sarah adamowicz - pros and cons of collecting specimens for barcoding vs. sampling existing...
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Discussing the pros and cons of fresh sample collections versus museum collections for DNA barcoding.TRANSCRIPT
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Pros and Cons of Collecting Specimens for Barcoding vs. Sampling Existing Collections
Sarah Adamowicz, Assistant Professor
Biodiversity Institute of Ontario & Dept. Integrative BiologyUniversity of Guelph
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1- Scientific perspective
2- Logistical issues
3- Financial considerations
Museum Specimens vs. Fresh Specimens
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Scientific Perspective: What Is Your Goal?
1. Barcode campaigns: generating the library
2. Targeted taxonomic questions
3. Environmental barcoding & biomonitoring
4. Other applications: e.g. bio-surveillance, food safety, marketplace fraud, invasive species
5. Site or regional biodiversity surveys
6. Ecological questions
7. Evolutionary questions
8. ????
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Taxonomic-focused campaigns• aim to be comprehensive• will enable identification• assist with applications• will facilitate other research directions
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Collections are a rich source of identified specimens
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Region-focused campaigns
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Churchill Northern Studies CentreChurchill Northern Studies Centre
Barcoding the Biota of Churchill, Manitoba, Canada
Sub Arctic
Low Arctic
High Arctic
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Comprehensive Habitat Coverage
Terrestrial
Nearshore Marine
Freshwater
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Field Course Students Contribute to Survey
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Red = Historical
Blue = Shared
Black = Contemporary
Microgastrinae wasps collected in either 2005-2007 or between 1930 and 1960 at Churchill
Fernandez Triana & Smith et al (2011) PLoS ONE 6(8): e23719
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Ecological Questions Regarding Biological Associations
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• For your goal, are there suitable specimens or tissues in a collection?
• Can you gain permission to sample the collection?
• Are there frozen tissues, pinned specimens, or fluid samples?
• How old are the specimens and how are they preserved?
2- Logistical Issues
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Museum specimens can yield shorter sequences
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Barcode information analysis
Full-length barcode
95-97% resolution
Mini-barcode zone
91-95% resolution
Meusnier et al. 2008
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Barcode (650 bp) Mini-barcode (130 bp)
Specimen success by age
>90% 5-10 years >90% Up to 200 years
Species resolution >95% 91-95%
Technology Sanger (ABI) Sanger (ABI)
NextGen (i.e. 454)
Applicability Barcode library
Routine barcoding
Museum samples
Environmental barcoding
Barcode vs. Mini-Barcode
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150 years old and key to a taxonomic puzzle
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• “Identification success” requires something to match to, reference library.
• The BARCODE data standard, such as employed by iBOL, requires longer sequences (> 500 bp).
• Therefore, typically one has to use multiple primer pairs and prepare contigs to gain longer sequences.
BUT…
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Canadian Centre for DNA Barcoding:http://www.dnabarcoding.ca/
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3- Financial Considerations
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Relative co
st per
samp
le
Complexity
Cost of laboratory analysis
Capacity (limited by total available staff hours to complete editing of processed samples)
Tradeoff: Capacity/Cost vs Complexity
- Evgeny Zakharov, Director of Laboratory Operations, Canadian Centre for DNA Barcoding
Fresh (12 steps/sample)
Mix (18 steps/sample)
Museum (24 steps/sample)
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Fresh vs Museum Pros/ConsMetric Malaise* Fresh/Recent Museum/OldProcurement cost √√√ √√ √√
Cost of laboratory analysis √√√√ √√√ √√√
Speed (processing time) √√√√ √√√ √√√
Sequence quality √√√√ √√√ √√
Data quality (species IDs) √√√ √√ √√√
Contamination Risk √√ √√ √√√
Capacity Utilization √√√ √√√ √√√
Taxonomic diversity √√ √√ √√√
Cost of voucher curation and sample prep √ √√√ √√
Barcode standard compliance √√√ √√√ √√
√√ √ Negative Score Positive Score √√√
*"easy" samples to work with, but risk of oversampling, thus meaning new biodiversity rich areas are to be targeted where no sampling was done before.
- Evgeny Zakharov
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Fresh vs Museum Pros/ConsMetric Malaise* Fresh/Recent Museum/OldProcurement cost √√√ √√ √√
Cost of laboratory analysis √√√√ √√√ √√√
Speed (processing time) √√√√ √√√ √√√
Sequence quality √√√√ √√√ √√
Data quality (species IDs) √√√ √√ √√√
Contamination Risk √√ √√ √√√
Capacity Utilization √√√ √√√ √√√
Taxonomic diversity √√ √√ √√√
Cost of voucher curation and sample prep √ √√√ √√
Barcode standard compliance √√√ √√√ √√
√√ √ Negative Score Positive Score √√√
*"easy" samples to work with, but risk of oversampling, thus meaning new biodiversity rich areas are to be targeted where no sampling was done before.
- Evgeny Zakharov
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To Collect or Not To Collect?
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