sarah adamowicz - pros and cons of collecting specimens for barcoding vs. sampling existing...

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?