Dr Sarah Adamowicz - Ecological studies
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Transcript of 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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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.