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Pros and Cons of Collecting Specimens for Barcoding vs. Sampling Existing Collections Sarah Adamowicz, Assistant Professor...
1- Scientific perspective 2- Logistical issues 3- Financial considerations Museum Specimens vs. Fresh Specimens
Scientific Perspective: What Is Your Goal? 1. Barcode campaigns: generating the library 2. Targeted taxonomic questions 3....
Taxonomic-focused campaigns <ul><li>aim to be comprehensive </li></ul><ul><li>will enable identification </li></ul><ul><li...
Collections are a rich source of identified specimens
Region-focused campaigns
Churchill Northern Studies Centre Barcoding the Biota of Churchill, Manitoba, Canada Sub Arctic Low Arctic High Arctic
Comprehensive Habitat Coverage Terrestrial Nearshore Marine Freshwater
Field Course Students Contribute to Survey
 
Red = Historical Blue = Shared Black = Contemporary Microgastrinae wasps collected in either 2005-2007 or between 1930 and...
Ecological Questions Regarding Biological Associations
<ul><li>For your goal, are there suitable specimens or tissues in a collection? </li></ul><ul><li>Can you gain permission ...
Museum specimens can yield shorter sequences
Barcode information analysis Meusnier et al. 2008 Full-length barcode 95-97% resolution Mini-barcode zone 91-95% resolution
Barcode vs. Mini-Barcode Barcode (650 bp) Mini-barcode (130 bp) Specimen success by age >90% 5-10 years >90% Up to 200 yea...
150 years old and key to a taxonomic puzzle
<ul><li>“ Identification success” requires something to match to, reference library. </li></ul><ul><li>The BARCODE data st...
Canadian Centre for DNA Barcoding: http://www.dnabarcoding.ca/
3- Financial Considerations
Tradeoff: Capacity/Cost vs Complexity Relative cost per sample Complexity Cost of laboratory analysis Capacity (limited by...
Fresh vs Museum Pros/Cons √√ √  Negative Score Positive Score  √√√ *&quot;easy&quot; samples to work with, but risk of ove...
Fresh vs Museum Pros/Cons √√ √  Negative Score Positive Score  √√√ *&quot;easy&quot; samples to work with, but risk of ove...
To Collect or Not To Collect?
 
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Sarah Adamowicz - Pros and Cons of Collecting Specimens for Barcoding vs. Sampling Existing Collections

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Discussing the pros and cons of fresh sample collections versus museum collections for DNA barcoding.

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

  1. 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. 2. 1- Scientific perspective 2- Logistical issues 3- Financial considerations Museum Specimens vs. Fresh Specimens
  3. 3. 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. ????
  4. 4. Taxonomic-focused campaigns <ul><li>aim to be comprehensive </li></ul><ul><li>will enable identification </li></ul><ul><li>assist with applications </li></ul><ul><li>will facilitate other research directions </li></ul>
  5. 5. Collections are a rich source of identified specimens
  6. 6. Region-focused campaigns
  7. 7. Churchill Northern Studies Centre Barcoding the Biota of Churchill, Manitoba, Canada Sub Arctic Low Arctic High Arctic
  8. 8. Comprehensive Habitat Coverage Terrestrial Nearshore Marine Freshwater
  9. 9. Field Course Students Contribute to Survey
  10. 11. 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
  11. 12. Ecological Questions Regarding Biological Associations
  12. 13. <ul><li>For your goal, are there suitable specimens or tissues in a collection? </li></ul><ul><li>Can you gain permission to sample the collection? </li></ul><ul><li>Are there frozen tissues, pinned specimens, or fluid samples? </li></ul><ul><li>How old are the specimens and how are they preserved? </li></ul>2- Logistical Issues
  13. 14. Museum specimens can yield shorter sequences
  14. 15. Barcode information analysis Meusnier et al. 2008 Full-length barcode 95-97% resolution Mini-barcode zone 91-95% resolution
  15. 16. Barcode vs. Mini-Barcode 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
  16. 17. 150 years old and key to a taxonomic puzzle
  17. 18. <ul><li>“ Identification success” requires something to match to, reference library. </li></ul><ul><li>The BARCODE data standard, such as employed by iBOL, requires longer sequences </li></ul><ul><li>(> 500 bp). </li></ul><ul><li>Therefore, typically one has to use multiple primer pairs and prepare contigs to gain longer sequences. </li></ul>BUT…
  18. 19. Canadian Centre for DNA Barcoding: http://www.dnabarcoding.ca/
  19. 20. 3- Financial Considerations
  20. 21. Tradeoff: Capacity/Cost vs Complexity Relative cost per sample Complexity Cost of laboratory analysis Capacity (limited by total available staff hours to complete editing of processed samples) - Evgeny Zakharov, Director of Laboratory Operations, Canadian Centre for DNA Barcoding Fresh (12 steps/sample) Mix (18 steps/sample) Museum (24 steps/sample)
  21. 22. Fresh vs Museum Pros/Cons √√ √ Negative Score Positive Score √√√ *&quot;easy&quot; 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 Metric Malaise* Fresh/Recent Museum/Old Procurement 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 √√√ √√√ √√
  22. 23. Fresh vs Museum Pros/Cons √√ √ Negative Score Positive Score √√√ *&quot;easy&quot; 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 Metric Malaise* Fresh/Recent Museum/Old Procurement 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 √√√ √√√ √√
  23. 24. To Collect or Not To Collect?

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