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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 Biology University of Guelph. Museum Specimens vs. Fresh Specimens. 1- Scientific perspective 2- Logistical issues
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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 Biology University of Guelph
Museum Specimens vs. Fresh Specimens 1- Scientific perspective 2- Logistical issues 3- Financial considerations
Scientific Perspective: What Is Your Goal? 1. Barcode campaigns: generating the library2. Targeted taxonomic questions3. Environmental barcoding & biomonitoring4. Other applications: e.g. bio-surveillance, food safety, marketplace fraud, invasive species 5. Site or regional biodiversity surveys6. Ecological questions7. Evolutionary questions8. ????
Taxonomic-focused campaigns • aim to be comprehensive • will enable identification • assist with applications • will facilitate other research directions
Barcoding the Biota of Churchill, Manitoba, Canada Churchill Northern Studies Centre Sub Arctic Low Arctic High Arctic
Comprehensive Habitat Coverage Terrestrial Freshwater Nearshore Marine
Microgastrinae wasps collected in either 2005-2007 or between 1930 and 1960 at Churchill Red = Historical Blue = Shared Black = Contemporary Fernandez Triana & Smith et al (2011) PLoS ONE 6(8): e23719
2- Logistical Issues • 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?
Mini-barcode zone 91-95% resolution Full-length barcode 95-97% resolution Barcode information analysis Meusnier et al. 2008
BUT… • “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.
Canadian Centre for DNA Barcoding: http://www.dnabarcoding.ca/
Tradeoff: Capacity/Cost vs Complexity - Evgeny Zakharov, Director of Laboratory Operations, Canadian Centre for DNA Barcoding
Fresh vs Museum Pros/Cons *"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. √√ √ Negative Score Positive Score √√√
Fresh vs Museum Pros/Cons *"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. √√ √ Negative Score Positive Score √√√