Marine Scotland Science

Proposed PhD studentships for the next round of SUPER DTP

Contents - Brief project title outlines

Project 1 Identifying the mechanisms involved in marine ecosystem responses to climate change.

Project 2 Ocean acidification impacts on the west coast of Scotland

Project 3 Fish killing flagellates in Scottish waters

Project 4 Modelling the impact of spatial fishery closures on commercially exploited shellfish stocks.

Project 5 Production of wild salmonids in Scotland

Project 6 Using environmental DNA to estimate salmon abundance in Scotland

Project 7 Sea trout in Scotland: genomic basis of anadromy and patterns of anadromy across the country

Project 8 The use of genomic tools to define effective population sizes of salmon in Scotland

Project 9 Immunogenetic status of salmonid populations in Scotland

Project 10 Killer whale predation of harbour seals in the coastal waters of Scotland: investigating the ecological drivers and consequences of an apex predator-prey interaction

Project 11 Harbour porpoise habitat associations: comparing east and west Scotland

Project 12 Influence of vessel traffic on cetaceans using the Scottish North Sea region

Project 13 Ocean multi-use at floating offshore windfarms to reduce conflicts with fisheries

Project 14 Movements and behaviour of diadromous fish in coastal waters

Project 15 Climate change impacts on seabirds in Scotland and opportunities for its mitigation

PROJECT 1 Proposed project title Identifying the mechanisms involved in marine ecosystem responses to climate change. Areas of interest Environmental dynamics, Biodiversity, Challenged Ecosystems, Estuarine/Marine Keywords Climate change, trophic interactions, Marine Ecosystems Brief description

The present-day rapid changes in the marine environment include a 0.6 to 1.5°C observed temperature increase in the North Sea over the last 3 decades and significant increases projected for the future decades. These temperature changes mean that the majority of marine biological processes are affected as most marine organisms are ectothermic (rely on environmental heat sources). Temperature effects on the physiology and phenology of marine organisms at the species level (e.g. spawning time, energetic requirements, growth, thermal tolerance) are widely reported, however differences in such responses among trophic levels may have a profound impact on the structure and productivity of marine ecosystems. Understanding how temperature affects the relative phenology and physiology of predators and prey is therefore of paramount importance for predicting climate change impacts on marine ecosystems.

Using environmental and biological data time-series, experimental work and

modelling, the proposed project aims at acquiring important knowledge on the effect of global warming on marine ecosystem structure and productivity in order to allow predictions of its consequences on biodiversity and ecosystem services but also to anticipate and advise on the appropriate management measures required to mitigate such effects. In particular, the project aims at quantifying the effects of temperature on the phenology and physiology of interacting species (fish, zooplankton), identify traits and mechanisms allowing resilience and model the consequences at the ecosystem level to improve their predictability and identify management scenarios to mitigate these effects. Proposed MSS supervisors Thomas Régnier, Dafne Eerkes-Medrano, Peter Wright Policy drivers The main legislative drivers for this project are the UK Marine Climate Change Impacts Partnership and Wildlife and Natural Environment (Scotland) Act 2011. Scottish Climate Change Adaptation Programme Ch3 Risks to the marine food chain.

PROJECT 2 Proposed project title Ocean acidification impacts on the west coast of Scotland Brief description Ocean acidification (OA) poses a serious risk to biota in the marine environment. A study from the Scottish Coastal Observatory monitoring site at Stonehaven has revealed shell dissolution of pteropod and pelagic gastropod larvae shells even when seawater was super saturated with aragonite (Leon et al., accepted). Preliminary studies from Stonehaven have also shown evidence of shell dissolution in bivalve larvae. The west coast is the location for much of the shellfish aquaculture and scallop fisheries in Scotland. MSS is in the unique position to lead a Ph.D. study to investigate the relationship between carbonate chemistry and shell integrity in bivalve larve and adult shellfish of commercial importance. Using carbonate chemistry data collected as part of the COMPASS project along with the plankton sample archive from the Scottish Coastal Observatory monitoring site at Loch Ewe, an assessment of shell dissolution of bivalve larvae of along with potential indicator species (pteropod and pelagic gastropod larvae) will be performed. Adult bivalves of commercial importance for the aquaculture and scallop fisheries will also be collected from the area and assessed for impacts for OA. Data collected will provide the first in-depth assessment of OA on both adult and larval shellfish on the west coast and will form the basis of key advice on OA impacts in Scottish waters for aquaculture and commercial shellfisheries into the future. Outputs will also contribute to national and international initiatives relating to OA via MCCIP assessments, ICES WGs and the Global Ocean Acidification – Observing Network. References Leon P., Bednaršek N., Walsham P., Cook K., Hartman S., Wall- Palmer D., Hindson J., Mackenzie K., Webster L., Bresnan E., (accepted) Relationship between shell integrity of pelagic gastropods and carbonate chemistry parameters at a Scottish Coastal Observatory monitoring site. ICES Journal of Marine Science. Proposed MSS supervisors Pablo Diaz, Lynda Blackadder and Pam Walsham

PROJECT 3 Proposed project title Fish killing flagellates in Scottish waters Brief description The farmed fish industry is worth more than £1bn to the Scottish economy. Harmful algal blooms pose a risk to this industry with losses recorded since 2000 associated with diatoms and dinoflagellates such as Chaetoceros and Karenia mikimotoi. Fish killing flagellates also pose a serious risk to the farmed fish industry. While the presence of potential toxin producing species have been recorded in Scottish waters, their small size (< 20µm) and poor preservation (making identification difficult) means little is known about their seasonality or ecology. This project aims to address this knowledge gap by investigating the diversity of these flagellate groups in Scottish waters, validating molecular techniques to facilitate routine identification and investigating mechanisms of harmful action on fish gill integrity. Using the plankton archive from the Scottish Coastal Observatory as well as archived samples already collected during 2006/2007, methods validated by this project will be applied to provide a first assessment of the seasonality of this group and if abundance and regional distribution has changed over time. Outputs from this project will provide improved advice to the aquaculture industry about the risk from this harmful algal group as well as best practise sampling protocols during mortality events to allow the causative organism to be accurately identified. Outputs will also feed into a number of national and international initiatives associated with harmful algae such as MCCIP, UK HAB Working Group, ICES-IOC Working Group on Harmful Algal Bloom Dynamics, IOC UNESCO Intergovernmental Panel for Harmful Algal Blooms (IPHAB) Fish Killing Algae Task Team. Proposed MSS supervisors Eileen Bresnan & Iveta Matejusova

PROJECT 4 Proposed project title Modelling the impact of spatial fishery closures on commercially exploited shellfish stocks. Brief description Scottish shellfish fisheries (scallops, crabs and lobsters) have significant value (landings worth over £150 million at first sale in 2018), and the economic benefits of these fisheries play an important role in supporting coastal/rural communities in Scotland. Most of these species have sedentary adult stages confined to specific seabed habitats, but annually release larvae that drift passively in the water column for periods of days-weeks. Habitats are patchily distributed, and only larvae which settle on appropriate habitat will survive and contribute to the population into the future. The linkages between patches is currently not well understood but is clearly a key factor in the population dynamics and requires consideration when identifying potential fishery management measures such as gear restrictions, minimum landing sizes and spatial closures. In addition, the population dynamics are also likely to be affected by the development of marine renewable energy systems, especially wind-farms. Scallop habitats off the east coast of Scotland will be particularly affected: exclusion zones around renewable sites may offer protection from fishing while fishing effort displacement may result in more intensive exploitation of stocks in other areas. The aims of the project are to identify which patches of habitat are sources and which are sinks, and to identify whether spatial closures (including those created by the development of renewable energy schemes) can contribute to sustainable management of scallop fisheries. Addressing these issues will require the development of spatial models of population dynamics of these exploited stocks – linking simulated larval dispersal patterns to models of the growth, survival and spawning of individuals which settle on suitable habitat. Outputs will contribute to the Scottish Government’s commitments to ensuring that commercial shellfish stocks are harvested sustainably and in addition, to marine spatial planning, in particular advising on the potential fishery/stock impacts of future renewable energy developments. Proposed MSS supervisors Helen Dobby

PROJECT 5 Proposed project title Production of wild salmonids in Scotland Brief description Populations of wild salmon in Scotland are in decline and now at lowest levels on record. The is an urgent need to increase production of salmon in freshwater systems, protect against environmental change and moderate impacts of factors affecting salmon where possible. This process can be underpinned by improved knowledge of the genetics and environment of salmon and there are strands of work that would work well as PhD studentship projects. As such two clusters are proposed and a number of possible projects are provided as examples: Cluster 1. Environmental factors affecting production of wild salmonids in Scotland 1. effects of impoundment and inter-basin transfer on hydrological and thermal regime and consequences for salmon. 2. interactions between temperature and hydrology on fish productivity and bioenergetics. 3. interactions between temperature and hydrology of abundance of invertebrates and their availability as fish food. 4. using river connectivity models to predict impacts of beavers on production of wild salmon. 5. prediction of runoff in ungauged catchments as inputs to river temperature and juvenile salmon density modelling. Cluster 2. Genetics factors affecting production of wild salmonids in Scotland 1. The fitness of farm-wild hybrid salmon in Scotland 2. Landscape genetics and population structure of salmon in Scotland 3. The use of genetic tools to define effective salmon population size in Scotland 4. Sea-trout in Scotland: genetic basis of anadromy and patterns of anadromy across the country 5. eDNA and salmon abundance in Scotland 6. Population connectivity of salmon in the NE of Scotland. Relevant references Pawluk, et al. 2019. Sea lice loads correlate with the diversity at the Major

Histocompatibility Complex-related loci in farmed Atlantic salmon, Salmo salar. Journal of Fish Diseases, 42: 1091-1093.

Tonteri, et al. 2010. Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune-relevant loci. Molecular Ecology, 197: 1273-1282. Dionne, et al. 2009. MHC standing genetic variation and pathogen resistance in wild Atlantic salmon. Phil Trans Roy Soc B: Bio Sci, 364(1523): 1555-1565.

Proposed MSS supervisors John Armstrong, David Morris, John Gilbey Policy drivers Conservation of wild salmon together with the sustainable growth of the aquaculture industry relies on understanding the interactions between wild and farmed fish. Increasing understanding of the risks associated with adaptive changes in wild populations associated with the industry, will help in the sustainable management of industry and conservation of wild stocks

PROJECT 6 Proposed project title Using environmental DNA to estimate salmon abundance in Scotland Areas of interest Assessment, conservation Keywords eDNA, conservation limits, biomass Brief description Estimation of the status of juvenile salmon populations is currently achieved through time consuming, logistically challenging and expensive electrofishing procedures. This project aims to assess the potential of environmental DNA (eDNA) procedures to estimate the biomass of juvenile salmonids at discrete and spatially defined locations on a river network. The work would initially focus on rigorous calibration of the techniques at Marine Scotland reference sites (the Girnock and Baddoch) where there is detailed understanding of chemical, hydrological, hydraulic and thermal characteristics. These sites also have detailed information on adult returns, egg deposition and juvenile densities obtained from electrofishing and recently developed novel spatial statistical river network models. As such they provide perhaps the best model system for testing the eDNA approach in the UK. The work would then expand to other locations on the Aberdeenshire Dee where information is available to calibrate the tool at sites with a wider range of environmental conditions. This work will be supported by recently developed water quality and river temperature models as appropriate. The overall aim of the project is to assess whether e-DNA can be directly related to spatially delineated estimates of juvenile salmonid biomass obtained from traditional electrofishing approaches and to understand how local calibration relationships are affected by water volume, residence time and rates of degradation which are in turn expected to relate to water quality including river temperature. Project structure

• Obtain e-DNA samples from sites distributed across the Girnock and Baddoch burns of the Dee considering pre-existing data on fish abundance.

• Develop a cost effective laboratory and/or bankside assay and screening procedure for quantification of the eDNA collected.

• Examine eDNA persistence times using experimental laboratory based analysis of differing environmental influences.

• Screen eDNA from the model systems and using the assay developed.

• Assess relationships between e-DNA concentrations and juvenile salmonid biomass estimated from electrofishing for a range of upstream distances thereby assessing the spatial extent of any assessments.

• Relate the spatial extent of correlations between e-DNA and electrofishing estimates of biomass to river temperature, hydrochemistry and hydraulic conditions (velocity, residence times) at the sample locations. .

• Devise and implement an eDNA collection/screening survey at a number of new sites in the larger Dee system where biological and environmental metrics are known.

• Integrate the findings to explore the potential of eDNA sampling to be used to assess juvenile salmonid biomass in Scotland.

Relevant references Carraro et al 2018 Estimating species distribution and abundance in river networks using environmental DNA. PNAS 115:11724-11729 Tillotson et al 2018. Concentrations of environmental DNA (eDNA) reflect spawning

salmon abundance at fine spatial and temporal scales. Biological Conservation, 220: 1-11.

Evans & Lamberti 2018. Freshwater fisheries assessment using environmental DNA: A primer on the method, its potential, and shortcomings as a conservation tool. Fish Res, 197: 60-66.

Doi et al 2017. Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshwater Biology, 62(1): 30-39.

Proposed MSS supervisors Iveta Matejusova, John Gilbey, Iain Malcolm Policy drivers Although e-DNA is not able to determine absolute juvenile fish numbers or life-stages, it has the potential to provide an indication of biomass where suitable calibrations could be developed. Although recently developed juvenile assessment procedures are based on counts of fish from electrofishing, it is possible that new metrics of population health could be developed based on biomass. It has been hypothesised that e-DNA approaches could be extended from existing indicators of presence and absence to also include biomass. If it was possible for eDNA to be used in such a way and if it were possible to develop new assessment benchmarks then such an approach could provide a far more cost effective assessment of the status of fish populations in rivers in the same way as recently developed for standing waters.

PROJECT 7 Proposed project title Sea trout in Scotland: genomic basis of anadromy and patterns of anadromy across the country Areas of interest Assessment, conservation, interactions Keywords anadromy, trout, mapping Brief description Understanding the genomic architecture of adaptive traits associated with different life history paths is vital to the successful management of different stock components. Genome wide association studies (GWAS) have already been used to identify adaptive genetic markers to aid management of Atlantic salmon and this project will seek to utilise the same approach to try to understand anadromy in brown/sea trout, Salmo trutta, and to develop a bespoke set of genetic markers associated with the migratory tendency in this species in Scotland. Once markers have been selected and validated, surveys of trout populations will be undertaken to examine population structuring and patterns of anadromy in rivers, and the interaction of anadromous traits, genetic propensity to migrate and environmental variables. The work would aim to enhance understanding of migratory trout in Scotland, with a view to allowing enhanced knowledge-based management of this threatened resource. Project structure

• Identifying, collating and preparing samples of resident brown and anadromous sea trout from a number of rivers across Scotland to perform initial genome wide screening and validation.

• Carry out GWAS to identify a panel of markers associated with anadromy.

• Validate those markers on new samples from a number of populations.

• Carry out Scotland-wide screening of juvenile trout populations using newly collected and/or samples already held.

• Screen juveniles at panel of genetic markers and determine patterns of population structure and anadromy.

• Examine Scotland-wide patterns of anadromy and environmental variables.

• Examine the influence of aquaculture on patterns of anadromy. Relevant references Ferguson et al. 2019. Anadromy, potamodromy and residency in brown trout Salmo

trutta: the role of genes and the environment. Journal of Fish Biology. Early Access.

Narum et al. 2011. Candidate Genetic Markers Associated with Anadromy in Oncorhynchus mykiss of the Klickitat River. Transactions of the American Fisheries Society, 140(3): 843-854.

Proposed MSS supervisors David Morris, Eef Cauwelier Policy drivers Elucidating basic population structure of sea trout populations will help in the assessment of wild stocks, as well as identifying origin of sea trout in the marine environment. Conservation of sea trout relies of understanding the patterns of anadromous fish across the country such that anadromous components can be identified and managed effectively. Further, sustainable growth of the aquaculture industry relies on understanding the interactions between wild sea trout populations and farmed fish. Increasing understanding of the risks associated with adaptive changes in wild populations associated with the industry will help in the sustainable management of industry and conservation of wild stocks.

PROJECT 8 Proposed project title The use of genomic tools to define effective population sizes of salmon in Scotland Areas of interest Assessment, conservation Keywords Genomics, stock assessment, conservation limits Brief description Building on previous work began at MSS FFL this project will investigate the utility of using genomic tools to define effective population sizes (Ne) of salmon in Scotland. The project will combine unique datasets held at FFL at both the Scotland-wide scale and tributary/river scale with genotype data to develop a genomic tool for estimating effective population sizes across the various environments seen in Scotland. High-density genome-wide marker genotyping and/or whole genome sequencing will be used to examine large proportions and/or entire genomes of groups of salmon from model populations. Such populations will be chosen where there are robust estimates of census numbers of fish from quantitative electrofishing and/or adult traps. Effective population size estimates will then be made based on the genomic data and genetic linkage information, and such estimates corroborated using the census data. Once calibrated using the model systems the approach will be extended to cover a range of habitat types and again compared to census counts derived by quantitative electrofishing. The ultimate aim of the work would be to identify a cost-effective genetic tool for estimating effective population size which can be used across the range of habitats found in Scotland. Project structure

• Identification of model sites and high-density genome-wide marker genotyping and/or whole genome sequencing of fish at the sites

• Calculation of contemporary effective population size and back-calculation of historic trends

• Corroboration of genomic estimates with known census data where possible

• Development of most efficient set of genomic markers to give power to obtain robust estimates of effective population size.

• Assessment of marker panel across a wide variety of habitat types in Scotland

• Refinement of tool to give cost-efficient robust estimates of effective population size across the country

Proposed MSS supervisors John Gilbey, Stuart Middlemas Policy drivers The main legislative policy drivers for this project are the Conservation of Salmon Regulations 2016. Current efforts in estimating the conservation status of Atlantic salmon involve combining the results of multiple methods as there is currently no single method that does not have some form of drawbacks. The use of genetic methods of determining population size are used elsewhere in the management of salmonids and could prove a valuable additional technique to assessing conservation status on Scotland. In addition, recent developments have shown that changes in salmon populations can also be inferred from contemporary samples, giving important information on trends over time when there are concerns about the state of salmon stocks. Relevant references Lehnert, S. J., Kess, T., Bentzen, P., Kent, M. P., Lien, S., Gilbey, J., Clément, M., et

al. 2019. Genomic signatures and correlates of widespread population declines in salmon. Nature Communications, Accepted.

Barría, A., Christensen, K. A., Yoshida, G., Jedlicki, A., Leong, J. S., Rondeau, E. B., Lhorente, J. P., et al. 2019. Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array. Frontiers in Genetics, 10: 498-498.

Hollenbeck, C. M., Portnoy, D. S., and Gold, J. R. 2016. A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci. Heredity, 117(4): 207-216.

PROJECT 9 Proposed project title Immunogenetic status of salmonid populations in Scotland Areas of interest Aquaculture interactions Keywords Aquaculture, adaptation, immune genes, conservation Brief description To assess genetic diversity that captures information relevant to the conservation of populations, it is sensible to use genetic markers associated with ecologically important traits. MHC and other immune-related genes could provide measures of the immunological fitness of salmon populations of conservation interest and the adaptive potential of these populations when threatened by disease outbreaks. Exposure to parasites and/or pathogens associated with aquaculture can result in strong selective pressures being exerted on wild individuals. For example strong associations have been found between sea-lice loading and MHC and other immune related loci in farmed Atlantic salmon. Such associations mean there is also the potential for significant anthropogenic driven immunogenetic changes in wild populations exposed to these pathogens. These changes may reduce genetic diversity and be exacerbated at a population level when coupled with the observed reductions in salmon marine survival. Reduced immunogenetic diversity is of concern as it reduces the resilience of a population to stressors (e.g. climate change or exposure to novel pathogens/ strains) making it more susceptible to extinction. This project would seek to use genetic materials collected as part of the National Electrofishing Programme for Scotland (NEPS) introgression program to characterise immune gene diversity in the wild in Atlantic salmon around Scotland and examine levels of diversity, selection and adaptation specifically associated with the aquaculture regions around the country. The outputs of the project will inform studies examining selective breeding and disease resistance (e.g. sea lice) within the aquaculture industry, and provide an understanding of the resilience of salmon populations around Scotland to disease which is of importance to conservation measures and fisheries management. Project structure

• Screen tissue samples from fish collected from across Scotland as part of the National Electrofishing Project for Scotland (NEPS) at immune related loci shown or suspected to potentially be involved in adaption to pathogens and/or parasites associated with farming and examine findings in regard to the patterns of aquaculture associated with the collection site

• Perform genome scans to identify genomic regions associated with immunological adaptation to pathogens and/or parasites associated with aquaculture

• Examine temporal patterns of adaptation to pathogens and/or parasites using historic material (scales/tissue) held at MSS FFL and the genetic and genomic markers found to be associated with adaptive responses

• Examine introgression into wild populations through escapes and interbreeding of farmed gene variants associated with resistance to pathogens and/or par from aquaculture lines selected for such resistance/genes using samples from the NEPS project.

Relevant references Pawluk, et al. 2019. Sea lice loads correlate with the diversity at the Major Histocompatibility Complex-related loci in farmed Atlantic salmon, Salmo salar. Journal of Fish Diseases, 42: 1091-1093. Tonteri, et al. 2010. Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune-relevant loci. Molecular Ecology, 197: 1273-1282. Dionne, et al. 2009. MHC standing genetic variation and pathogen resistance in wild Atlantic salmon. Phil Trans Roy Soc B: Bio Sci, 364(1523): 1555-1565. Proposed MSS supervisors David Morris, John Gilbey Policy drivers Conservation of wild salmon together with the sustainable growth of the aquaculture industry relies on understanding the interactions between wild and farmed fish. Increasing understanding of the risks associated with adaptive changes in wild populations associated with the industry, will help in the sustainable management of industry and conservation of wild stocks.

PROJECT 10 Proposed project title Killer whale predation of harbour seals in the coastal waters of Scotland: investigating the ecological drivers and consequences of an apex predator-prey interaction Areas of interest Marine Mammals Brief description This project will use a combination of Passive Acoustic Monitoring, visual observations, photo-identification and citizen science to assess the extent of killer whale predation of harbour seals and the role this plays in the local population declines of harbour seals. It will also determine the behaviour of killer whales in the vicinity of known seal haul outs, potential ecotype divisions and prey between killer whale clans. In studying these predator-prey interactions in situ, the project will provide an important insight into the consequences of multiple stressors on ecological communities. Proposed MSS supervisors Ross Culloch, Ewan Edwards or Kate Brookes Policy drivers Harbour seal populations, including those identified as qualifying features of Special Areas of Conservation (SACs), have undergone significant declines, with predation being identified as a potential contributory cause. The killer whale population is small and vulnerable with several knowledge gaps identified in the cetacean conservation strategy. Scotland has a requirement to monitor killer whales through OSPAR.

PROJECT 11 Proposed project title Harbour porpoise habitat associations: comparing east and west Scotland Areas of interest Marine Mammals Brief description Using data collected across several acoustic monitoring projects (e.g. ECOMMAS, JOMOPANS, COMPASS, MarPAMM), a comparison between harbour porpoise habitat associations in the east and west coast of Scotland will be undertaken. These regions have considerably different habitats (e.g. sandy vs. rocky substrates) that will support a varying and potentially diverse range of prey species, for example. Understanding the distribution and relative use of these two areas by harbour porpoise, and the relevant ecological drivers for this, is important in the context of management and protection of the species Proposed MSS supervisors Ross Culloch, Ewan Edwards or Kate Brookes Policy drivers To better inform monitoring and management of harbour porpoise both in the Inner Hebrides and the Minches SAC, and outside it. To address the knowledge gaps identified in the cetacean conservation strategy, e.g. the importance of supporting habitat

PROJECT 12 Proposed project title Influence of vessel traffic on cetaceans using the Scottish North Sea region Brief description This project will use acoustic data collected through Marine Scotland Science’s ECOMMAS project, along with AIS and VMS data to investigate the extent to which shipping traffic influences how cetaceans use the region. This project will consider whether, and the extent to which, noise generated by shipping may affect cetaceans in Scottish waters. ECOMMAS data include cetacean click detections and broadband recordings, which can also be used to monitor noise levels from shipping. Proposed MSS supervisors Ross Culloch, Ewan Edwards or Kate Brookes Policy drivers Under the EU Marine Strategy Framework Directive, and through OSPAR, Scotland has a requirement to monitor underwater noise levels, its impact on the marine environment and to consider management to reduce the impact of this.

PROJECT 13 Proposed project title Ocean multi-use at floating offshore windfarms to reduce conflicts with fisheries Brief description To explore multi-use as a mean of reducing potential conflicts from floating offshore wind farms with other marine users (e.g. fisheries). To better understand the environmental effects and changes in ecosystem structure of excluding mobile fisheries from a floating offshore wind farm e.g. quantify changes in benthic and fish communities, study the localised recovery of the benthos with associated spill-over effects from enhanced local production into adjacent areas; and explore mitigation options e.g. alternative harvesting methods (static gears). Proposed MSS supervisors Andronikos Kafas and Marion Harrald Policy drivers The Scottish Government is committed to the continued growth of the renewable energy sector in Scotland. Offshore wind is a large scale technology with the potential to play a pivotal role in Scotland’s energy system over the coming decades. The development of technologies such as floating wind, which offer scope for development in deeper water, have significant potential to contribute offshore wind energy supply at affordable prices. In light of large-scale floating wind farms and broad incompatibility with mobile fishing gears, demonstrating the multi-use potential of floating windfarms with other marine users, such as commercial fisheries, as well as study the environmental effects will be crucial for sustainable development.

PROJECT 14 Proposed project title Movements and behaviour of diadromous fish in coastal waters Areas of interest Diadromous Fish Brief description Scotland is a stronghold for diadromous fish species such as Atlantic salmon and sea trout which are important receptors in the context of marine renewables and other developments. Understanding how developments may interact with them is key to environmental risk assessment and identifying possible mitigation measures. There is limited information on the movements and behaviour of salmon and sea trout on the east coast of Scotland where most of the marine renewables development is currently taking place. Acoustic tracking of salmon and sea trout smolts moving out of rivers in the east of Scotland has or will shortly be undertaken, with fixed arrays of receivers used to detect smolt as they migrate into the marine environments. These data will be used to investigate smolt dispersal and subsequent use of areas for on-growing. Although the Ythan is a very important sea trout river, no tracking has previously been carried out on its sea trout and the work would allow comparison with data currently being obtained from other areas including west coast situations with complex coastal topography. The project would capitalise on acoustic arrays and receivers being put in place as part of the European Offshore Wind Deployment Centre Scientific Research Programme or otherwise available and would involve working closely with the local Fisheries Trusts. Subsequently, the PhD could continue to build on the Ythan sea trout tracking work or move on to other studies on the movement and behaviour of diadromous fish in coastal waters. Proposed MSS supervisors Robert Main and David Morris Policy drivers To understand the potential for interaction between marine developments and diadromous fish species, which are species of high conservation importance, as is required under European and national obligations for Habitats Regulation and Environmental Impact Assessments.

PROJECT 15 Proposed project title Climate change impacts on seabirds in Scotland and opportunities for its mitigation Brief description This project would model the potential impacts of forecast climate change scenarios on seabird species distribution and abundance within Scotland, identifying key changes that may occur and opportunities for mitigation or adaptive management approaches that could be put in place. Proposed MSS supervisors Jared Wilson or Tom Evans Policy drivers Scotland supports internationally important numbers of seabirds that are legally protected. The relevant legislation and policy drivers include the EU Birds Directive, the EU Marine Strategy Framework Directive, and the Marine Scotland Act 2010.