptera) and Australian Crambidae (Lepidoptera) have now been obtained and DNA extractions and amplification of COI have been performed on most. Larvae and adults associations have been completed through the use of DNA barcoding for the Baetidae (>50 species), over 25 species of Crambidae (Lepidoptera: Acentroptinae), 5 species of Coloburiscidae (Ephemeroptera) and 18 species of Caenidae (Ephemeroptera). The use of molecular tools has greatly increased the speed and ease in which life stage associations can be made. The molecular studies have also highlighted the presence of numerous cryptic species and areas of endemism such as Tasmania and the high altitude areas of the Alps. Presented 3 papers at Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Manuscripts revising the Baetidae and Coloburiscidae are nearing completion. Morphological descriptions of over 50 species are virtually completed for publication. Three papers have been published on the Australian Baetidae and two are near completion. Dichotomous and electronic (LUCID) keys to species of Baetidae have been prepared and updated after the workshop at the second taxonomic workshop held in February 2010. Dichotomous and electronic (LUCID) keys to adult mayfly genera have been prepared and updated since the taxonomic workshop. The keys are currently on the TRIN wiki and the baetid key is to be published by the Museum of Victoria. Data was provided for the electronic (LUCID) Family key.

Taxonomy of Mayflies and Aquatic Invertebrates – Final Report: June 2007 to March 2011 - 25 -

Attended the TRIN ‘Field Day' on 31 August in Canberra to showcase and raise awareness of the various TRIN tools developed over the past 3 years. This was well attended and all participants were impressed with the keys and the advances made through the TRIN project. The fact that in three years the aquatic project had increased the number of known species of the Australian mayflies (Ephemeroptera) by 30% is a clear indication of the project success. Papers and publications include:

Webb JM and Suter PJ (2010) Easing the burden – DNA barcoding, the taxonomic impediment, and the systematics of aquatic insects. Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Mynott JH, Webb JM and Suter PJ (2010) Testing the species validity and larval associations of the alpine stoneflies, Riekoperla (Plecoptera: Gripopterygidae). Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Shackelton M, Webb JM and Suter PJ (2010) Using genetic data to associate life stages of homometabolous insects. Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Webb JM, Suter PJ (2010a) Identification of larvae of Australian Baetidae. Museum of Victoria Science Reports 15, 1-39. Webb JM, Suter PJ (2010b) Revalidation and redescription of Bungona illiesi (Lugo-Ortiz & McCafferty) (Ephemeroptera: Baetidae) from Australia, based on mitochondrial and morphological evidence. Zootaxa 2481, 37-51. Webb JM, Suter PJ (2010c) New combinations for the Australian species of Baetis (Ephemeroptera: Baetidae), with a new synonym. Zootaxa 2668, 63-65.

The third TRIN taxonomy workshop was held from the 8-9th February 2011 and included keys to the Australian Leptophlebiid genera (Ephemeroptera), Australian species of the stonefly genus Riekoperla (Plecoptera), the fairy shrimps of Australia (Crustacea) and the non chironomid aquatic dipterans (Diptera). Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives:

Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

Using a combination of morphological and molecular characters, the generic status of the Australian Baetidae has been clarified with >50 species associated and descriptions are being prepared. This has increased the number of described species of Australian mayflies by 30%. Keys to species available on the Wiki in both dichotomous and electronic formats. An honours project has clarified the taxonomy of the stonefly genus Riekoperla using both molecular and morphological characteristics. The student received an H1 honours result and has a postgraduate scholarship to revise the taxonomy and phylogeny of the Australian Gripopterygidae (Plecoptera). The generic status of the lepidopteran Family Crambidae has been determined and the revision is being written up as a PhD thesis to be completed at the end of 2011. The first key to adult Australian Mayfly genera since the mid 1950s was updated in both dichotomous and electronic formats.



The use of DNA barcoding techniques has improved our ability to identify and delimit species, discover cryptic species, and associate adult and larval stages. However, the morphological descriptions of the large number of new species recognised still takes considerable time to prepare. By using electronic journal Zootaxa descriptions have been published at a faster rate.


Biolink has continued to be used for managing specimen data. Keys for the adults of the genera of mayflies and species of all genera of Baetidae (Cloeon still in review) have been placed on the TRIN wiki and presented at the Taxonomic workshop. Keys presented at the TRIN “Field Day” in Canberra.


http://wiki.trin.org.au/Mayflies/TaxonomicWorkshops


Keys made available at multiple sites including the Museum of Victoria (Linked to the TRIN website) and the TRIN wiki. Manuscripts published in Zootaxa. Two honours and 3 postgraduate students currently continuing taxonomic research directly as an outcome from this project




7. Development of mayfly web products

Dec 2009

Dichotomous and LUCID keys prepared and presented at second Taxonomic Workshop in Feb 2010. Keys on TRIN wiki. Three dichotomous keys published on Museum of Victoria’s website, URL link via TRIN website. Adult Family key completed. Publications in Zootaxa available.

14. Field work Sept 2009 – ongoing Field work completed.

15. Databasing specimens ongoing Continuing to database fresh material and historical specimens

16. Collection of phenotypic data (morphology) Dec 2009

Completed for Baetidae to enable key preparation. Preparation of descriptions of new species for publication completed.

17. Collection of genotypic data (molecular) June 2010

Completed for Baetidae except for a small number of nuclear loci for phylogeny ofCentroptilum and the generic phylogeny.

18. Development of taxon concepts (genera and species) Dec 2009 Completed for all Baetidae


http://wiki.trin.org.au/Mayflies/TaxonomicWorkshops

19. Preparation of datasets for taxon interactive keys Dec 2010 Completed. Interactive keys on TRIN wiki and

presented at the second taxonomic workshop.

20. Analysis of data (parsimony, ML, Bayesian) ongoing Completed. All generic data analysed and formed

the basis of the generic keys.

21. Development of phylogenetic hypotheses Aug 2009 Completed for Australian Baetidae and Caenidae

22. Assembly of taxonomic descriptions ongoing

Descriptions of new species of Baetidae and Coloburicidae completed and manuscripts almost ready for Zootaxa.

24. Preparation of manuscripts Aug 2009 –

ongoing

Two manuscript published in Zootaxa. Descriptions of new species of Baetidae and Coloburicidae completed.


Specifics of What

Museum Victoria, Richard Marchant Publication of keys produced by taxonomic workshops

Dr Faye Christidis, JCU John Dean, EPA Victoria

Collaboration initiated to revise the leptophlebiid genus Jappa.

Jean-Luc Gattolliat, Musee de Zoologie Lausanne

Collaboration on phylogeny of Baetidae and Caenidae

Linkages to Outcomes Progress in identifying/linking with target areas of the Department of Environment, Water, Heritage and the Arts or the Australian Government for project outcomes: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Dr Richard Marchant, Museum Victoria Publication of keys from Taxonomic Workshop held in Albury-Wodonga

Issues Any issues associated with the project: New Technician appointed part time in early 2010 and took up full-time position in May 2010 after completion of honours thesis. Early career researcher left project in November to take up employment with The Barcoding for Life project at the University of Quelph, Canada. The project continues with further postgraduate and honours projects.


Highlights Two highlights from the last period (May 10 to end):

• Increase of 30% of described Australian mayflies as a product of this project.

• Publication of significant taxonomic problems associated with Australian mayflies involving synonymys which have only been possible to solve using molecular and morphological techniques.

Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Three papers published on the Australian Baetidae and two are near completion. Dichotomous and electronic (LUCID) keys to species of Baetidae and to adult mayfly genera have been prepared and updated. The keys are currently on the TRIN wiki and the baetid key is to be published by the Museum of Victoria. Attended the TRIN ‘Field Day' on 31 August in Canberra to showcase and raise awareness of the various TRIN tools developed over the past 3 years. This was well attended and all participants were impressed with the keys and the advances made through the TRIN project. The fact that in three years the aquatic project had increased the number of known species of the Australian mayflies (Ephemeroptera) by 30% is a clear indication of the project success. Papers and publications include:

Webb JM and Suter PJ (2010) Easing the burden – DNA barcoding, the taxonomic impediment, and the systematics of aquatic insects. Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Mynott JH, Webb JM and Suter PJ (2010) Testing the species validity and larval associations of the alpine stoneflies, Riekoperla (Plecoptera: Gripopterygidae). Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Shackelton M, Webb JM and Suter PJ (2010) Using genetic data to associate life stages of homometabolous insects. Australian Entomological Society 41st Annual General Meeting and Scientific Conference Perth WA Sept 26-30 2010. Webb JM, Suter PJ (2010a) Identification of larvae of Australian Baetidae. Museum of Victoria Science Reports 15, 1-39. Webb JM, Suter PJ (2010b) Revalidation and redescription of Bungona illiesi (Lugo-Ortiz & McCafferty) (Ephemeroptera: Baetidae) from Australia, based on mitochondrial and morphological evidence. Zootaxa 2481, 37-51. Webb JM, Suter PJ (2010c) New combinations for the Australian species of Baetis (Ephemeroptera: Baetidae), with a new synonym. Zootaxa 2668, 63-65.

The third TRIN taxonomy workshop was held from the 8-9th February 2011


Project:

Australian Mangrove and Salt Marsh Species

Final Report

Australian Mangrove and Salt Marsh Species

FINAL REPORT

Context Information

Project Title Australian Mangrove and Salt Marsh Species: a resource of mangrove and salt marsh biodiversity for the Australian region



Project Team Project Leader Brendan Lepschi

Host Organisation Centre for Plant Biodiversity Research

Project Team Member Role in Project Organisation Expertise in Project FTE

Brendan Lepschi Project Leader Centre for Plant Biodiversity Research

Plant Taxonomist / ANH Curator

0.1

Emma Clifton Project Officer Centre for Plant Biodiversity Research

Project coordinator 0.5 (CSIRO funding)

Judy West TRIN Leader Centre for Plant Biodiversity Research

TRIN Liaison Plant Systematist

Nominal

Jim Croft Project Mentor Centre for Plant Biodiversity Research

Biodiversity Informatics Nominal

John Busby Project Mentor Centre for Plant Biodiversity Research

Plant ecologist / Informatics

0.3 (Volunteer)

Murray Fagg Science Communication and Outreach

Centre for Plant Biodiversity Research

Image Resources Nominal

Collaborators Member Role in Project Organisation Expertise in Project FTE

Chris Cargill Collaborator Curator of Cryptogam Herbarium at ANBG

Cryptogam taxonomist Nominal

Heino Lepp Collaborator ANBG associate Lichen and fungal expert

Nominal

Australian Mangrove and Salt Marsh Species – Final Report: June 2007 to March 2011 - 31 -

Leo Joseph Collaborator Australian National Wildlife Collection, CSE

Biogeography and ecology of Australian birds

Nominal

Angela Frost Collaborator Australian National Wildlife Collection, CSE

Biogeography and ecology of Australian birds

Nominal

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: Adding capacity to the mangrove and saltmarsh wiki:

o Addition of semantic links, allowing species pages to be connected together through biological interactions and mapping these interactions through a dynamic food web.

o Addition of 25 locality profile pages with localised species lists and Google maps. For example: http://wiki.trin.org.au/Mangroves/Moreton_Bay

Addition of over 100 images of plants and animals. Over 1000 additions to species lists including plants, mammals, reptiles, fish, insects,

crustaceans, molluscs, annelids, nematodes, flatworms and lichens. Addition of 500 ‘stub’ species profiles with information including nomenclature, locality,

location, links and biological interactions. Addition of 20 comprehensive species profiles for High and Medium fidelity mangrove and

saltmarsh plant species. Attended and demonstrated at TRIN field days in Canberra and Cairns. Currently undertaking project with CPBR interns to record pollination interactions between

mangrove plants, birds and insects. Currently liaising with numerous experts and institutions to provide comprehensive species lists

and profiles for vertebrates, molluscs, fungi and lichens, insects, and crustaceans. Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

The continued compilation of species lists, profiles and species interactions will help identify knowledge gaps. The development of semantic links between species will improve understanding of interactions between organisms in mangrove and saltmarsh ecosystems.


Continuing to bring together information in the form of species profiles, species lists, images and interactive keys, on a vulnerable and important ecological community. This will assist with sustainable management and highlight areas needed for further research.


The Australian Mangrove and Saltmarsh Resource is developing into a one-stop-shop for mangrove and saltmarsh information. We are implementing a system that allows for the capture of all information available on mangrove and saltmarsh biodiversity, including interactions between species.



Information collated for the Australian Mangrove and Saltmarsh species project continues to be made available on the TRIN wiki. Collated information continues to be modified to ensure its accuracy, add to detail and improve delivery format.


The projects framework for data format and delivery continues to be refined. The framework and methodology developed in this project could be used for other ecosystems.

Milestones Progress against outcomes and deliverables (outputs), including any milestones, for the period; activities to achieve these; associated completion dates. An explanation of any delays that have occurred, including the reasons for those delays and action proposed to take to address the delay and the expected effects (if any) the delay will have on the project (including subsequent Milestones and the overall completion of the project) (use milestones listed in the Work Plan): Milestone Completion

Date Details – what did you achieve and what did you produce

16. Collection of phenotypic data (morphology) June 2010 The development of Mangrove and Saltmarsh

species lists continues in all major groups.

22. Assembly of taxonomic descriptions Throughout

Addition of 20 comprehensive species profiles for H and M fidelity mangrove and saltmarsh plant species.

Liaise with other collections, institutions and experts Throughout

Over 100 images obtained from individuals. Species list of over 250 lichens obtained from ANBG. Currently liaising with numerous experts and institutions to provide comprehensive species lists and profiles for vertebrates, molluscs, fungi and lichens, insects, and crustaceans. Liaising with various experts on the taxonomy of various organisms, such as molluscs and crustaceans.


Specifics of What

Curators of CSIRO biodiversity collections • Australian Plant Image Index (Murray Fagg) • Australian National Fish Collection (Peter Last) • Australian National Herbarium (Brendan Lepschi,

Chris Cargill, Heino Lepp)

Mangrove and saltmarsh species information, images and multimedia.


• Australian National Insect Collection (David Yeates) • Australian National Wildlife Collection (Leo Joseph) State and Territory Museums and Herbaria Mangrove and saltmarsh species

information Members of informal network of mangrove experts Mangrove and saltmarsh species

information Related networks (OzEstuaries) Mangrove and saltmarsh species

information Linkages to Outcomes Progress in identifying/linking with target areas of the Department of Environment, Water, Heritage and the Arts or the Australian Government for project outcomes: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Atlas of Living Australia, Mr Donald Hobern Creation of species level content.

DEWHA through ABRS and ERIN Access to mangrove information (for use in State of Environment reporting and reporting into international conventions, e.g. Convention on Biological Diversity, Ramsar).

Biological Collections (including Museum Victoria, Australian Museum, Western Australian Museum, Orange Scientific Collections Unit and others)

A national mangrove information capability will provide context for their jurisdiction-specific activities.

Issues Any issues associated with the project: Engaging mangrove and saltmarsh researchers to voluntarily contribute their data, information, time and expertise continues to be a challenge. We are continuing to search for additional funding to help facilitate the collaboration of other professionals in the field. Highlights Two highlights from the last period (May 10 to end): • Addition of semantic links, allowing species pages to be connected together through biological

interactions and mapping these interactions through a dynamic food web. • Significantly expanding the content of the project to include species lists and profiles for

vertebrates and invertebrates. Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: TRIN field days presented an excellent opportunity to showcase the resource and receive valuable feedback.


Project:


Final Report


FINAL REPORT

Context Information

Project Title Biodiversity Information Management Framework

Duration of the entire project July 2007 to May 2011


Project Team Project Leader Jim Croft

Host Organisation Collections and Information management, Australian National Herbarium Centre for Plant Biodiversity Research (CPBR)

Project Team Member Role in Project Organisation Expertise in

Project FTE

Jim Croft Project Leader Centre for Plant Biodiversity Research

Leader ANH Informatics

0.1

Margaret Cawsey Project Manager CSE, Gungahlin Biodiversity Informatics

0.6

Garry Jolley-Rogers

Researcher Centre for Plant Biodiversity Research

Informatics and systems analysis

1.0

Paul Alexander


Biodiversity Informatics

1.0

Paul Harvey



1.0

Nunzio Knerr Spatial database manager


Spatial analysis 0.1

Brendan Lepschi ANH Curator CSIRO Plant Industry Taxonomist 0.1

Bronwyn Collins Technical officer Centre for Plant Biodiversity Research

APNI Databaser 0.1

David Yeates Project Leader, Insect Families Key

CSIRO Sustainable Ecosystems

Insect Systematist 0.1

Greg Whitbread IBIS manager Centre for Plant Biodiversity Research


0.1

Jo Palmer Technical officer Centre for Plant Biodiversity Research

ANH Collection Manager

0.1

Biodiversity Information Management Framework – Final Report: June 2007 to March 2011 - 36 -

John Hook Software manager


Database Applications

0.1

Maggie Nightingale Content Manager Centre for Plant Biodiversity Research

ANHSIR Database 0.1

Kirsten Cowley Technical officer Centre for Plant Biodiversity Research

APNI Database 0.1

Murray Fagg APII manager Centre for Plant Biodiversity Research

Curator of Images 0.1

Steve Shattuck Project Leader, Ants


Informatics 0.1

Judy West Researcher Centre for Plant Biodiversity Research

Taxonomist Nominal

Siobhan Duffy Web developer Centre for Plant Biodiversity Research

LUCID and Web Applications

Nominal

Temi Varhese Programmer Centre for Plant Biodiversity Research

TRIN Wiki consolidation

0.25

Asad Sultan Programmer Centre for Plant Biodiversity Research

TRIN Wiki consolidation

0.15

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: 1. Employment of programmers to work on the Wiki/Taxon Profile Toolkit 2. Maintenance and enhancement of existing systems e.g. Wiki, Key Server, hosts and domain 3. Documentation on the taxonomic workflow 4. Application of collaborative technologies to the taxonomic workflow and publication 5. Prototype solutions to identified bottlenecks in the practice of taxonomy e.g. TRINpin, Linked

Lab Book, tool for manipulating and visualising of phylogenies 6. Specification of a meta taxon profile (a data model for arbitrary taxonomic information); the

Wallace Core 7. Collaboration with the ALA in the development of a Taxon Profile Toolkit; a tool for creation of

well-structured taxon profiles 8. Collaboration with the ALA on mobilising data from existing systems into the Wiki using the

Taxon Profile Toolkit 9. Communication with taxonomists in hub projects to document informatics requirements 10. Communication with immediate stake holders (principally with Government agencies) 11. Communication with national and international collections and taxonomy bodies and projects 12. Short-term informatics requirements for taxonomic projects 13. Develop priorities and work out strategies to address the medium- and long-term informatics

requirements for taxonomic projects 14. Conceptualisation of information framework 15. Identification of standards and technologies 16. Migration of existing electronic products to the web


17. Assist with interactive keys to insect families and rainforest key; publish The Rainforest Key and The Orchid Rainforest Key online (Dec 2010), EUCLID online (Jul 2011) and The Pea Key on CD (Feb 2011), promote all keys

18. Implementation of Australian National Wildlife Collection specimen database data service to the ALA via OZCAM

19. Web services for ANHSIR, APNI and APII 20. Enhancements to ANIC web services (BioLink) within the Ants Project 21. Participation in ALA, TDWG and GBIF working groups 22. Participation in HISCOM and FCIG 23. Participation in conferences such as the CERF conference and TDWG 2010 24. Assist with the organisation of the TRIN Field Days and participate on the days Contribution to Hub Outcomes A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

o Consolidating an information infrastructure, which enables secure and convenient web-based collaboration, accessible to taxonomists anywhere in the world, consolidation involved:

• working with CSIRO IM&T to ensure domain architecture and wiki services function appropriately

• contributing to the Foswiki code base, to ensure that the developing features continue to be tailored for taxonomic collaboration and the capture and delivery of biodiversity information

• Developing tools to capture, manipulate, visualise and deliver taxonomic information

• Implementing highly scalable, structured data storage and retrieval within the wiki with a MongoDB (i.e. no-SQL) datastore

• Implementing fuzzy natural language searching for disambiguation and discovery (through SOLR)

o Building the Wallace Core - a meta taxon profile framework which

• encodes common meaning to profile elements, giving a means to translate and link information about taxa across disciplines; and

• provides an exchange vocabulary for information about taxa

o Building a Taxon Profile Toolkit; a streamlined system for building semantically enabled structured taxon profiles, using linked data and allowing the capture of taxon profile information for repurposing for multiple uses and users.

o Engaging with national and international biodiversity information management projects



o Consolidating an information infrastructure, which enables secure and convenient web-based collaboration, accessible to taxonomists anywhere in the world, consolidation involved:




• Implementing highly scalable, structured data storage and retrieval within the wiki with a MongoDB (i.e. no-SQL) datastore

• Implementing fuzzy natural language searching for disambiguation and discovery (through SOLR)

o Documenting the taxonomic workflow to identify and target solutions to data capture and management issues

o Building the Wallace Core - a meta profile framework which

• has tools to cross-walk and collate information across profiles from different sources


• provides an exchange standard for information about taxa

o Building and publishing online as open source software; Wiki-based tools to deliver and compile taxonomic information i.e. a Taxon Profile Toolkit; a streamlined system for semantically enabled structured documents

o Presenting the Taxon Profile Toolkit in a form that can be understood and curated by domain experts such as Taxonomists:

• Guiding the creation of profiles in the collaborative Taxon Profile Toolkit framework

• Providing tools for the import of taxon profiles into the Wiki Taxon Profile Toolkit

• Providing a space for hosting existing profile data in a form that can be easily revised

• Assisting taxonomists to use the toolkit to research, capture and publish their data

o Providing taxon profile data from the Taxon Profile Toolkit in a form that can be consumed by web services from partners (e.g. the ALA and IBIS)


o Engaging with the Atlas of Living Australia to incorporate the Taxon Profile Toolkit and Linked Lab Book strategies into the Australian biodiversity informatics framework

o TRINpin • Managing the IP and patent application for

the TRINpin • Experimental testing and writing a paper

describing the uses and longevity of the TRINpin

o Linked Lab Book • Specifying and plugging in wiki

augmentation • Liaising with partners who will test the

linked lab book • Data migration and modelling

o Collaborative Phylowidget (tool for interacting with phylogenetic trees)

• Implemented in the wiki o Implementing the ANWC database data service to

the ALA via OZCAM o Implementing semantic and multimedia data

management strategies that can be generalised to other organisations

• WebDAV • WikiDraw • Semantic Links Plugin • Extending the Semantic Links Plugin to

include a citation capability o Engaging with international biodiversity information

management projects in matters of standards and protocols


o Engaging with international biodiversity information management projects in matters of standards and protocols

o Promoting, implementing and contributing to shared and common communications protocols

o Engaging with user communities and helping them capture and publish their information

o Documentation of user needs and use-cases o Developing online interactive identification keys

• Australian Tropical Rainforest Plants Key (Edition 6), Australian Tropical Rainforest Orchids, The Pea Key, EUCLID

o Building the capacity to represent linked data


o Communicating with TDWG, HISCOM, FCIG, ALA, ABRS to ensure nationally consistent and interoperable standards and approach to species descriptive data

o Consolidating an information infrastructure, which enables secure and convenient web-based


collaboration, accessible to taxonomists anywhere in the world, consolidation involved:




• Implementing MongoDB within the wiki platform to provide scalable, structured data storage and retrieval

• Implementing fuzzy natural language searching for disambiguation and discovery (SOLR)

o Consulting with taxonomists to provide solutions to user needs, e.g. with:

• the Mangroves project; forms to build taxon profiles, use linked data sourced directly from APNI, AVH, and APII, and embed interactive keys into wiki documents

• Establishment of hosting for unfunded non-TRIN projects include Thysanoptera, Sea slugs, sponges, marine invertebrates and for the Herbarium Curators Group etc.

o Building and publishing online as open source software; Wiki-based tools to deliver and compile taxonomic information i.e. a Taxon Profile Toolkit; a streamlined system for semantically enabled structured documents

o Developing interactive identification keys and making them available on the web.








o Conceptual and actual development of Information architecture

o Building the Wallace Core - a meta profile framework which

• has tools to cross-walk and collate information across profiles from different sources



• provides an exchange standard for information about taxa

o Taxon profile toolkit and support for communities to use it

o Building and publishing online as open source software: Wiki-based tools to describe and define the framework, providing new ways to deliver and compile taxonomic information i.e. a Taxon Profile Toolkit; a streamlined system for semantically enabled structured documents







o Documenting the taxonomic workflow to identify and target solutions to data capture and management issues

o Documenting information storage requirements o Continuing the project; strategic alliance with the

ALA to carry the project through to the next phase; arrangement has been reached to extend the Biodiversity Informatics Project for another 15 months

o Development of interactive identification keys available on web





2. Model the taxonomic process

31 May 2011

o Documenting on the Wiki the translation of old workflow into modern workflow methodologies

• Trial runs of pinning workflows for the TRINpin

• Specification of testing regimes • Draft of the TRINpin paper

o Identify modern technologies relevant to each step • IP and patent application management for the

TRINpin • Collaboration with Queensland Museum

researchers in the use of the Taxon Profile Toolkit as a research tool for Sponge taxonomy

3. Build and populate internet information framework

31 May 2011

o Publish online as open source software: Wiki-based tools to describe and define the framework.

o Providing new ways to deliver and compile taxonomic information i.e. a Taxon Profile Toolkit; a streamlined system for semantically enabled structured documents

• Phylowidget; visualising phyogenies and getting responses from Identify Life to get back a key to that clade.

• WikiDraw; a tool for collaborative image annotation

o Mobilise data from existing systems into the Wiki • Import molecular and specimen Acacia data

from MS Access into the Linked Lab Book • Converting the mangroves profiles from static

pages into the Taxon Profile Toolkit structured documents

• Converting the sponges data from Excel to Taxon Profile Toolkit structured documents

• Converting Latin Glossary from MS Access to an online searchable resource

o Prototype solutions to identified bottlenecks e.g. Linked Lab Book – building linkages to Galaxy and other tools for genetic analysis; TRINpin, the Taxon Profile Toolkit itself; incorporation of semantic links for documentation of taxa and their relationships; tools for including citations in taxon pages;


implementing of MX for the documentation, development and testing of operational taxonomic units i.e. taxonomic research.

o Monitor and encourage Wiki use, adapting the system to make it more user-friendly; document the application and the process

• Improved the Foswiki WYSIWYG editor • implemented semantic links • Implemented user-definable rich, structured

document object data models • Engaged with active projects and continually

adapting and developing solutions to meet their needs e.g. Mangroves, Sponges, Latin Glossary

o Promote shared and common communications protocols e.g. Taxon Profile Toolkit, use of name services from Australian Nomenclators, common GUIDS for names, building the facility to use standard biodiversity-related resources (e.g. APNI, AFD etc) on the web as they become available

o Identify and apply technologies and strategies for the needs of the taxonomic projects; Collaborating with IM&T, ARCS for long term storage, Key server, ENTkey web presence, collaboration tools e.g. EVO, Google Wave, Twitter; EVO for remote microscopy

o Development and documentation of a multimedia strategy for taxonomy; remote microscopy, ARCS and IM&T and both failed hopelessly, working with the ALA on developing a storage strategy, all hopeless.

o ANWC database data service to the ALA via OZCAM commenced as of September 2010. The strategy of on-line delivery to OZCAM via TAPIR has been abandoned by OZCAM as the process is too slow. The current strategy is to continue delivery via csv files until a new strategy has been devised. We will work with CSIRO IM&T to “automate” delivery of csv files once a OZCAM develops a protocol for managing this approach.

4. Adapt existing electronic products for regional web applications

31 May 2011

o Maintained keys on the key server; installed updates, interacted with CBIT on application enhancement, bug testing, etc.

o Assisted with the development of the rainforest key for web and DVD - online release launched Dec 2010 in conjunction with the Cairns TRIN Field Day, companion key to Australian Tropical Rainforest Orchids also released online Dec 2011; publish on DVD Feb-Mar 2011

o Publish EUCLID online (Jul 2011) and The Pea Key on CD (Feb 2011), promote keys

o Communicated with TDWG, HISCOM, FCIG to ensure nationally consistent and interoperable standards and approach to species descriptive data


o Represented TRIN in the development of existing software products and contribute enhancements

5. Development of interactive key to insect families

6. Development of interactive key to plant genera

31 May 2011

o Maintained infrastructure for on-line key to insect families

o Maintained keys on the key server; install updates, interact with CBIT on application enhancement, bug testing, etc.

o Because of the lack of external funding, there has been no progress on the Plant Genera Key.

o Communicated with TDWG, HISCOM, FCIG to ensure nationally consistent and interoperable approach to species descriptive data


Specifics of What

DEWHA (in particular ERIN, SPRAT, ANHAT) DAFF, BRS, ABRS, CSIRO, ANIC, ANWC CHAH, CHAFC, CHAEC

o Alert to potential and impact of species based data

o Alert to specific resources of species based information

o Identification of unmet needs for species based information

DEWHA (in particular ERIN, SPRAT, ANHAT) DAFF, BRS CHAH, CHAFC, CHAEC HISCOM, FCIG EDIT, GBIF, TDWG, ALA Universities

o Alert to potential and impact of species based data

o Alert to specific resources of species based information

o Identification of unmet needs for species based information

o Identification of new ways of communication species level data

o Ensure adoption of current information standards and procedures

CHAH, CHAFC, CHAEC HISCOM, FCIG EDIT, GBIF, TDWG, ALA Universities

o Alert to new resources for species based information

o Development of new ways of collection managing and delivering species level information

o Adoption of current biodiversity information management standards and protocols



Specifics of What

DEWHA (in particular ERIN, SPRAT, ANHAT) DAFF, BRS, ABRS, CSIRO, ANIC, ANWC CHAH, CHAFC, CHAEC

o Foundation species level data for environmental policy making, decision making and natural resource management

o Two way communication and advice on policy directions

o Information resources for biodiversity policy development and natural resource program management

DEWHA (in particular ERIN, SPRAT, ANHAT) DAFF, BRS CHAH, CHAFC, CHAEC HISCOM, FCIG EDIT, GBIF, TDWG, ALA Universities

o Targeted species level information for conservation and natural resource management

o Ensure adoption of current information standards and procedures

o Community validation of species level information

CHAH, CHAFC, CHAEC HISCOM, FCIG EDIT, GBIF, TDWG, ALA Universities

o Access to raw data materials for research o Information management tools for research o Access to research results o Communications infrastructure o Adoption of current information standards and

procedures Issues Any issues associated with the project: • Sporadic and inconsistent support from CSIRO IM&T has seriously impeded our ability to meet

milestones and support our collaborators. • Delays with lawyers are holding up the patent for the TRINpin • Lack of clarity with intellectual property and partnering e.g. 6 week delay in getting an invoice for

necessary work on MongoDB because CSIRO protocols cannot handle open source software (CSIRO Legal was most helpful)

• Lack of engagement from the TRIN taxonomic projects meant we didn’t get the feedback we required and thus the TRIN taxonomic projects did not reap the benefits they could have realised; all significant advances for our project are coming through collaboration with non-TRIN projects. This was exacerbated by a late start to the Biodiversity Informatics Project, due to the difficulty attracting suitably qualified staff


Highlights Two highlights from the last period (May 10 to end): • A strategic alliance with the Atlas of Living Australia to carry the project through to the next

phase; arrangement has been reached to extend the Biodiversity Informatics Project for another 15 months which clearly demonstrates the relevance of our work within the Australian Biodiversity Informatics framework and community.

• The innovative development of the Wiki within the semantic web context, including the Taxon Profile Toolkit; It now includes many innovative capabilities that currently do not exist in any equivalent project with the promise of great potential as partners start to use it in the coming year

• Collaboration with the Mangrove Project with regard to implementation of linked data e.g. with APNI; extension of this approach to similar capability

• The patent for the TRINPIN; demonstrates that we have developed innovative, modern solutions to accelerate the capture and delivery of taxonomic data

Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: • Paul Harvey contributed significantly to the development of the open-source Foswiki code-

base, with enduring benefit for the future • Jim Croft, Margaret Cawsey and Greg Whitbread attended the International TDWG conference

in Woods Hole, USA in September-October 2010. • Margaret Cawsey, Garry Jolley-Rogers, Greg Whitbread, Paul Alexander and Paul Harvey

attended the specify workshop in October 2010. • Paul Harvey and Garry Jolley-Rogers demonstrated The Taxon Profile Toolkit and Laurie’s

Latin Glossary at the TRIN field day in Canberra 31/08/2010. • Paul Alexander demonstrated the Wallace Core meta taxon profile at the TRIN field day in

Canberra 31/08/2010. • Margaret Cawsey presented and demonstrated the use of PDAs and other technologies for

mobile capture of field data at the TRIN field days in Canberra 31/08/2010 and Cairns 9/12/2010.

• Siobhan Duffy demonstrated interactive identification keys at the TRIN field days in Canberra 31/08/2010 and Cairns 9/12/2010

• Margaret presented at and Garry Jolley-Rogers attended the CERF conference in May 2010. • Margaret Cawsey attended the FCIG and joint FCIG/CHAFC meeting in Tasmania November

2010 as FCIG representative of the Australian National Wildlife Collection. • Greg Whitbread and Jim Croft attended the HISCOM and joint HISCOM/CHAH meeting in New

Zealand in November 2010. • Paul Harvey presented at the Linux Conference Australia in Brisbane in January 2011.


Project:


Final Report


FINAL REPORT

Context Information

Project Title Australian Insect Families on the Web



Project Team Project Leader Dr David Yeates

Host Organisation CSIRO Sustainable Ecosystems


Project Organisation Expertise in Project FTE

Dr David Yeates Project Leader


Insect systematist 0.2

Dr Steven Shattuck

Researcher CSIRO Sustainable Ecosystems

Informatics 0.1

Dr John Trueman Researcher Australian National University

Informatics 0.1

Ms Fiona Spier Technical officer


Insect technician 0.6 (Nov 08-Jun 10)

Ms Dena Paris Technical Officer


Web-based skills 0.6 (March 09 – June 10)

Ms Anne Hastings Technical Officer


Graphic design and illustrator

0.3 (Mar 09 – June 10)

Dr Adam Slipinski Researcher CSIRO Sustainable Ecosystems

Insect systematist 0.1

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: Activities focussed in the following four areas during this period: 1) finalising the keys themselves, determining the final form of the last few keys to be developed (route or matrix). 2) Continuing to add content, mostly references to literature and images. 3) Working with users to further enhance the design to improve the user experience. 4) Working with the TRIN Knowledge Management team to roll out user testing workshops to undergraduate students and other user groups.

Australian insect families on the web – Final Report: June 2007 to March 2011 - 49 -

Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

Continuing to streamline the operation of the keys.


These keys will allow for the rapid identification of the fauna, and this is of use as a stage in determining whether taxa are new to science or already described.


Information and images are input into BIOLINK, allowing them to be exposed on the web and used by the keys as needed, or other web based biodiversity outreach projects such as the Atlas of Living Australia.


User testing workshops continually test user interactions with the product and suggest areas of modification to enhance the user experience.


Initiatives to ensure the continued maintenance and upgrade of the servers that deploy the keys are underway.




5.1 Development of interactive key to insect families

May 2010

User testing conducted both informally and formally. Technical specifications modified in order to modify keys under Milestone 5.2. Some technical specifications are limiting within Lucid, and need to be modified by CBIT.


May 2010

User testing conducted both informally and formally. User experience around the overall look and feel of the front page modified, also modified the way that users access the various order-level keys.


June 2010

Continue to ensure that information resources generated in the project are stored securely, and can be made available for other data harvesters such as the Atlas of Living Australia.


Project Collaboration

Progress in working with target areas of the Department of Environment, Water, Heritage and the Arts or other Commonwealth Government Departments or State agencies: Specifics of Who (Department, Section, Contact Person)

Specifics of What

DEWHWA, ABRS, Helen Thompson Further development of key content, and development of keys at genus and species level

John Trueman, (Australian National University), Andy Austin (Univ Adelaide), Lyn Cook and Shaun Winterton, (University of Queensland), Donald Hobern (ALA), Gerry Cassis (Univ NSW).

Testing of web site and keys in undergraduate and other teaching

Entomological taxonomists developing digital or web based keys that could be deployed on the web site

Forming partnerships with these researchers to store and deploy keys on Hub web site

Linkages with Outcomes

Progress in identifying/linking with target areas of the Department of Environment, Water, Heritage and the Arts or the Australian Government for project outcomes: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Issues

Any issues associated with the project: Consistent user feedback is the need for more content around glossaries and vocabularies for all orders, as provided for the Diptera key. Highlights Two highlights from the last period (May 10 to end): • User testing workshops held with ANU undergraduates provided valuable feedback and

assisted in improving the process of key creation • Display of key at TRIN Field days in Canberra Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Display of key at TRIN Field days in Canberra


Project:

Communication and Knowledge Exchange

Final Report

Communication and Knowledge Exchange

FINAL REPORT

Context Information

Project Title Communication and Knowledge Exchange



Project Team Project Leader Dr Judy West

Host Organisation Centre for Plant Biodiversity Research, CSIRO Plant Industry



Judy West Project leader

CPBR CSIRO Plant Industry

Networking and liaison 0.2

Helen Eddy-Costa

Knowledge Broker


Linking research with stakeholders 1.0

Kathryn Farry

Communication Officer


Communicating outcomes and outreach activities

1.0

Murray Fagg Botanical Information & Outreach

CPBR CSIRO Botanical Interpretation 0.1

Siobhan Duffy

Graphic designer


Graphic / web design 0.3

Bronwyn Bergersen

Project Officer


Administrative duties Assistance with administering end user questionnaire and focus groups

0.5 to December 2010

Communication and Knowledge Exchange – Final Report: June 2007 to March 2011 - 53 -

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: Communication Strategy The C&KE team met regularly, with the Communication Strategy being a main point of focus at these meetings. Throughout TRIN, the strategy centred on interacting with endusers, and providing information online, e.g. interactive ID keys, newsletters, Wiki interaction etc. The two TRIN Field Days reflected this Strategy as it invited stakeholders and endusers to experience TRIN products in a hands-on environment, showed where they will be of benefit. TRIN’s Summary documents, ”Accelerating discovery…’, Issues 1 & 2 brings together the main findings outcomes, protocols and products. Issue 1 has been distributed to endusers and relevant audiences, and Issue 2 will be released April 2011. Communication Action Plan The Knowledge Exchange component of the plan focussed on stakeholder liaison and feedback on output requirements: continuation of analysis of questionnaire and focus group data and report on findings; development of concept and outline of eight manuscripts for publication in peer reviewed journals. Completion of testing and feedback workshops with stakeholders, including university undergraduate students, for assessing the outputs developed, testing identification keys from 5 TRIN projects as well as a wiki resource, including key testing at ANU with undergraduate entomology students. Test reports published on TRIN Knowledge Exchange wiki The Communication Action Plan was developed and refined of plan as informed by stakeholder liaison and feedback from the KE project- which partly led to the Field Days being held. We continue to raise awareness of TRIN research outcomes through our events and online publications. We evaluated the success of the plan through short questionnaires available at the Field Days. Events: August 2010 – First TRIN Interactive Field Day held at the ANBG Canberra; all TRIN projects and products had a booth display and/or presented a short talk; also had booths for non-TRIN biodiversity online tools and resources; successful day, positive feedback; the range of participants/institutions attending included DEWHA/SEWPac, ACT Govt, ANBG, ABRS, National Parks, DAFF, private and environmental consultants. September 2010 – assisted with the Tree of Trees outdoor display and promotion in collaboration with the CPBR, ALA and ANBG October 2010 – TRIN represented at the ANBG Open Day, highlighting the small terrestrial vertebrate reintroduction work done at Mulligan’s Flat; identification tools also on display December 2010 – Second TRIN Interactive Field Day held at JCU in Cairns; northern focus that included TRIN products on display and talks, as well as a range of identification keys and other biodiversity online tools and resources; participants were end-users who got a lot out of the day and would like to see more of these kinds of events; the range of participants/institutions attending included Australian Tropical Herbarium, JCU, Cairns Regional Council, DERM, GHD, Girringun Aboriginal Corporation, Johnstone Ecological Society, Qld Parks and Wildlife Service, Skyrail, TNQ TAFE; Wet Tropics Management Authority, private and environmental consultants; great success; tied it in with the web launch of the Australian Tropical Rainforest Plants – Edition 6 and the Australian Tropical Rainforest Orchids keys.


Website Content was updated after each Progress Report iteration Evaluation of website usage: website updates and maintenance of content including project updates, TRIN Field Day photo galleries, news and events, products and publications; website stats. Monitor online enquiries: online enquiries monitored, record kept and actioned, 12 enquiries from July 2010 Wikis Maintenance of content of TRIN, Knowledge Exchange and Communication project wikis. Support biodiversity informatics project with wiki use across TRIN by using it for project updates. Knowledge Exchange project discussion forums initiated on the wiki, participants of product workshops invited to comment on preliminary reports of identification tool usability testing workshops. Mechanisms for users to provide feedback on key usability set up for on-line identification tools. Toolkit for testing identification keys with users published on the TRIN Knowledge Exchange wiki. Meetings and Reports Assisted with organisation of Steering Committee, Management Team meetings Assisted with collation and preparation of Progress Reports to CERF secretariat. Prepared Final Report and assessment of TRIN performance Report on findings of Knowledge Exchange project under development, in the form of journal publications. Eight manuscripts outlined and will be written up and submitted for publication in peer reviewed journals between February 2011 and February 2012, as part of a PhD by publication through the Australian National University. Prepare TRIN Summary document, Accelerating discovery: the products, outcomes and protocols from the Taxonomy Research & Information Network to assist with identifying and preserving Australia’s biodiversity. July 2010 – Issue 1; project based; compiled and published on TRIN website as an interactive PDF, included Vodcast and workshop video April 2011 – Issue 2; objective based; compiled and published on TRIN website as interactive PDF. Collaboration With other CERF Hub Knowledge Brokers: collective reflection on experiences in knowledge brokering for research in environmental management and development of a brief to CERF to outline the key findings from the experiences and lessons learned of translation of research into policy and practice, including knowledge brokering, by Commonwealth Environment Research Facilities (CERF) Hubs and their knowledge brokers and to better inform the planning, implementation, maintenance and evaluation of knowledge brokering, in the National Environmental Research Program (NERP) and future SEWPaC funded programs. With users of taxonomic information to identify usability issues in identification tools for further development/improvement of TRIN products Potential collaboration initiated with the Atlas of Living Australia, the National Focal Point for the Global Taxonomy Initiative (located in SEWPaC) and the Australian Biological Resource Study (ABRS). With professional communications units in participant institutions to maintain consistency of external communication across TRIN e.g. ALA.



The product testing and feedback workshops, including the TRIN Interactive Field Days, conveyed the work we have done in those areas that are addressing gaps in knowledge.


Communication activities have marketed TRIN and its products to relevant users and stakeholders. This has helped illustrate the new methods and ways of conducting taxonomic research, and has done so in an integrated manner with the taxonomic projects.


Ensuring a broad range of user communities are identified, scoped and considered. Feedback to the projects from the testing workshops and the Field Days assists in the delivery framework of TRIN products.


Conduct testing and feedback workshops with stakeholders, for assessing the outputs, implementation finalised July 2010, testing identification keys from 5 TRIN projects as well as a product of the MTSRF Project, Status and Trends of Biodiversity and Ecosystem Services - The Rainforest Plant Key. Set up discussion and feedback forums linked to online published TRIN identification tools for ongoing feedback, particularly for those users who were not able to participate in the workshops. Ongoing analysis of data collected by questionnaire and focus groups and product testing workshops yielding insights into how users use taxonomic information to do identifications and associations of experience of users and frequency of use of taxonomic information with perceived importance of types of information and delivery of information. Results presented to the TRIN Field Day in Cairns December 2010 and discussed with the ALA, ABRS and National Focal Point of the Global Taxonomy Initiative. Involvement of TRIN taxonomic researchers in testing and feedback workshops provided an environment for researchers and users to learn from each other: needs, problems, barriers to uptake of research outputs, solutions.


Outcomes of the Knowledge Exchange project re user community needs and priorities will inform the Australian taxonomic community for future use. Toolkit for testing identification keys with users developed and published on the TRIN Knowledge Exchange wiki as a legacy for future key developers to use as a resource.


Milestones Progress against outcomes and deliverables (outputs), including any milestones, for the period; activities to achieve these; associated completion dates. An explanation of any delays that have occurred, including the reasons for those delays and action proposed to take to address the delay and the expected effects (if any) the delay will have on the project (including subsequent Milestones and the overall completion of the project) (use milestones listed in the Work Plan): Milestone Completion


3. Build and populate internet information framework

Ongoing

Management of content of web site and wikis (TRIN and projects), including project updates.

30. Integration strategy Ongoing Action plan for remaining six months focused on delivering final outcomes, e.g. summary document, field days etc.

34. Stakeholder liaison

Activities completed February 2011, Publication to be completed February 2012

Stakeholder liaison and feedback on output requirements; enduser/researcher workshops - continued analysis of questionnaire and focus group data; eight methods and results papers framed and outlined with a view to submitting all manuscripts for publication in peer reviewed journals by February 2012 as part of a PhD by publication through the Australian National University - testing prototype taxonomy products – workshops completed July 2010, reports published on the TRIN Knowledge Exchange wiki, toolkit for testing identification keys with users published on the TRIN Knowledge Exchange wiki. - evaluation of taxonomy products – rollout of taxonomy products implemented with TRIN field days in August and December 2010 Monitor online enquiries, record, forward for action

35. University Undergraduate Courses

Workshops combined with enduser/researcher workshops. University students participated in workshops at the Centre for Plant Biodiversity Research (botany summer interns from various universities), ANU (third year entomology students), University of Adelaide, Curtain University, University of New South Wales, Macquarie University, University of Melbourne (entomology students), James Cook University (botany and vertebrate students). University teaching and technical support staff at universities exposed to TRIN products through these testing workshops.



Specifics of What

State and Commonwealth departments of environment and agriculture, NRMs and CMAs

• Liaison and feedback on output requirements for conservation and biosecurity – user product testing workshops and TRIN field days.

CERF secretariat and other CERF Hubs • With other CERF Hub Knowledge Brokers: collective reflection on experiences in knowledge brokering for research in environmental management and development of a brief to CERF to outline the key findings from the experiences and lessons learned of translation of research into policy and practice, including knowledge brokering, by Commonwealth Environment Research Facilities (CERF) Hubs and their knowledge brokers and to better inform the planning, implementation, maintenance and evaluation of knowledge brokering, in the National Environmental Research Program (NERP) and future SEWPaC funded programs. • With CERF secretariat: follow up meetings to discuss further KB brief and how it may assist with informing planning of knowledge brokering for NERP.

• CERF liaison was included in the planning and location of the 2nd field day.


Specifics of What

State and Commonwealth departments of environment and agriculture, NRMs and CMAs

• Developing relationships with these target areas as users of taxonomy information, through product testing workshops and TRIN field days.

SEWPaC: CERF Secretariat • Regular feedback and conversations with Secretariat on Communication Plan and Activities

SEWPaC: Australian Biological Resources Study (ABRS) and National Focal Point for the Global Taxonomy Initiative located in the International Biodiversity Policy and Ecosystem Science Section, Parks Australia,

• Initiated discussion on end user needs assessment relating to taxonomic and biodiversity information that has been undertaken as part of TRIN, as a useful reference in both the Australian context in reporting to the CBD, as well as in the GTI context.

Atlas of Living Australia (ALA) • Exploring ideas and opportunities for integrating findings from the Knowledge Exchange Project into the work of the ALA: http://www.ala.org.au/.


http://www.ala.org.au/

Identified particularly the value of user feedback to development of the Identify Life Project: http://www.identifylife.org/.

Issues Any issues associated with the project: • During the course of TRIN, the Knowledge Exchange Project evolved from one of only

servicing the taxonomic research projects to additionally being a research project in its own right, with the taxonomic research projects as the case studies. The Knowledge Broker enrolled in a PhD with the Australian National University, Centre for the Public Awareness of Science on a part-time basis in August 2009. At the fulfilment of her contract with TRIN, the Knowledge Broker will continue the PhD by publication on a full-time basis from February 2011 with a view to submitting all manuscripts for publication by February 2012. The PhD candidature will be supported by an ANU Scholarship and hosted by a CSIRO Studentship.

• Project Officer took another job December 2010 before end of contract • Delay in delivering reports, journal articles, final keys from some projects made it difficult to

‘market’ or create a media splash on single outcomes- field days worked better due to lack of maturity of some research

Highlights Two highlights from the last period (May 10 to end): • Submission of brief to CERF December 2010; a collaborative document on behalf of all CERF

Hub Knowledge Brokers: CERF Hub: Knowledge Brokering for Translation of Research into Policy and Practice - Lessons Learned

• The 2 TRIN Field Days provided the opportunity to interact with the ‘client’ and policy makers (in Canberra) and provided a variety of endusers and stakeholders a well-received overview of TRIN’s achievements and capability (in Cairns).

Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: • Presentation of results of Knowledge Exchange project to TRIN field day Cairns December

2010 and seeking of feedback from field day participants • Submission of abstract for an oral presentation to the XV111 International Botanical Congress

(IBC2011) November 2010: A “model process” for understanding the needs of users of taxonomic information.

• Submission of brief to CERF December 2010; a collaborative document on behalf of all CERF Hub Knowledge Brokers: CERF Hub: Knowledge Brokering for Translation of Research into Policy and Practice - Lessons Learned

• Toolkit for testing identification keys with users published on the TRIN Knowledge Exchange wiki


http://www.identifylife.org/

Project:

Small Terrestrial Vertebrates: Clarifying Taxonomic Status

Final Report

Small Terrestrial Vertebrates: Clarifying Taxonomic Status

FINAL REPORT

Context Information

Project Title Small Terrestrial Vertebrates: Clarifying Taxonomic Status



Project Team Project Leader Dr Leo Joseph

Host Organisation Australian National Wildlife Collection, CSIRO Sustainable Ecosystems (CSE)



Dr Leo Joseph Project Leader

Australian National Wildlife Collection, CSE

Director 0.1

Dr Ken Aplin Scientific Leader


Morphological Taxonomy of Australian Mammals and Reptiles

0.5

Dr Fred Ford ECR Australian National Wildlife Collection, CSE

Rodent Evolution and Systematics

1.0

Mr Robert Palmer Curatorial Assistance


Collection Manager 0.5

Prof Stephen Donnellan

Research Scientist

Evolutionary Biology Unit, South Australian Museum

Molecular Analysis 0.1

Dr Terry Bertozzi Research Scientist

Evolutionary Biology Unit, South Australian Museum

Molecular Analysis 0.1

Ms Leanne Wheaton

Researcher Evolutionary Biology Unit, South Australian Museum

Molecular Technical Assistance

0.8

Prof Alan Cooper Research Scientist

Australian Centre for Ancient DNA, University of Adelaide

Ancient DNA Analysis 0.1

Dr Kyle Armstrong Molecular Technician

Australian Centre for Ancient DNA, University of Adelaide

Ancient DNA Technical Analysis

0.8

Ms Vicki Thomson PhD Student Australian Centre for Ancient DNA, University of Adelaide

Rodent Molecular Phylogeny

1.0

Small Terrestrial Vertebrates: clarifying taxonomic status – Final Report: June 2007 to March 2011 - 61 -

Collaborators Member Role in

Project Organisation Expertise in Project

Dr Paul Doughty Collaborator Dept. of Terrestrial Vertebrates, Western Australian Museum

Reptile and Amphibian Taxonomy

Dr Mark Hutchinson

Collaborator Department of Herpetology, South Australian Museum

Reptile Taxonomy

Dr Scott Keogh Collaborator Botany and Zoology, Australian National University

Genetic Analysis and Amphibian Taxonomy

Mr Mark Adams Collaborator Evolutionary Biology Unit, South Australian Museum

Genetic Analysis

Mr Andrew Hugall Collaborator School of Earth and Environmental Sciences, University of Adelaide

Genetic Analysis

Dr Susan Fuller Collaborator School of Natural Resource Sciences, Queensland University of Technology

Genetic Analysis of Melomys Rodents

Ms Litticia Bryant Associated PhD Candidate

School of Natural Resource Sciences, Queensland University of Technology

Taxonomy of Melomys Rodents

Dr Glenn Shea Collaborator Department of Veterinary Anatomy, University of Sydney

Reptile Taxonomy

Dr Patrick Couper Collaborator Department of Herpetology, Queensland Museum

Reptile Taxonomy

Mr Ross Sadlier Collaborator Department of Herpetology, Australian Museum

Reptile Taxonomy

Mr Steve Hamilton Associated PhD Candidate

School of Biological Sciences, University of New South Wales

Taxonomy of Pogonomys Rodents

Dr Kristopher Helgen

Collaborator Department of Mammalogy, United States National Museum, Washington

Mammal Taxonomy

Dr Harold Parnaby Collaborator Vertebrate Ecology Unit, NSW NPWS

Bat Taxonomy

Dr Nicolas Vidal Collaborator Department of Systematics and Evolution, Museum Nationale d’Histoire Naturelle, Paris

Molecular Analysis of Blindsnakes

Prof Blair Hedges Collaborator Dept. of Biology and Astrobiology Research Center, Pennsylvania State University

Molecular Analysis of Blindsnakes

Dr Adam Skinner Collaborator University of Adelaide Phylogenetics and biogeography. Diversification through time analyses.


Mr Graham Medlin Collaborator S.A. Museum taxonomy of Australian rodents

Mr Matt McDowell Associated PhD Candidate

Flinders University taxonomy of Australian rodents

Dr Alex Baynes Collaborator W.A. Museum taxonomy of Australian rodents

Dr Marion Anstis Collaborator Unaffiliated taxonomy of Australian frogs

Assoc Prof William Breed

Collaborator Department of Anatomy and Histology University of Adelaide

taxonomy of Australian rodents

Dr Paulina Jenkins Collaborator Department of Mammalogy, Natural History Museum, London

Taxonomy of Australian marsupials and rodents

Dr Mark Blacket Collaborator University of Melbourne Taxonomy of Planigale

Dr John Woinarski Collaborator NT Department of Natural Resources Environment, the Arts and Sport

Taxonomy of Planigale

Dr Sandy Ingleby Collaborator Department of Mammalogy, Australian Museum, Sydney

Taxonomy of Acrobates

Dr Jeannette Hope

Collaborator Unaffiliated Original mammal fauna of southeastern Australia

Mr Gavin Perri Associated PhD Candidate

School of Archaeology and Anthropology, Australian National University

3D morphometric analysis

Dr Adrian Manning Collaborator CRES, Australian National University

Theory and practice of faunal reintroduction

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: Numerous molecular and morphometric datasets were integrated during this period to reveal high levels of cryptic diversity in many different groups of vertebrates, including both ecologically generalized and highly specialized groups. The results demonstrate the need for a complete taxonomic review of the Australian mammal and reptile faunas, and the vulnerability of the many aspects of biological science and environmental management that rest up the presumption of a solid taxonomic foundation. All problems with use of the micro-ct Scanner were resolved during this period, allowing rapid progress to be made on numerous projects. The ct scanner is the cornerstone of our approach to modernisation and provision of globally accessible morphometric taxonomy and legacy data sets. Major analytical advances with microCT datasets and application to both rodent and marsupial problems demonstrated the phenomenal discriminatory power of true 3D, fine resolution morphometrics. This powerful approach became fully functional, with rapid progress now possible on morphometric and anatomical studies of the smallest, most problematic groups of Australian mammals. Numerous publications were progressed through our own efforts and those of collaborators and associated students. Several important publications appeared in 2010, and more have been submitted or near completion.



Numerous molecular and morphometric datasets were integrated during this period to reveal high levels of cryptic diversity in many different groups of vertebrates, including both ecologically generalized and highly specialized groups. Although taxonomic knowledge has been advanced for many groups, the results demonstrate the need for a complete taxonomic review of the Australian mammal and reptile faunas, and the vulnerability of the many aspects of biological science and environmental management that rest up the presumption of a solid taxonomic foundation.


The resolution of issues relating to the microCT scanner and the initiation of sophisticated 3D morphometric analyses of demonstrably superior discriminatory power has been a major part of the last years work. The facility is now capable of assisting in a vast array of studies, and in encouraging the development of similar facilities elsewhere. See also below for PDA.


Continued collaboration with Margaret Cawsey in the Biodiversity Informatics team has lead to further refinement and extension of the PDA data collection technology, with applications in both field and laboratory. Furthers links have been fostered with the ALA to establish open-access to all of the taxonomic resources (literature, datasets, images) captured during the life of this project.

Ensure information is provided in a form, which meets end user needs, and ensure uptake of the product.

The LUCID key to Australian rodents was tested in several contexts during this period and refined to make it more effective and relevant.


See above comments on ct scanner and ALA collaborations.


Milestones Progress against outcomes and deliverables (outputs), including any milestones, for the period; activities to achieve these; associated completion dates. An explanation of any delays that have occurred, including the reasons for those delays and action proposed to take to address the delay and the expected effects (if any) the delay will have on the project (including subsequent Milestones and the overall completion of the project). (use milestones listed in the Work Plan): Milestone Completion Date Details – what did you achieve

and what did you produce

16. Collection of phenotypic data Assessment of the ‘original’ mammal fauna of northern NSW to central Queensland, including the historically important Hunter Valley, Liverpool Plains and Darling Downs;

Fieldwork commenced by September 2008, completed by August 2009. DONE

No further field work was undertaken. Curation, sorting and analysis focussed on the important collections from the Southern Tableland and Liverpool Plains.

Capture and analysis of Micro-CT imagery for 1) taxonomic revision of Pseudomys delicatulus group; 2) taxonomic revision of Egernia inornata group; 3) generic revision of Australian native rodents; 4) taxonomic revision of possum genus Acrobates; 5) taxonomic revision of Crinia riparia group; 6) taxonomic revision of Aprasia fusca group; 7) generic revision of Australian Typhlopidae (blind snakes); 8) taxonomic revision of Planigale maculata group.

May 2009 for project 1. DONE

July 2009 for projects 2. DONE

December 2009 for projects 3-4. DONE

August 2010 for projects 5-8 DONE for Projects 5,6. Objective abandoned for Project 7. February 2011 for Project 8.

All software issues for use of the micro-CT scanner for detailed morpohometric analyses (Procrustes, Fourier Transformation) were resolved by mid-2010 and sophisticated work completed on morphometric data sets for the delicate mice, Acrobates and Pseudomys oralis/higginsi. Plans to scan blind snake skulls for generic revision were abandoned due to initiation of a similar project by collaborators Hutchinson and Skinner of S.A. Museum, using facilities at Uni. Adelaide. Scans also completed for analysis of cranial morphometrics of Planigale; analysis pending. Type specimens of Pseudomys and Acrobates examined at NHML in May 2010; scanned as part of CERF Extension project in October 2010.

Descriptions of new taxa using traditional morphometric approaches for 1) rodent genus Melomys and an allied, new genus; 2) Australian members of rodent genus Uromys; 3) marsupial genus Petauroides; 4) varanid genus Odatria; 5) Delma australis group

Project 1 completed in 2009.

September 2009 for projects 2-4. DONE

January 2010 for project 5. DONE

All Australian museum holdings examined and documented for Projects 1-3. Regionally-based morphometric datasets assembled for projects 4-5.


17. Collection of genotypic data Sequencing of modern DNA samples at SA Museum for 1) marsupial genus Acrobates; 2) rodent genus Uromys; 3) Aprasia fusca group; 4) Planigale maculata group.; 5) members of the Egernia inornata group; 6) members of the Egernia depressa group; 7) members of the Egernia stokesii group; 8) members of the skink genus Eremiascincus.

Sequence data collection for Projects 1-3 completed May 2010. Commenced May 2010 for Projects 3-8. Completed December 2010. DONE

All available fresh tissues sequenced for Project 1 (ND2, 12Srna, BRCA1), Project 2 (cyt b, D-loop), Project 3 (ND2), Project 4 (12sRNA, D-loop), Projects 5-8 (ND4).

Sequencing of modern DNA samples at MNHN (collaborator Dr N. Vidal) for Australian Ramphotyphlops.

1st 500 samples done by April 2010, remaining 600 samples to be done by 2011 DONE

All available fresh tissues sequenced for 12sRNA, 16sRNA, cyt b. Tree topology and preliminary morphological assessments suggest presence of c. 26 additional cryptic species in Australia, more than currently recognised (25 spp.).

Sequencing of ancient DNA samples at ACAD, Uni Adelaide for: 1) marsupial genus Acrobates; 2) mosaic tailed rat genera Melomys and Uromys; 3) rodent genus Pogonomys; 4) marsupial genus Dasyurus; 5) marsupial genus Petauroides; 6) Planigale maculata group; 7) extinct members of Australian rodent radiation (associated PhD student V. Thomson); 8) members of Pseudomys australis/auritus and Pseudomys oralis groups (associated PhD student V. Thomson); 9) rare or extinct members of the Egernia inornata group.

Sequence data collection for projects 1-6 completed in May. 2010. DONE for Projects 1-6; completion expected March 2011 for Projects 7-8

Extensive and crucial ancient DNA datasets generated for key marsupial and reptile groups, using improved ancient DNA protocols developed during this project. Progress on rare/extinct arid-zone Australian rodents hindered by poor condition of ancient DNA. Better results now coming from new samples from the Liverpool Plains; project will be completed by V. Thomson

24. Preparation of manuscripts 1) Taxonomic revision of the Carlia longipes group (Donnellan with collaborator P. Couper)

DONE Donnellan, S.C., P.J. Couper, K. M. Saint & L. Wheaton, L. (2009) Systematics of the Carlia ‘fusca’ complex (Reptilia: Scincidae) from northern Australia. Zootaxa 2227: 1–31. Two species of lizard resurrected from synonymy.

2) Taxonomic description of two new members of the Egernia (Liopholis) inornata group (Aplin, Donnellan, Armstrong, with collaborators B. Maryan, P. Doughty)

To be submitted by October 2010. Submitted in late January to BMC Biology

Two new species identified. Status of two other species (L. slateri and L.virgata) clarified, both with new rating as the most critically endangered of all Australian reptiles.

3) Taxonomic revision of the Aprasia fusca group (Aplin, Armstrong, Donnellan with collaborator M. Adams)

To be submitted by October 2010. Slight delay but due for submission by end February 2011.

Five new species in W.A.; range of Aprasia rostrata enlarged to include NW Cape, with downgrading of IUCN status recommended.


4) Taxonomic revision of the Crinia riparia group of myobatrachid frogs (Donnellan with collaborator M. Anstis)

To be submitted by December 2010. Slight delay but due for submission by end February 2011.

A new species of Crinia in the northern Flinders Range, S.A.

5) A new genus of mosaic-tailed rat from the Wet Tropics of Australia (Aplin with PhD student L. Bryant and collaborator S. Fuller)

Slight delay, pending publication of molecular component (under review with Molecular Phylogenetics and Evolution). Taxonomic paper in advanced draft, submission as soon as molecular study accepted.

First entirely new genus and species of Australian mammal since 1975; a Wet Tropics endemic.

6) Taxonomic revision of the ‘delicate mice’ of northern and eastern Australia (Ford with collaborator W. Breed).

Delayed pending microCT scan of type specimens in London and completion of ancient DNA results. Both now completed; manuscript due for submission by end February 2011.

Two species resurrected from synonymy; hybrid origin of Pseudomys pillagensis demonstrated.

7) A new generic arrangement of the Australian native rodents, based on combined morphological and molecular evidence (Ford and Aplin).

On hold pending successful deployment of interactive key. Type material in NHM, London scanned in Dec 2010; completion of the manuscript by May 2011

Three genera resurrected from synonymy; content of Mastacomys enlarged; one new genus described.

8) Taxonomic revision of the Australian members of the murid genus Uromys (Aplin, Donnellan with collaborator K. Helgen);

To be submitted by October 2010. Delayed pending receipt of morphometric analysis from collaborator Helgen. Submission now anticipated for April 2011.

One species of Uromys resurrected from synonymy, a Wet Tropics endemic.

9) A historical, ecological and taxonomic review of the terrestrial mammal fauna of southeastern Australia (Ford, Aplin, with collaborator J. Hope).

To be submitted by October 2010. Delayed due to lack of access to J. Hope collection (illness). Effort diverted into detailed analysis of Douglas Cave (near Queanbeyan) fauna and other newly curated collections from Wee Jasper. Full analysis now anticipated for completion in May 2011.

Presentation of key findings to Royal Zoological Forum, Sydney October 2010.


10) A multi-gene phylogenetic framework of the Australian blindsnakes, including their relationship with other globally-distributed typhlopid blindsnakes (Donnellan, Aplin with collaborators N. Vidal and B. Hedges)

Published online in Biology Letters 31 March 2010

Published online in Biology Letters 31 March 2010.

11) Taxonomic revision of the marsupial genus Acrobates (Aplin, Armstrong, with collaborators S. Ingleby and P. Jenkins);

To be submitted by October 2010. Delayed pending analysis of scanned images. Completed December 2010. Manuscript to be submitted to Proc Roy Soc, London B in early February 2011.

A cryptic species identified in the iconic Feathertail Glider. Most previous work on ecology, physiology, reproduction in this genus now thrown into doubt because of broad sympatry including key study sites near Melbourne.

12) Taxonomic revision of the marsupial genus Petauroides (Aplin; Armstrong with collaborators B. Arbogast; A, Taylor;

To be submitted by October 2010. Delayed pending completion of genetic investigation by collaborators Arbogast and Taylor. Taxonomic findings will be submitted to coincide with meeting of American Society of Mammalogists, June 2011.

Greater Glider shown to be complex of four parapatric species, with concordant geographic patterns of genetic and morphological variation. Three species to be resurrected from synonymy (all named as subspecies).

13) Revision of E. frerei group (Donnellan with collaborators R. Sadlier and P. Couper).

To be submitted by October 2010. Delayed pending receipt of morphometric analysis from collaborators Couper and Sadlier. Submission now anticipated for May 2011.

Two new species to be named.

14) Taxonomic revision of the Planigale maculata group (Aplin with collaborators M. Adams, M. Blacket and J. Woinarski)

Submitted by May 2010 for MS 13-16. Delayed pending completion of ancient DNA. Two manuscripts in advanced draft: 1. new generic molecular survey; 2. description of two new species from the Pilbara.

Three species will be resurrected from synonymy. Eight new species to be named. Generic total taken from 5 to 16.


15) Generic revision of Eremiascincus, and description of a new species from the Pilbara (with collaborator P. Doughty and international collaborator S. Mecke)

First part published in Zootaxa in 2009. Second paper submitted to Zootaxa in February 2011.

Mecke, S. Doughty, P. and Donnellan, S.C. (2009). A new species of Eremiascincus (Reptilia: Squamata: Scincidae) from the Great Sandy Desert and Pilbara Coast, Western Australia and reassignment of eight species from Glaphyromorphus to Eremiascincus. Zootaxa 2246: 1–20. One new species of lizard; generic reallocation of eight others. Part II. One more new species.

16) Use of microCT and 3D morphometrics for discrimination of closely related rodent species Ford and PhD student G. Perri).

Manuscript to be submitted February 2011.

Important demonstration of the discriminatory power of 3D morphometric analyses.

17) Decision analysis for community reconstruction through faunal reintroduction (with collaborator A. Manning)

Manuscript to be submitted February 2011.

General model for Australian context where much of native fauna declined long ago.

18) Taxonomy of the spiny-tailed skinks (genus Egernia) (Donnellan with collaborator P. Doughty)

Manuscripts to be submitted to Zootaxa in February 2011.

Three new species of the Egernia depressa complex.

19) Phylogenetic affinities of extinct Australian murine rodents (PhD student V. Thomson)

Publication schedule is contingent on progress of PhD candidate but MS should be completed by April 2011

Good progress made with aDNA from Liverpool Plains samples.

20) ‘Original’ population genetic structure of Australian rodents based on analysis of modern and ancient DNA (PhD student V. Thomson)

Publication schedule is contingent on progress of PhD candidate but MS should be completed by April 2011.

Comprehensive mtDNA phylogeography of Pseudomys oralis, including many extinct populations sampled by ancient DNA. Major implications for translocation programs.

21) ‘Original’ population genetic structure of Australian Dasyurus based on analysis of modern and ancient DNA (PhD student S. Hamilton)

Publication schedule is contingent on progress of PhD candidate S. Hamilton. Progress delayed by deferral of study. Resumed January 2011.

Continental phylogeography of Western Native Cat, including many extinct populations sampled by ancient DNA. Major implications for translocation programs

22) Taxonomic revision of the rodent genus Pogonomys including description of a new species from Australia (PhD student S. Hamilton

Publication schedule is contingent on progress of PhD candidate S. Hamilton. Progress delayed by deferral of study. Resumed January 2011. Expect to finalise taxonomic publication by May 2011.

Australian Pogonomys is Wet Tropics endemic.

23) Taxonomic revision of Australian Melomys ((PhD student L. Bryant)

Submitted to Molecular Phylogenetics and Evolution in March 2010. Accepted pending revision.

Phylogeographic analysis of two lineages within Australian Melomys. Clarified status of IUCN listed M. rimicola of Bramble Cay, Torres Strait.



Specifics of What


Specifics of What

Issues Any issues associated with the project: All problems with use of the micro-ct Scanner were resolved during this period, allowing rapid progress to be made on numerous projects. The ct scanner is the cornerstone of our approach to modernisation and provision of globally accessible morphometric taxonomy and legacy data sets. The support made available through the CERF Extension project funded two extended visits by Ford to scan type material of Australian mammals held in the Natural History Museum London; the ongoing value of this resource for taxonomic research in Australia is immeasurable. In the meantime, we have focussed our efforts on publications that were not contingent on microCT datasets, including most of those dealing with herpetofauna, and in preparing all other components of manuscripts. Highlights Two highlights from the last period (May 10 – End): Major analytical advances with microCT datasets and application to both rodent and marsupial problems demonstrated the phenomenal discriminatory power of true 3D, fine resolution morphometrics. This powerful approach became fully functional, with rapid progress now possible on morphometric and anatomical studies of the smallest, most problematic groups of Australian mammals. Integration of modern genetic data, ancient DNA sequences, and traditional morphometrics of the skink genus Liopholis lead to recognition of two relictual new species in northern Australia, and two in Central Australia, both of which were named in the late 1960s but have not definitely been seen for 50 years. Both should be raised to the highest level of conservation concern; if not already extinct, they surely rate as Australia’s most critically endangered reptiles.


Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: • Catalyst (November 2010) filming in lab and field for story on mammal diversity and declines –

due for broadcast mid-2011. • Seminar to Zoology Department, Natural History Museum, London (Dec 14 2010) – Fred Ford • Radio interview ABC666 (November 2010) – interview about mammal declines • Australian Mammal Society meeting, Canberra, July 2010, individual presentations by Ken

Aplin and Fred Ford. • Royal Zoological Forum ‘Impacts of climate change’, Sydney October 2010 joint presentation

by Ken Aplin and Fred Ford. • Presented and demonstrated at both TRIN Field Days in Canberra and Cairns by Ken Aplin

and Fred Ford.


Project:


Final Report


FINAL REPORT

Context Information

Project Title Systematics of Environmental Weeds


Dates for which this progress report applies May 2010 to November 2010

Project Team Project Leader Dr Richard Watts

Host Organisation Centre for Plant Biodiversity Research CSIRO Plant Industry

Member Role in


Dr Richard Watts

ECR CPBR, CSIRO Plant Industry, Canberra

Population genetics & Phylogenetics

1.0

Dr Joe Miller

Research Scientist

CPBR, CSIRO Plant Industry, Canberra

Phylogenetics & genetics advice

0.3

Dr Judy West

Research Scientist

CPBR, CSIRO Plant Industry, Canberra

General oversight & Systematics

nominal

Dr Andrew Young

Research Scientist

CSIRO Plant Industry, Canberra

Population genetics advice nominal

Brendan Lepschi

Curator ANH, CPBR Weeds expertise, Taxonomy 0.2

John Connors

Technical Officer

CPBR, CSIRO Plant Industry

Technical officer, Web-based identification products, Field work

0.5

Caroline Chong

Technical Officer

CPBR, CSIRO Plant Industry

Molecular techniques 1.0

Michael Day

Collaborator Alan Fletcher Research Stn QLD Dept Primary Industries Brisbane

Lantana Biocontrol

Rieks Van Klinken

Collaborator CSIRO Sustainable Ecosystems

Mesquite expert

Louise Morin

Collaborator CSIRO Sustainable Ecosystems

Plant Pathologist, Biocontrol of Chrysanthemoides and Moraea

Tara Hopley

PhD Student CSIRO Plant Industry, Canberra

Willows research 0.5

Systematics of Environmental Weeds – Final Report: June 2007 to March 2011 - 73 -

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: 1. Project expansion – Mesquite (Prosopis spp.)

• Engage a PhD candidate to continue this project. Due to our inability to attract a suitable candidate we discontinued our efforts to recruit a PhD candidate. Instead we engaged a part-time technical assistant to perform seedling growth trials as part of a study into the consequences of hybridisation for mesquite management.

• Manuscript In Press 2. Project expansion - other WONS

• Engage in discussions with national coordinators to identify needs and seek synergisms with existing capability. We presented our work to the annual forum for the WONS Coordinators held by DAFF in Canberra and asked for input into critical needs for genetic research. As a result of this consultation process we initiated a study into hybridisation and origins of bitou bush and boneseed (Chrysanthemoides monilifera subspp.) in Australia. The justification for this project is that these two weeds have differing invasive ecologies and that while moderate success in biocontrol of bitoubush has been acheived, no agents for boneseed have ever been identified. As a consequence, hybridisation between the two weeds has the potential to erode past efforts due to the introgression of agent resistance into the bitou bush population, and to lead to the evolution of new weed forms.

• Manuscript In Press

• Initiate genetic profiling project for Chrysanthemoides monilifera. Genetic profiling of bitou bush and boneseed demonstrated that ongoing hybridisation between the two weeds is occurring in Australia. Native range materials supplied as part of a new collaboration with Louise Morin (CSIRO Entomology) enabled us to localise the likely origins of the Australian boneseed population to a small region on the eastern slopes of Table Mountain outside Cape town, South Africa. This information is being used to justify eradication programs in Victoria and to inform ongoing searches for suitable control agents for boneseed.

3. Project expansion - other weeds

• Develop collaboration with Saggitaria and bring Gleditsia triacanthos work to completion. We are in ongoing communication with Saggitaria workers but elected not to enter into a formal collaboration. All Gleditsia experimental work is completed and we expect to see that written up for publication early in 2011.

• Initiated genetic profiling project for Cape tulip (Moraea spp.). As part of our new Chrysanthemoides collaboration with Louise Morin we initiated a genetic profiling project for one- and two-leafed Cape tulips. The goal of this project is to describe Australian diversity and to identify native range origins for improved biological control agent discovery. We have extracted DNA from Australian accessions and from representatives of populations throughout the native range in South Africa. We are currently developing markers suitable for the project goals.


4. Communication • Give presentations of results to national meetings of weed management and policy

workers and publish work in peer reviewed scientific journals. Ensure uptake of work into weed management strategies. Presented with Michael Day at 17th Australasian Weeds Conference held in Christchurch, 26-30 September, 2010. ‘Utilization of molecular tools to unravel the geographical origins of invasive weeds in Australia’ Workshop had a heavy management focus. Also led to an ‘ad-hoc’ talk on barcoding of weeds.

5. Staffing

• Caroline Chong joined the project in place of Bron Matheson as a technical assistant. Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

Our work and data analysis has provided a scientific basis for actions by weed managers and a new geographic focus for biocontrol discovery efforts


Our methods have proven highly transferrable to new weed problems. Our ongoing success has been recognised by weed managers and weed scientists, who actively sought to collaborate with us.


Work is being integrated into the TRIN web management system to permit rapid dissemination of the knowledge we are generating.


Information was delivered in collaboration with major end users. Communications with WONS coordinators to obtain input into their knowledge requirements led to rapid uptake. We have given seminar presentations of our work to biocontrol scientists and systematic biologists to raise awareness of our work and obtain feedback.


The tools we developed provide a universally applicable and rapid method for the genetic profiling of other weeds with complex introduction histories. We are actively educating end users in the capability that we have developed to encourage the uptake of our work.




Details – how you are going to achieve it and what you are going to produce

17. Collection of genotypic data

20. Analysis of data 31/12/2009 n/a


24. Preparation of manuscripts

25. Submission of manuscripts

31/6/2010

Preparation and submission of a manuscript describing AFLP results for Gleditisia triacanthos is expected to be completed in 2011 following employment of a short-term post doc.





24. Preparation of manuscripts

25. Submission of manuscripts

31/6/2010

A manuscript for reproductive biology components of Salix cinerea is in preparation. Manuscripts describing results for Lantana is in late stages of preparation, a manuscript describing the Chrysanthemoides research is well under way and awaiting final results from the expanded survey.


Specifics of What

Michael Day, QLD DEEDI Biocontrol of Lantana

Kym Johnson QLD DEEDI Lantana National Coordinator – policy wording and implications of research


Hillary Cherry, NSW DPI Bitou bush and bone seed National Coordinator – research priorities and implications

Robin Adair, VIC DPI State-wide Leader Weed Sciences – hybridisation of bitou bush and boneseed and its implications


Specifics of What

Issues Any issues associated with the project: Manuscripts are still In Prep and will be completed beyond end of the project. Highlights Two highlights from the last period (May 10- Nov 10): • Presented with Michael Day at 17th Australasian Weeds Conference held in Christchurch, 26-

30 September, 2010. ‘Utilization of molecular tools to unravel the geographical origins of invasive weeds in Australia’

• This work has changed the way people think and has brought home what can be done- it is not that hard to get quick, useful results from sequencing methods

Communication & capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: • TRIN Field Day seminar presentation and stall • Presented with Michael Day at 17th Australasian Weeds Conference held in Christchurch, 26-

30 September, 2010. ‘Utilization of molecular tools to unravel the geographical origins of invasive weeds in Australia’


Project:

Emerging Priorities/DNA Barcoding for Taxonomy

Final Report

Emerging Priorities / DNA Barcoding for Taxonomy

FINAL REPORT

Context Information

Project Title Emerging Priorities/DNA Barcoding for Taxonomy

Duration of the entire project 20 December 2009 to 4 December 2010


Project Team Project Leader Dr Joe Miller

Host Organisation Centre for Plant Biodiversity Research, CSIRO Plant Industry



Project FTE

Joe Miller Project Leader

Centre for Plant Biodiversity Research, CSIRO Plant Industry

Plant Systematics 0.3

Stephen Cameron Systematics entomologist

CSIRO Sustainable Ecosystems Insect Systematics 0.2

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: During this final period of the DNA barcoding for Taxonomy project we have finalized our data collection. All projects have made important contribution effort to develop barcodes for Australian biodiversity. The project generated data from many diverse organisms including trees, grasses, fish, flies, fungi, termites, ants, beetles and butterflies. The primary objective was to generate DNA sequences that can be used to generate DNA barcode libraries and because of this project we have many solid datasets. For example the two labs that have been focusing their efforts on grasses have made substantial impact on the available sequences that can be used to identify grasses. Although the project had a much faster timeframe than normal for a research project, our initial goals were very close to the actual data collected. We were in most cases able to generate data from multiple representatives of each species to give a snapshot of diversity within the species. It is critical to understand within species diversity for identification within the barcode libraries. For example an unidentified specimen may not have a perfect DNA barcode match to a single entry in a barcode library however if multiple species samples are present then a near match may allow confidence in the barcode identification. The activities of this time period involved the termination of the last DNA sequences, data analysis, manuscript preparation (see below) and submission of data to international data repositories. An important highlight to the project is the successful bid by the TRIN Grass Barcoding group to bring the International Barcoding conference to Australia (Adelaide) next year. This meeting will provide an opportunity to showcase the successful TRIN barcoding projects on the international stage and will provide momentum for furthering this important work in Australia.

Emerging Priorities/DNA Barcoding for Taxonomy – Final Report: June 2007 to March 2011 - 79 -


The taxa -selected to be barcoded in this study were chosen based on taxonomic gaps. These include under-studied groups such as rare Acacia species, weedy invasive grasses, under studied native hardwood tree species, potentially overfished marine biota and important pollinators and insects that provide important ecosystem services.


DNA barcoding is reliant on DNA sequence databases. Unknown specimens are sequenced to determine the barcode and this DNA sequence is compared to a known reference database of barcodes from which an identification is made. The only way to accelerate this process is the high-throughput development of the barcode reference databases. This is the goal of the present study. After this project is complete Australia will have several robust barcode libraries that will allow the accelerated identification. This work is integrated in that the genetic barcode is tied to a vouchered specimen that has been expertly identified to species by a taxonomist.


The labs involved in this barcoding project are distinguished taxonomic labs in Australia. All labs have attached natural history collections with the taxonomic expertise needed to identify the organism. Without this expertise the DNA barcodes would be of little use. The project leader is working with the TRIN bioinformatics team in the development of a Linked Lab book. This will facilitate streamlined data capture and export to DNA sequence databases such as BOLD and Genbank.


The major goal of the first six months has been the generation of barcoded reference database DNA sequences. The submission of the DNA sequence is a time consuming process. The most efficient way of contributing this data to the Genbank database is a single large submission. This will take place near the end of the project.


The project has developed active collaborations among several labs, most of which are new. We have also further developed our DNA barcoding protocols which will be published and will provide for more efficient DNA barcoding.





Emerging Priorities Project as per “Annexure A” the workplan outline on DNA Barcoding for Taxonomy;

− Completion and delivery of 70% of barcodes for each group

February 2011

The project has now successfully completed the DNA sequencing portion of the barcoding project. This was an extremely diverse project with many types of organisms sequenced: trees, grasses, termites, fish, rust, ants, flies, beetles and butterflies. There were several subprojects that attempted a defined number of barcodes with replication of more than one sample per species and usually more than one gene per sample. Overall we were able to sample more species than we proposed in the original project. However we were not able to sequence as many individuals per species in many cases. This primarily was due to difficulties of obtaining appropriate material. We made up for this slight shortfall by sequencing mores species and in many cases, such as the grasses and trees, sequencing more genes. Overall the data generated in this project contributes to the development of DNA libraries, and is already being used in many ways, including barcode identification and determining evolutionary relationships among organisms. There is building momentum in Australia for DNA barcoding much of which came out of this project.


Specifics of What

Peter Last/Bob Ward – Fish Systematist from CSIRO Marine & Atmospheric Research (CMAR).

Darren Crayn – Plant molecular systematist from the Australian Tropical Herbarium, JCU

We obtained a total of 3,065 sequences: 1,535 of rbcL, 1025 of matK, 505 of trnH-psbA . Species barcoded (≥ 2 replicates) rbcL: 500 Species barcoded (≥ 2 replicates) matK: 317 Species barcoded (≥ 2 replicates) trnH-psbA: 199


Hugh Cross – Molecular biologist from the University of Adelaide

601 species from 1,956 specimens have been sequenced. For these 64% of the specimens have a completed rbcL region and 50% have matK. Additionally 25% have ITS which was an additional marker deemed important to clarify significant barcodes for the grasses.

Dan Murphy / Anna Syme – Plant molecular systematists from the Royal Botanic Gardens Melbourne.

DNA barcoding of grasses: 617 specimens representing 255 species, resulting in a total of 1194 sequences of three gene regions.


Specifics of What

David McLaren, Aaron Dodd, Charles Grech, Department of Primary Industries, Victoria.

DNA barcoding of stipoid grasses; in particular, molecular identification of Mexican feather grass.

CSIRO Ecosystem Sciences, Dr Dan Metcalfe Considerable value added to Wet Tropics forest plots through vouchering of tagged trees and addition of DNA barcodes to the baseline data for these plots.

DEWHA, Australian Biological Resources Study, Michael Preece

Provision of samples and DNA barcodes for many tropical rainforest groups enhances ABRS goals to document the diversity of Australia’s biota, through providing 1) novel identification tools; 2) vouchered samples for taxonomic studies; and 3) sequence data that are already being utilised in several studies on taxonomic problems in Australian tropical rainforest plants.,

DEWHA, Australian Natural Heritage Assessment Tool, Anthony Whalen

Discussions around the provision of DNA barcode data for assessments of phylogenetic diversity in areas of NE Qld of Departmental interest, e.g. Cape York Peninsula.


Issues Any issues associated with the project: The major issues in generating the data can be summarized below. The project timeline was insufficient to achieve the target: Several subprojects were slowed due to the slow delivery of contracts and the need to hire personnel to do the work. This was exacerbated by the extremely tight schedule of the project. Difficulties with DNA extraction: All projects had a high number of target species. For the plant work this required the use of herbarium plants for DNA extraction. Many of these were ultimately unsuitable for DNA and required additional time in the lab and in sample collection. The rust work was additionally complicated by the lack of robust published protocols for DNa extraction from dry field collected rust spores. Difficulties with generating data: Poor success was accounted with PCR amplification, especially for the grasses due to the extreme taxonomic diversity (more than 90 families) of samples in this study. Universal matK primers are not yet available. An additional complication to the DNA barcoding of grasses was identified during this project. There appear to be at least two copies of rbcL in some Poaceae taxa requiring cloning to differentiate, which went beyond the capability of the project. Taxonomic identification difficulties: For many grass species it has been difficult to obtain authoritatively identified voucher material, especially recent collections. Also, when identifications are checked by taxonomists initial identifications are often found to be mistaken due to the specialised knowledge needed to correctly identify. This requires extra time and diligence in confirming identifications by expert taxonomic botanists prior to processing specimens for DNA barcoding. Highlights Two highlights from the last period (May 10 to end):

Highlight: Invasive grass identification to limit incursion We were able to use DNA barcoding of grasses to identify an incursion of Mexican Feather Grass in Australia. This species is a weed of national significance and our results received considerable publicity and resulted in plant material confiscated by the Department of Primary Industries in Victoria being rapidly identified. Our team’s work was nominated for the DPI David McAlpine Science Award in October 2010.

Highlight: Biodiversity Analysis of Tropical Rainforest Richness We used DNA barcode data to improve estimates of plant diversity patterns in Australian tropical rainforests. Until now, analysis of diversity across entire floras has been limited to calculating taxonomic (e.g. species) richness. The barcode dataset we have compiled allows phylogenetic diversity – which measures evolutionary distinctiveness - to be calculated for the first time. This will lead to much more meaningful assessments of conservation value. Talks given at international conferences (Flora Malesiana 2010 in Singapore, and Association for Tropical Biology and Conservation in Bali) generated a lot of interest and discussion with other colleagues from around the world. Several collaborative linkages were developed with colleagues undertaking similar but smaller scale projects in Singapore, China and Papua New Guinea. Productive discussions took place to establish standard methods in these projects to enhance data complementarity. Our intention is to link these projects together to use barcode data to examine patterns of diversity in forest plots along a latitudinal transect from China through SE Asia and Malesia to Australia.


Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Media exposure for the project also increased public awareness in the work including: Costion C. TRIN Field Day – James Cook University Cairns Campus: “DNA Barcoding of Trees in

Queensland”

Miller, J.T TRIN Field Day, ANBG October 2010

Miller, J.T Acacia Tree of Tree Phylogeny Display, Floriade, Sept 2010

Miller, J.T, Acacia Tree of Tree Phylogeny Display, ANBG, Sept-Nov 2010

Murphy, D.J. (26 February 2010). Interview with Libby Price ABC Country Hour, Melbourne studio.

Murphy, D.J. (9 April 2010). Alumni Profile, The University of Melbourne Alumni News. http://cms.unimelb.edu.au/?a=293661

Publications in review

Gallagher, R. et al. (2011) Genome size as a predictor of invasion success and trait variation in Australian acacias. Diversity and Distributions, 17 (in review).

Miller, J.T., D. M. Murphy, G. K. Brown, D. M. Richardson and C. E. González-Orozco (in review). The evolution and phylogenetic placement of invasive Acacia species Diversity and Distributions, 17 (in review).

Richardson, D.M., Carruthers, J., Hui, C., Impson, F.A.C., Miller, J.T., Robertson, M.P., Rouget, M., Le Roux, J.J. & Wilson, J.R.U. (2011). Human-mediated introductions of Australian Acacia species—a global experiment in biogeography. Diversity and Distributions, 17 (in review).

Formal Presentations Cameron, S.L. & Evans, T.E. Phylogenomics of termites. Meeting of the Entomological Society of

America, San Diego, CA, USA, December 2010. Costion C. Association for Tropical Biology & Conservation Conference 2010 – Bali – “The

Australasian Floristic Interchange” Barcode data used to infer phylogenies and biogeographic history of Australian plant lineages

Costion C. Australian Tropical Forest Institute Seminar – James Cook University Cairns Campus: “DNA Barcoding for Estimating Species Diversity in the Tropics”

Costion C. Flora Malesiana Conference 2010 – Singapore – “DNA Barcoding for Estimating Species Diversity in the Tropics”

Miller, J.T Australian Systematic Botany Society, Christchurch,NZ December 2010

Miller, J.T Human-mediated introductions of Australian Acacia species—a global experiment in biogeography, Stellenbosch South Africa, October 2010

Miller, J.T, International Legume Conference, August 2010, Argentina


http://cms.unimelb.edu.au/?a=293661

Transition Project:

Generalised mobile field data recording application for hand-held device (PDA, Smartphone, Netbook, etc.)

Final Report

Generalised mobile field data recording application for hand-held device (PDA, Smartphone, Netbook, etc.)

TRANSITION PROJECT – FINAL REPORT

Context Information

Project Title Generalised mobile field data recording application for hand-held device (PDA, Smartphone, Netbook, etc.)

Duration of the entire project July 2010 to March 2011 – anticipated to May 2011

Dates for which this progress report applies July 2010 to March 2011

Project Team Project Leader Dr Jim Croft




Project FTE

Jim Croft Leader. research coordination

Centre for Plant Biodiversity Research, DEWHA

0.05

Margaret Cawsey Project design and direction

CSIRO Sustainable Ecosystems Survey design, database design and management, design of forms for field data capture

0.2

Garry Jolley-Rogers

Software engineer

CSIRO Plant Industry, CPBR 0.1

Greg Whitbread Systems engineer

Australian National Botanic Gardens, DEWHA, CPBR

0.1

Paul Harvey Programmer CSIRO Plant Industry, CPBR 0.1

Nunzio Knerr Geospatial technician

DSIRO Plant Industry, CPBR 0.1

Gaia Resources Environmental Technology Consultants

Programmer Gaia Resources Environmental Technology Consultants

software consultants, HTML5

.5

Generalised mobile field data recording application for hand-held device – Final Report: June 2007 to March 2011 - 86 -

Project description This project extends TRIN’s hand-held PDA application and generalises its platforms and the biological domains in which it can be applied. The application will extend to take advantage of inbuilt Wifi and G3 network connectivity increasingly available in these devices and similarly, digital image capture and mobile GPS and other spatially aware technologies. The project will investigate generalised extensions to enable the use of the application by other biological collections e.g. botanical and entomological collections. Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: In July 2010 it became clear that the Atlas of Living Australia-funded software for Citizen Science could be readily adapted for the collection of scientific collection/survey data. Accordingly, rather than reinventing wheels, it was decided to co-invest with the ALA in this adaptation, employing the original contractor, Gaia Resources Environmental Technology Consultants, to continue the work. This altered the whole approach to the project, as the programming environment was already defined to be HTML5, which currently runs on all mobile operating systems except Microsoft Windows Mobile – although this will change in future. The focus of the project in this period has been on the design of the mobile data capture system with regard to the survey designs required to collect these types of data, whether collected in the field or in the laboratory, and the development of a pilot system, which was completed by December 31/12/2010. The results and analysis were presented and demonstrated the TRIN field day in Cairns, on 9/12/2010. The project has been extended to 31/05/2011, to allow for field testing and adaptation of the pilot system. Planning for this process has commenced. Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

o Expansion of the PDA application to a greater range of organisms (beyond vertebrates), platforms (other mobile devices e.g. iPhones, iPads, Tablets, Smartphones), operating systems (beyond Windows Mobile OS), and data collection environments (lab as well as field) will greatly influence biological collecting processes well beyond the TRIN network and will enhance data management and availability of information.




o Integration of mobile data capture technologies with collection management databases to accelerate the rate of entry of taxonomic data into these databases, and thus their availability to taxonomic and other user-communities for analysis, research, policy-making etc.

o Effective, open source, free, generic mobile data capture technologies will facilitate a wider range of users and use-cases.



o Integration of mobile data capture technologies with collection management databases will accelerate the rate of entry of taxonomic data into these databases, and thus their availability to taxonomic and other user-communities for analysis, research, policy-making etc.


o Integration of mobile data capture technologies with collection management databases will accelerate the rate of entry of taxonomic data into these databases, and thus their availability to taxonomic and other user-communities for analysis, research, policy-making etc.


o Effective, open source, free, generic mobile data capture technologies will facilitate a wider range of users and use-cases and produce a user-community actively involved in the enhancement and adaptation of the software for other research and data-capture purposes.





Recruitment- Advertise, select, recruit

July 2010 o In July 2010 it became clear that the Atlas of Living Australia-funded software for Citizen Science could be readily adapted for the collection of scientific collection/survey data. Accordingly, it was decided to co-invest with the ALA in this adaptation, employing the original contractor, Gaia Resources Environmental Technology Consultants, to continue the work.

o This changed the whole approach to the project, as the programming environment was already defined to be HTML5, which currently runs on all mobile operating systems except Microsoft Windows Mobile – although this will change in future.

o Due to other commitments, the meeting between TRIN, ALA and Gaia Resources participants could not be arranged until 30/08/2010

Workplan- Refine workplan, timeline July 2010 n/a Analysis- Analyse, document existing workplan

July 2010 n/a

(Evaluation- Evaluate alternative platforms) Workplan- Refine workplan, timeline AND Analysis- Analyse, document existing workplan

August 2010

o Meeting between TRIN, ALA and Gaia Resources participants determined the HTML5 approach, based upon the ALA Citizen Science software. Gaia Resources to collaborate with Margaret Cawsey on workplan and requirements for mobile data collection system for science.

o The workplan and protocols documented on 9/09/2010.

(Migration- Migrate to selected platforms) Platform selection

October 2010

o Mobile test platforms selected and purchased: Android phone and iPad.


(Extension- Extend application to botany/entomology) Redesign of HTML5 citizen science software to meet the requirements of scientific data collection.

November 2010

o November 16-18 Margaret Cawsey worked with Gaia Resources in Perth,

• refining the protocols and design from 9/09/2010

• Developing and testing a pilot system

• Analysing survey design, download and usability of the pilot system

Evaluation- Evaluate project, future development potential

November 2010

o Pilot system evaluated for future development potential

Promotion- Release for other institutions or projects

December 2010

o Progress presented by Margaret Cawsey at the TRIN field day in Cairns on 9/12/2010

o Pilot system 31/12/2010 Project Collaboration Progress in working with target areas of the Department of Environment, Water, Heritage and the Arts or other Commonwealth Government Departments or State agencies: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Atlas of Living Australia Funding for software development

Gaia Resources Environmental Technology Consultants

Development of software


Specifics of What

Australian National Herbarium Test client Australian National Botanic Gardens Test client Australian National Insect Collection Test client Australian Biological Resources Study- Bush Blitz

Test client


Issues Any issues associated with the project: o The approach to the project underwent complete redesign when it was realised that the Atlas of

Living Australia-funded software for Citizen Science could be readily adapted for the collection of scientific collection/survey data. Accordingly, rather than reinventing wheels, it was decided to co-invest with the ALA in this adaptation, employing the original contractor, Gaia Resources Environmental Technology Consultants, to continue the work. This rendered many of the original milestones inapplicable and changed the original timeline (see next point also). The project has been extended until 31/05/2011 in order to achieve the required outcomes.

o The project has been time-constrained due to Margaret Cawsey’s prior commitments and absence for 2 months during the project timeline, and the prior commitments of the contractor.

o By 31/12/2010 the pilot data capture system was ready for testing but the time constraints and lack of expedition opportunities among the Collections have not permitted the system to be tested with a variety of Collections/organisms and in a variety of data collection environments. This will happen before 31/05/2011.

Highlights Two highlights from the last period (July 10 to end):

1. Prototype system design accomplished and online form design and download tested, 16/12/2010.

2. Analysis of software and hardware constraints with regard to mobile data capture presented at the TRIN field day in Cairns 9/12/2010.

Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Margaret Cawsey presented and demonstrated the analysis and results of the project at the TRIN field day in Cairns, on 9/12/2010.


Transition Project:

Developing a benchmark invertebrate group for biodiversity modelling

Final Report

Developing a benchmark invertebrate group for biodiversity modelling


Context Information

Project Title Developing a benchmark invertebrate group for biodiversity modelling: phylogenetics and databasing of the dung beetle (Scarabaeidae) genus Lepanus



Project Team Project Leader Dr David Yeates

Host Organisation Australian National Insect Collection, CSIRO Sustainable Ecosystems Project Team Member Role in


Project FTE

Dr David Yeates Leader, Research Coordination

CSIRO Sustainable Ecosystems Systematics & Spatial modelling

0.05

Dr Nicole Gunter Postdoctoral fellow, Molecular Systematics

CSIRO Sustainable Ecosystems Beetle Systematics - molecular

0.1

Mr Tom Weir Senior Curator, Morphological Taxonomy

CSIRO Sustainable Ecosystems Beetle Systematics - morphological

0.05

Dr Stephen Cameron

Molecular Systematics

CSIRO Sustainable Ecosystems Molecular Systematics

0.05

TBA – Technical assistant

Database and molecular lab technician

CSIRO Sustainable Ecosystems 0.5

Developing a benchmark invertebrate group for biodiversity modelling – Final Report: June 2007 to March 2011 - 93 -

Project description Biodiversity modelling methods such as Generalised Dissimilarity Modelling (GDM) are increasingly incorporating phylogenetic as well as species distribution data to more effectively model biodiversity. Developing and testing these methods rely on the existence of benchmark groups for which the taxonomy, phylogenetic relationships and distributional databasing are complete. Few groups of Australian organisms are so well known and at present no invertebrate examples are available. We propose to complete such a dataset for the native dung beetle genus Lepanus Balthasar which consists of 24 described species and 22 undescribed provisional species. Significant digital specimen database records have already been entered into institutional databases around Australia, funded by DEWHA. Distributed throughout most of non-arid, mainland Australia and with the most diversity in the montane wet tropics of Queensland, Lepanus can also be used as a model for the effects of topological heterogeneity and climate change in geospatial modelling systems. We aimed to complete the databasing of Lepanus specimens held in the Australian National Insect Collection (ANIC), and to develop a phylogeny of the group partly by attempting to extract sequence data from existing pitfall trap collected holdings and by collecting fresh material from throughout its range.

Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: We have found that Lepanus species are most reliably characterised by the distinctive shape of the pygidium. Based on this as a primary character, the species can be divided up into 12 assemblages (see table 1). There are variations within the groupings and some groupings are more homogeneous than others, but pygidium structure provides a hypothesis to investigate genetic relationships within the genus. The number of recognisable but as yet undescribed species within the genus has also increased from 22 to 56. Suitability of different specimen types for DNA extraction was assessed with DNA successfully recovered from freshly collected or archival ethanol-stored specimens but not pit-fall trap specimens. Interestingly, the 28S gene was readily amplified from archival specimens but not CO1; both genes were readily amplified from fresh beetles. Phylogenetic analysis of species with both COI and 28S sequence data was performed on 27 Lepanus spp. (131 specimens) representing 10 of the 12 species assemblages (see fig 1). Species assemblages were generally well supported including monophyletic clades for species assemblages 1, 4, 5, 8 and 11. Associations between all species in assemblages 3 and 12 currently remain unsupported due to limited resolution of the tree; however clades containing multiple species in both complexes are supported. The only relationship which is supported that does not correspond to species assemblage is that of CYP3 and CYP5 (Assemblages 6 & 9), however assemblage 6 is only represented by a single specimen. Further taxon or gene sampling is likely to resolve these relationships. While 28S could be amplified from a wider range of specimens, including ones stored for years in 70% ethanol this gene alone could not resolve relationships within the genus. This highlights the need for fresh collections in a project of this type.



Forest dung beetles are a poorly known group in general, however work on Lepanus has also expanded the knowledge base of groups useful for geospatial modelling to include an invertebrate saprovore and an inhabitant of temperate forests.


By conducting molecular diversity assessments alongside morphological descriptions this has improved the confidence with which structures such as the pygidium can be interpreted for delimiting species limits.


By databasing all museum specimens of this genus to include newly recognised species we are ensuring that the geographic and geospatial information on this species is advanced at the same rate as taxonomic discovery


Geospatial modelling uses require both phylogenetic trees and data based spatial series of the species in a given group. Few groups satisfy both requirements and by progressing this group we serve their needs.


All specimens of the genus held in three major collections (ANIC, AM & QM) have been sorted and assigned to an improved informal taxonomy ahead of formal species descriptions in the coming year. This data has been instrumental in developing the project to the point that it has been supported by the ABRS Bush Blitz program. This will support the taxonomic career of Dr Nicole Gunter a postdoc for whom this is her first competitive grant.

Milestones Progress against outcomes and deliverables (outputs), including any milestones, for the period; activities to achieve these; associated completion dates. An explanation of any delays that have occurred, including the reasons for those delays and action proposed to take to address the delay and the expected effects (if any) the delay will have on the project (including subsequent Milestones and the overall completion of the project)



Databasing - ANIC Enter distributional and identification data for ANIC - approx. 2000

December 2010

2228 Lepanus records representing 5485 specimens have been databased (each individual collection date and locality constitutes a single record which may be represented by multiple specimens – individual beetles).


QM/AM Collections assessments

Search bulk collection holdings of the QM and AM for additional Lepanus specimens and pin, label, identify and database the specimens found.

October 2010

• Sorted bulk EtOH collections at AM (contained 59 specimens representing 12 spp.)

• Tom has sorted pinned collection of both AM and QM

• Revision of morphological diversity in the group has lead to the recognition of a further 34 undescribed species.

Assess DNA utility of existing collections

Assess the utility of specimens in hand, both those stored in 80% ethanol plus dried pinned specimens, for extracting DNA for use in molecular phylogenetics. Also identify which genes can be amplified from existing collections versus those freshly collected.

November 2010

• Limited success of DNA amplification from non-optimally preserved specimens.

• DNA was extracted from 105 specimens from existing collections (ANIC and AM).

• Two genes were amplified with varying success. 28S (LSU r DNA) was sequenced for 22 of 105 specimens while only 15 of 105 specimens had COI sequences generated.

Collect fresh samples for DNA amplification

Collections will be undertaken of additional material from several localities in Queensland known to represent gaps from previous collecting efforts. Additionally fresh material will be obtained for molecular phylogenetics

December 2010

Additional material representing 17 spp. has been collected by Geoff Monteith and Nicole Gunter. Over 100 specimens from these recent collections are included in the molecular phylogenetics.

Molecular Phylogenetics

A phylogenetic analysis will be undertaken of all available sequence data (from pitfall specimens which are usable plus freshly collected specimens) for use as a preliminary phylogeny in geospatial modelling.

December 2010

• Species boundaries have been investigated using sequence data generated for 2 genes (28S and COI).

• 28S sequences have been generated for 98 specimens representing 22 spp.

• COI sequences have been generated for 75 specimens representing 16 spp.

• 60 specimens representing 15 spp. have sequence data for both genes.

• Out group data has also been generated for closely related genera including Aptenocanthon and Sauvagesinella.

• Intra- and inter- specific variation investigated


• 28S has supported genetic differences between some species complexes (i.e. villosus/ sp. nov.1 nr villosus and palumensis/ sp. nov NQ8) but does not provide enough resolution to separate some closely related spp. (i.e. nitidus/dichrous complex and ustulatus/globulus).

• Levels of inter-specific variation between Lepanus spp. are higher for COI. All spp. including those not resolved by COI are genetically distinct.

• Preliminary phylogeny of specimens with both genes sequenced support suspected relationships of Lepanus spp. based on morphology.


Specifics of What

Dr Geoff Monteith, Queensland Museum Field collections, taxonomy of the group Dr Chris Reid, Australian Museum Taxonomy of the group Linkages with Outcomes Progress in identifying/linking with target areas of the Department of Environment, Water, Heritage and the Arts or the Australian Government for project outcomes: Specifics of Who (Department, Section, Contact Person)

Specifics of What

Issues

Any issues associated with the project: Highlights Two highlights from the last period (July 10 to end): Completion of the molecular tree for Lepanus allowing us to test the utility of morphological features used in species limits for the first time. Awarding of further funding through the ABRS Bush Blitz program to add an extra gene and to add representatives of the currently unrepresented species groups to this study.


Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Entomological Society of America 2011- Nicole Gunter- Success rates and optimisation of DNA amplification of old and non-optimally preserved beetle specimens (Lepanus: Scarabaeidae) Table 1: Species assemblages of Lepanus based on pygidial characteristics. Species in bold are included in the phylogenetic analysis. Assemblage Characteristics Species 1 Large species with transverse sinuate

fold across base of pygidium. ustulatus, NQ11, globulus, NQ2, and CYP8.

2 Small species with transverse sinuate fold across base of pygidium.

storeyi, NSW2 and NSW3.

3 Pygidium simple, without depression, smooth, entirely nitid.

monteithi, CYP2, NQ5, CYP1, NT1, australis, SQ2, SQ3, latheticus, NQ6 and CQ3.

4 Pygidium simple, without depression, not smooth or nitid.

vestitus, villosus, NQ21, NQ7 and loftyensis.

5 Pygidium with large flat central area which is rugulose and contrastingly matt.

nitidus, dichrous, NQ9 and NQ10.

6 Pygidium with a depression with sharp edges and usually a tubercle in the depression.

pygmeaus, CYP5, NQ26, CYP7, NT4, CYP6, NQ28, WA2, NQ29, WA4, NT2 and NQ27.

7 Pygidium with depression without well defined lower lip or edge.

pisoniae, NQ12, NQ13, NQ14, NQ3, NQ15, NQ16, NQ17, NQ18, NQ19 and NQ20.

8 Pygidium with depression with sharp lower lip or edge and with a pit in the upper angle.

furcifer and NQ2.

9 Pygidium with depression with sharp lower lip or edge and no pit in upper angle.

parapisioniae, NQ23, NQ24, SQ1, CYP3, politus and SQ4.

10 Large species with pygidium with a transverse groove at base that extends right across.

illawarensis, penelopae, WA1 and NSW5.

11 Small species with pygidium with a transverse groove at base that may or may not extend right across.

arator, NQ1, NQ22, glaber, WA3 and CQ2.

12 Pygidium with a well defined depression without any sharp edges.

palumensis, NQ8, NQ4, CYP4, occidentalis, gelasinus, bidentatus, NSW4, NT3,CQ4 and NQ30.


Fig.1 Phylogenetic relationships within Lepanus, a combined analysis of 28S and CO1. Species group assemblages based on pygidium structure are colour coded.


Transition Project:

Rapid Assessment of Species Boundaries of Potential Rare and Threatened Plant Species

Final Report

Rapid Assessment of Species Boundaries – Final Report: June 2007 to March 2011 - 101 -

Rapid Assessment of Species Boundaries of Potential Rare and Threatened Plant Species


Context Information

Project Title Rapid Assessment of Species Boundaries of Potential Rare and Threatened Plant Species


Dates for which this progress report applies July 2010 to end

Project Team Project Leader Dr Joe Miller




Project FTE

Dr Joe Miller Leader and Advisor, molecular taxonomy

CSIRO Plant Industry Plant Systematics 0.1

Dr Mark Clements

Advisor, orchid morphological taxonomy

SEWPAC Orchid taxonomy 0.1

Nigel Swarts Molecular and genome research and analyses

Independent contractor Orchid population genetics

1 (six months)

Project description Conservation agencies require information covering a range of variables relating to population status and biological characteristics. Requests to comment on the taxonomic status of putatively threatened plant species often has little data for assessment. This project utilised methodologies and protocols developed during the TRIN weeds taxonomy and DNA barcoding to rapidly assess the species status of plants that are potentially rare or threatened in order to inform agencies responsible for legislative decisions, such as SEWPAC. Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: Consideration of the conservation status of species is dependent on information that is often not readily available. Conservation agencies, including DEWHA, require information covering a range of variables relating to population status and biological characteristics. Biologists and particularly


taxonomists are often requested to comment on the taxonomic status of putatively threatened plant species, but in many cases there is little data to assess the claims. Thus decisions are sometimes taken at both Federal and State levels about the listing of endangered species with inadequate or no scientific data to support species definitions. This TRIN extension project utilised the methodologies and protocols developed during the TRIN research relating to invasive weed taxonomy and DNA barcoding to rapidly assess the species status of plants that are potentially rare or threatened in order to inform agencies responsible for legislative decisions on threatened species. This short term project had as a goal the analysis of 200 plants in a population genetic study. We were very fortunate to undertake the project during a wet Spring and to have many interested collaborators who helped collect material. In the end we were able to collect and process 600 samples averaging 15 samples per population for nearly 30 populations of the Caladenia reticulata orchid complex. This included material from the type location in South Australia and material from VIC, NSW and TAS. This material was collected in October-November 2010. We had help in collecting material from several interested parties including Victorian conservation officers and other orchid taxonomists who saw value in the project. We were fortunate in being able to hire an experienced researcher in Caladenia population genetics, Nigel Swarts. Swarts had previously worked on another group of Caladenia species and for that work had generated microsatellite markers. Swarts was able to use these markers on the Caladenia reticulata orchid complex with good results. We had five microsatellite markers of which four show good levels of variation and one marker that is less variable and less informative. Due to the unexpected large amount of data that we were able to collect we are still analyzing the data. Our preliminary data suggests that there is a large amount of gene flow among populations and taxa within the Caladenia reticulata orchid complex. This suggests that long distance pollinator activity is connecting gene flow among populations. We are in the process of using metrics to determine the extent of the gene flow which will provide the basis of defining the species. We plan on having a manuscript to review by the end of May 2011. Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

We have investigated the genetic variation within Caladenia reticulata orchid complex which contains three species listed as endangered.


Our data was generated by the application of methodologies developed in other TRIN projects namely DNA barcoding and Invasive species (Lantana) projects. These methodologies and a precise project definition have allowed the rapid (6 month) assessment of genetic variation for a group of species which could easily take years of research using morphology alone.


We are using best practices derived from past TRIN DNA barcoding and invasive species projects. All data will be published in a peer review journal.


We are developing an informational email (eventually on the website) which we will send to interested parties, and relevant State and Commonwealth species listing divisions. We will also send this information to our list of collaborators that helped collect the material.

This email will contain materials, methods and results of our work. It will be an easily digested portion of the research paper.


This project is an example of rapid assessment of species boundaries. We feel it will leave a legacy and we will use it as an example in future grant applications to investigate species boundaries of rare and endangered plant species.




Rapid Assessment of species boundaries of rare and threatened plant species.

Application of recently developed rapid molecular/genetic protocols to assess the genetic analysis of rare species and their closest relatives in order to determine the taxonomic status of a species in question.

December 2010

• Successfully transferred protocols from the DNA barcoding and invasive species project. Most importantly the microsatellite DNA markers from an allied group proved informative in the Caladenia reticulata orchid complex

• We were able to collect and process 600 samples averaging 15 samples per population for nearly 30 populations of Caladenia reticulata orchid complex. This included material from the type location in South Australia and material from VIC, NSW and TAS. This material was collected in October-November 2010.

Application of protocols to exemplar plant group

Genetic assessment to be applied to the orchid complex Caladenia reticulata

December 2010

• Our preliminary data suggests that there is a large amount of gene flow among populations and taxa within the Caladenia reticulata orchid complex. This suggests that long distance pollinator activity is connecting gene flow among populations. We are in the process of using metrics to determine the extent of the gene flow which will provide the basis of defining the species. We plan on having a manuscript to review by the end of May 2011.



Specifics of What

Noushka Reiter – Biodiversity Officer, DSE Victoria

Collaborator and organiser of collections of targeted species of Caladenia throughout Victoria

Lachlan Farrington – SA Government Provided material of targeted Caladenia in South Australia, in particular Kangaroo Island and Adelaide Hills


Specifics of What

SEWPAC, Species Listing Section, Saravan Peacock and Michael Deering

Contacted and wish to discuss results and methodologies

Issues Any issues associated with the project: Due to the short term of the project we were not able to recruit our preferred researcher to Canberra. However this has not been an impediment as Swarts is a highly motivated scientist and has been able to focus on the project without other obligations. Swarts’ effort has been key to the success of the project. Highlights Two highlights from the last period (July 10 to end):

• A highlight of the project was the successful transfer of polymorphic markers from another Caladenia species complex to the Caladenia reticulata orchid complex. This greatly aided the quick start to the project. This was possible by the hiring of Nigel Swarts for the project. His experience in Caladenia population genetics was critical to the success of the project.

• The most important highlight to the project was the exceptionally favourable growing season for Caladenia species. We were able to collect populations of plants that had not been seen in flower for several years. Importantly this allowed us to have a more comprehensive set of material to answer the species delimitation question than we thought possible at the beginning of the project.


Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: We have contacted the SEWPAC Species Listing Section (Saravan Peacock and Michael Deering). We hope to meet with a representative of this department to discuss our results soon.


Transition Project:

3D digital type collection for Australian Small Terrestrial Vertebrates

Final Report

3D digital type collection for Australian Small Terrestrial Vertebrates


Context Information

Project Title 3D digital type collection for Australian Small Terrestrial Vertebrates

Duration of the entire project August 2010 to December 2010

Dates for which this progress report applies August 2010 to end

Project Team Project Leader Dr Ken Aplin

Host Organisation Australian National Wildlife Collection, CSIRO



Project FTE

Dr Ken Aplin Project supervisor

CSIRO 0.1

Dr Fred Ford Early career researcher

CSIRO 1

Project description One of the impediments to taxonomic progress identified during TRIN is access to type specimens. The majority of Australian mammals are held in the National History Museum in London; they are not available for loan. This project obtained high resolution images of the mammal types in London using the Micro CT scanning technology; cutting down on cost and access to these specimens. Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: Two periods of ct scanning were conducted at the Natural History Museum, London, in September and December 2010. More than 100 type specimens were successfully scanned during these trips, including all marsupials of scannable dimensions, all smaller rodents and several genera of bats.

3D digital type collection for Australian Small Terrestrial Vertebrates – Final Report: June 2007 to March 2011 - 107 -


Availability of type material is essential for effective taxonomy on small mammals


Ready access to digital type specimens by Australian researchers will negate need for expensive travel and make integration of type material into taxonomic assessments straightforward


Simple loan access to type images via the ANWC means that types are accessed in the same way as any other specimen


A forthcoming publication will alert users to the collection and how to access it.


The collection represents a significant legacy; a collection of Australian type material in Australia, which would otherwise not have been possible, and which forms a significant component of our biological heritage.


Milestone Completion


Scan Types Travel to London/European collections and scan the type specimens of the listed target groups. Store unprocessed scans to hard drives.

Trip 1. By end of September

All smaller types of marsupials were successfully scanned on this trip

Reconstruct digital data sets

Digitally reconstruct data sets and create digital 3D volume renderings and metadata describing exact scanning and reconstruction protocols

Trip 2. By end of October

Reconstruction of files was achieved, and many had 3D renderings produced.


Create accessible product of public appeal for ALA

Create movies of each specimen that illustrate the key features (dorsal/lateral/ventral views, close up dentition etc). The movies may be the primary ALA product

End November

Copyright issues meant that movies etc for general public display require further negotiation with the NHM by the ALA.

Integrate type into taxonomic studies

Add type data that will permit taxonomic decisions arising from current CERF project work.

End December

Type material for Acrobates spp., Pseudomys delicatulus and its relatives, Pseudomys nanus and its relatives and Nyctimene spp. have been assessed as part of taxonomic studies, with full morphometric integration of Acrobates and P. delicatulus material into existing data sets.

Organise long-term curation of digital data sets and metadata

As necessary; establish standards, data storage, access protocols etc

End October Data storage has been organised, but not yet accessed


Specifics of What


Specifics of What

Issues Any issues associated with the project: Serious transport delays to and from London prevented the secondary goal of the project- scanning of type specimens held in Australian collections.


Highlights Two highlights from the last period (Aug 10 to end): The digital repatriation of priceless Australian type specimens, including e.g. scans of specimens such as the only existing specimen of Pseudomys glaucus. Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Departmental lecture for Zoology Department at The Natural History Museum London, December 14, 2010


Transition Project:

Conserving Australia’s genetic diversity – A Summit

Final Report

Conserving Australia’s genetic diversity – A Summit


Context Information

Project Title Conserving Australia’s Genetic Diversity – A Summit



Project Team Project Leader Dr Judy West

Host Organisation Parks & Biodiversity Science Branch, SEWPAC



Project FTE

Dr Judy West Leader & coordinator

Parks & Biodiversity Science, SEWPAC

0.05

Dr Linda Broadhurst

Advisor - science

Parks & Biodiversity Science, SEWPAC

Conservation geneticist

0.05

Peter Cochrane Advisor - policy

Director of National Parks, SEWPAC

0.05

Dr Iain Gordon Advisor - science

CSIRO Sustainable Ecosystems; Biodiversity Theme Leader

0.05

Dr Charlie Zammit Advisor - policy

Land and Coasts Division, SEWPAC

0.05

Project description The Summit was held to bring together Australia’s leading geneticists, biodiversity scientists and policy developers to explore the key elements for a more systematic approach to conserving Australia’s genetic diversity and bring the issue more sharply into focus in the context of policy directions that are increasingly adopting whole of landscape and multiple species approaches to conservation. Activities this period A summary of the work undertaken this period and an analysis of the effectiveness of the work: A three day summit held in October 2010 brought together a broad range of participants with a primary interest in improving the management of Australia’s biodiversity. The participants were selected from State and Federal government agencies and Australian research institutions for their experience in conservation genetics, policy and biodiversity management. The aim of the summit was to highlight the importance of genetic information and the types of information it can provide, and to develop ways of incorporating this information into policy and decision making to improve

Conserving Australia’s genetic diversity – A Summit – Final Report: June 2007 to March 2011 - 112 -

biodiversity outcomes. The summit highlighted two important outcomes – that genetic information is important and needs to be included in the decision-making process but that it needs to be in a form that is interpretable by policy and decision makers. A discussion paper summarising the outcomes of the summit and providing recommendations on how to incorporate genetic information into decision making and planning is being prepared and will be available for general comment by mid-2011. Contribution to Hub Objectives A description of how the work undertaken this period has contributed to meeting the Hub objectives: Close the knowledge gaps in key Australian taxonomic groups which are important for environmental management.

Knowledge of genetic diversity can assist with taxonomic delimitation


Incorporation of genetic, molecular and barcoding information through use of molecular markers and phylogenies have assisted in bringing together significant datasets to better understand some groups.



The discussion paper will be printed and available on the web in a form readily decipherable by policy makers to ensure uptake of the recommendations.


The discussion paper highlights the need for genetic taxonomic work to identify and appropriately manage cryptic species and species complexes.


Milestone Completion Date Details – what did you achieve and what did you produce

To hold a summit involving c. 30 participants in Canberra that will bring together conservation geneticists and biodiversity managers to: • Identify the ‘state of the art’ of

conservation genetics • Consider threats and risks to

genetic diversity

August/September 2010

Summit was held on 12-14 October 2010 and brought together 25 participants from Federal and State government agencies and research institutions including geneticists, biodiversity managers and policy makers. Presentations from researchers highlighted the role of


Identify gaps and opportunities for how approaches to conservation genetics can be better integrated into existing policy and program initiatives

that genetics can play in decision making while policy/managers presented information on how decisions are made and the types of information they require. Gaps in understanding and opportunities for including genetic information were discussed and a series of recommendations were devised.

Prepare policy relevant technical Proceedings for use by researchers and biodiversity planners and managers

December 2010

A discussion document is in preparation with the final draft being available for comment by the participants mid-March. This document will then be circulated to other researchers and stakeholders such as NGOs for comment. The final discussion paper for external comment is anticipated mid-2011.


Specifics of What

Approvals & Wildlife Division, Michael Deering Regulatory systems, endangered species listing

Land and Coasts Division, Emma Burns Ecological communities, stewardship

Marine Division, Paul Garrett Marine diversity

Parks Australia, Linda Broadhurst Genetic diversity Linkages with Outcomes Progress in identifying/linking with target areas of the Department of Environment, Water, Heritage and the Arts or the Australian Government for project outcomes: Specifics of Who (Department, Section, Contact Person)

Specifics of What

AWD; Land & Coasts; Parks Australia; Marine Uptake and incorporation into policy

Issues Any issues associated with the project:


Highlights Two highlights from the last period (July 10 to end): 1. Bridge-building between policy makers and biodiversity managers and geneticists to improve the exchange and interpretation of information between each. 2. Group of geneticists available for consultation by policy makers and biodiversity managers. Communication and capacity building e.g. Communication outputs (media release, poster etc), generated public awareness, community engagement or training opportunities: Media release proposed for discussion document release


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