Date post: | 25-May-2015 |
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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
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. 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. ????
Taxonomic-focused campaigns• aim to be comprehensive• will enable identification• assist with applications• will facilitate other research directions
Collections are a rich source of identified specimens
Region-focused campaigns
Churchill Northern Studies CentreChurchill 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 1960 at Churchill
Fernandez Triana & Smith et al (2011) PLoS ONE 6(8): e23719
Ecological Questions Regarding Biological Associations
• 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
Museum specimens can yield shorter sequences
Barcode information analysis
Full-length barcode
95-97% resolution
Mini-barcode zone
91-95% resolution
Meusnier et al. 2008
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
150 years old and key to a taxonomic puzzle
• “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…
Canadian Centre for DNA Barcoding:http://www.dnabarcoding.ca/
3- Financial Considerations
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)
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
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
To Collect or Not To Collect?