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Pros and Cons of Collecting Specimens for Barcoding vs. Sampling Existing Collections

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

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  1. 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

  2. Museum Specimens vs. Fresh Specimens 1- Scientific perspective 2- Logistical issues 3- Financial considerations

  3. 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. ????

  4. Taxonomic-focused campaigns • aim to be comprehensive • will enable identification • assist with applications • will facilitate other research directions

  5. Collections are a rich source of identified specimens

  6. Region-focused campaigns

  7. Barcoding the Biota of Churchill, Manitoba, Canada Churchill Northern Studies Centre Sub Arctic Low Arctic High Arctic

  8. Comprehensive Habitat Coverage Terrestrial Freshwater Nearshore Marine

  9. Field Course Students Contribute to Survey

  10. 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

  11. Ecological Questions Regarding Biological Associations

  12. 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?

  13. Museum specimens can yield shorter sequences

  14. Mini-barcode zone 91-95% resolution Full-length barcode 95-97% resolution Barcode information analysis Meusnier et al. 2008

  15. Barcode vs. Mini-Barcode

  16. 150 years old and key to a taxonomic puzzle

  17. 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.

  18. Canadian Centre for DNA Barcoding: http://www.dnabarcoding.ca/

  19. 3- Financial Considerations

  20. Tradeoff: Capacity/Cost vs Complexity - Evgeny Zakharov, Director of Laboratory Operations, Canadian Centre for DNA Barcoding

  21. 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 √√√

  22. 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 √√√

  23. To Collect or Not To Collect?

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