Ecological Analyses Using BOLD Sarah Adamowicz, Assistant Professor

1. Ecological Analyses Using BOLD Sarah Adamowicz, Assistant Professor Biodiversity Institute of Ontario& Dept. Integrative Biology University of Guelph

2. Types of Ecological Analyses BOLD Can Facilitate • 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

3. 1- Managing and co-analyzing multiple types of data • 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

4. BOLD Systems – Data Analysis

5. 2- Studying Biological Associations, e.g. between caterpillars and host plants

6. Host Specialists or Generalists? Smith M. A. et.al. PNAS 2008;105:12359-12364

7. Using BOLD to Study Associations • 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.

8. Diptera Larvae from Churchill Extra Info: Type of Pond

9. Churchill Mites Collected from Different Substrates Extra Info: Lichen Types

10. 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).

13. 4- Using BOLD to Inform Biodiversity Surveys The Case of Churchill, Manitoba, Canada Churchill Northern Studies Centre Sub Arctic Low Arctic High Arctic

14. Species Accumulation Curve Tool Available in BOLD Insect Orders Marine Taxa Number of Species/Clusters Number of Individuals

15. Species Accumulation Curve Tool Available in BOLD Insect Orders Marine Taxa Number of Species/Clusters Number of Individuals

16. Similar trends often shown when biodiversity quantified in different ways Accumulation of EPT Diversity in Churchill Accumulated species diversity Trichoptera Barcode Clusters Phylogenetic Diversity Morphospecies Ephemeroptera Plecoptera Number of Individuals Zhou et al. 2009. Frontiers in Zoology. 6, 30.

18. 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)

19. 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. Amateur Expert Jinjing Wang et al., in review

20. 6- Phylogenetic structure offers insight into ecological mechanisms Clustered Phylogeny • Species traits conserved within a lineage. • Clustered phylogeny: species coexisting are closely related. • Overdispersed phylogeny: species coexisting are not closely related. Overdispersed Phylogeny