Molecular Genetic Applications and Barcoding

1. Molecular Genetic Applications and Barcoding Andrew Lowe State Herbarium and Bioknowledge SA, DEH Earth & Environmental Science, University of Adelaide

2. Whatever has molecular genetics done for taxonomy?

3. Whatever has molecular genetics done for taxonomy? • Well quite a lot actually

4. Whatever has molecular genetics done for taxonomy? • Well quite a lot actually • Provided robust independent phylogenies to chart systematic and evolutionary relationships

5. Whatever has molecular genetics done for taxonomy? • Well quite a lot actually • Provided robust independent phylogenies to chart systematic and evolutionary relationships • Allowed integration of fossil data with molecular clock methods for date of divergence estimation

6. Whatever has molecular genetics done for taxonomy? • Well quite a lot actually • Provided robust independent phylogenies to chart systematic and evolutionary relationships • Allowed integration of fossil data with molecular clock methods for date of divergence estimation • Range of species and population level tools:

7. Whatever has molecular genetics done for taxonomy? • Well quite a lot actually • Provided robust independent phylogenies to chart systematic and evolutionary relationships • Allowed integration of fossil data with molecular clock methods for date of divergence estimation • Range of species and population level tools: • Speciation, hybridisation and phylogeography • Population genetics, gene flow, genetic cohesion

8. Whatever has molecular genetics done for taxonomy? • Have these methods made traditional morphological taxonomy redundant?

9. Whatever has molecular genetics done for taxonomy? • Have these methods made traditional morphological taxonomy redundant? • No – allowed new paradigm for testing trait evolution in relation to phylogenetic constraints and environmental change:

10. Whatever has molecular genetics done for taxonomy? • Have these methods made traditional morphological taxonomy redundant? • No – allowed new paradigm for testing trait evolution in relation to phylogenetic constraints and environmental change: • Trait evolution and adaptation • Coevolution and ecological dependence • Vicariance vs long distance dispersal • Radiation and extinctions

11. Whatever has molecular genetics done for taxonomy? • Have these methods made traditional morphological taxonomy redundant? • No – allowed new paradigm for testing trait evolution in relation to phylogenetic constraints and environmental change: • Trait evolution and adaptation • Coevolution and ecological dependence • Vicariance vs long distance dispersal • Radiation and extinctions • Potentially never had it so good with so many useful and integrative tools at our disposal?

12. Barcoding, what is it? • New spectra of the horizon

13. Barcoding, what is it? • What is it and what does it offer?

14. Barcoding, what is it? • What is it and what does it offer? • Use DNA markers to provide rapid estimation of species identity and diversity

15. Barcoding, what is it? • What is it and what does it offer? • Use DNA markers to provide rapid estimation of species identity and diversity • Companies interested in developing handheld devices to provide field identity and species description/information for rapid assessment

16. Barcoding, the threat • Is it a threat to taxonomy?

17. Barcoding, the threat • Is it a threat to taxonomy? Scenario 1 • Army of untrained environmental consultants descending on our ecosystems armed only with the information held in hand held devices

18. Barcoding, the threat • Is it a threat to taxonomy? Scenario 1 • Army of untrained environmental consultants descending on our ecosystems armed only with the information held in hand held devices • Taxonomists made unemployed as all species DNA information captured on data systems

19. Barcoding, the threat • Is it a threat to taxonomy? Scenario 1 • Army of untrained environmental consultants descending on our ecosystems armed only with the information held in hand held devices • Taxonomists made unemployed as all species DNA information captured on data systems • Art of taxonomy lost to future generations

20. Barcoding, the opportunity • Is it an opportunity for taxonomy? Scenario 2

21. Barcoding, the opportunity • Is it an opportunity for taxonomy? Scenario 2 • Allows rapid assessment of difficult groups, grasses, algae, bacteria, fungi – part of tool kit

22. Barcoding, the opportunity • Is it an opportunity for taxonomy? Scenario 2 • Allows rapid assessment of difficult groups, grasses, algae, bacteria, fungi – part of tool kit • New funding – environmental assessment

23. Barcoding, the opportunity • Is it an opportunity for taxonomy? Scenario 2 • Allows rapid assessment of difficult groups, grasses, algae, bacteria, fungi – part of tool kit • New funding – environmental assessment • Funding for species characterisation, particularly to document breadth of variation within species • Use archived specimens • Phylogeny, systematics, taxonomy

24. Barcoding, the opportunity • Is it an opportunity for taxonomy? Scenario 2 • Allows rapid assessment of difficult groups, grasses, algae, bacteria, fungi – part of tool kit • New funding – environmental assessment • Funding for species characterisation, particularly to document breadth of variation within species • Use archived specimens • Phylogeny, systematics, taxonomy • Taxonomists integral to barcode development

25. Barcoding, the opportunity • Is it an opportunity for taxonomy? Other opportunities • New phylogenetic distance metrics and species identity measures based on DNA information

26. Barcoding, the opportunity • Is it an opportunity for taxonomy? Other opportunities • New phylogenetic distance metrics and species identity measures based on DNA information • Access to previously non-analyzable material or poorly characterised systems • Stygofauna – barcoding and DNA chip technologies • Sediment cores and other ancient DNA materials

27. Barcoding, the opportunity • Is it an opportunity for taxonomy? Other opportunities • New phylogenetic distance metrics and species identity measures based on DNA information • Access to previously non-analyzable material or poorly characterised systems • Stygofauna – barcoding and DNA chip technologies • Sediment cores and other ancient DNA materials • Promotes importance of taxonomy to track change

28. Barcoding, how do we prepare If it is an opportunity, what do we need to do?

29. Barcoding, how do we prepare If it is an opportunity, what do we need to do? • Integrate specimen data and DNA banks (Atlas)

30. Barcoding, how do we prepare If it is an opportunity, what do we need to do? • Integrate specimen data and DNA banks (Atlas) • Online information system for barcodes (Genbank)

31. Barcoding, how do we prepare If it is an opportunity, what do we need to do? • Integrate specimen data and DNA banks (Atlas) • Online information system for barcodes (Genbank) • Muster and prepare Australia’s taxonomic community to meet the challenge (group, meetings)

32. Barcoding, how do we prepare If it is an opportunity, what do we need to do? • Integrate specimen data and DNA banks (Atlas) • Online information system for barcodes (Genbank) • Muster and prepare Australia’s taxonomic community to meet the challenge (group, meetings) • Form strategic international alliances • COBOL, Genome Canada – Australian Chapter

33. Barcoding, how do we prepare If it is an opportunity, what do we need to do? • Integrate specimen data and DNA banks (Atlas) • Online information system for barcodes (Genbank) • Muster and prepare Australia’s taxonomic community to meet the challenge (group, meetings) • Form strategic international alliances • COBOL, Genome Canada – Australian Chapter • Fund barcoding as component of taxonomy