Dr Sarah Adamowicz - Ecological studies

Ecological Analyses Using BOLD

Sarah Adamowicz, Assistant Professor

Biodiversity Institute of Ontario & Dept. Integrative BiologyUniversity of Guelph

1- Managing and co-analyzing multiple types of data

2- Studying biological, habitat, and geographical associations

3- Accessing published data and co-analyzing published data with your own

4- Accumulation curves and biodiversity inventories

5- Using BINs as proxies for species in ecological research

Types of Ecological Analyses BOLD Can Facilitate

• BOLD is a workbench

• Store and manage together collection data, geographic data, photographs, and sequences

• Use “Taxon ID Tree” with “matching photos and spreadsheet” option for quality control and to co-analyze sequence and photographic data

• Publish data easily in BOLD and to GenBank from BOLD

1- Managing and co-analyzing multiple types of data

BOLD Systems – Data Analysis

2- Studying Biological Associations, e.g. between caterpillars and host plants

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Host Species / Barcode species

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2 3 4 5 76 8 9 10 11 12 13 14 151

Smith M. A. et.al. PNAS 2008;105:12359-12364

Host Specialists or Generalists?

• Many types of biological associations can be elucidated using DNA barcodes (e.g. host/parasite; insect larva/host plant; male/female; juvenile/adult).

• Associations between genetic clusters and habitats or geographic regions.

• One way to do this is to put key information for your study in brief form into the “Extra Info” field. This can be shown on your “Taxon ID Tree” and can also be used to colourize your tree. Can follow up with statistical analysis.

Using BOLD to Study Associations

Diptera Larvae from ChurchillExtra Info: Type of Pond

Churchill Mites Collected from Different SubstratesExtra Info: Lichen Types

3- Accessing published data and co-analyzing published data with your own

• Use Taxonomy Browser to seek published sequence data.

• Use Search/Filter function to access full data (including locality information) for published records.

• Use “Merge Projects” function to merge and co-analyze specific projects.

• Can access some information using the ID engine (and you can then link to full information for published records).

Churchill Northern Studies CentreChurchill Northern Studies Centre

Sub Arctic

Low Arctic

High Arctic

4- Using BOLD to Inform Biodiversity SurveysThe Case of Churchill, Manitoba, Canada

Species Accumulation Curve Tool Available in BOLD

Insect Orders Marine Taxa

Number of Individuals

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Species Accumulation Curve Tool Available in BOLD

Insect Orders Marine Taxa

Number of Individuals

Nu

mb

er o

f S

pec

ies/

Clu

ster

s

Trichoptera

Ephemeroptera

Plecoptera

Barcode ClustersPhylogenetic DiversityMorphospecies

Number of Individuals

Zhou et al. 2009. Frontiers in Zoology. 6, 30.

Similar trends often shown when biodiversity quantified in different ways

Accumulation of EPT Diversity in Churchill

Informing Biodiversity

Surveys

•High incidence of singletons and doubletons suggests undersampling

•Can use barcode clusters as provisional species for biodiversity estimators (e.g. in software EstimateS)

5- Barcode clusters can be used as proxies for species for many types of ecological analyses

• BINs (Barcode Index Numbers = barcode clusters) are assigned to specimens with sequences >500 bp by BOLD.

• Can be used for many purposes.

• Biodiversity estimators.

• Complementarity indices.

Jinjing Wang et al., in review

Amateur Expert

6- Phylogenetic structure offers insight into ecological mechanisms

Clustered Phylogeny

Overdispersed Phylogeny

• Species traits conserved within a lineage.

• Clustered phylogeny: species coexisting are closely related.

• Overdispersed phylogeny: species coexisting are not closely related.