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

Whatever has molecular genetics done for taxonomy?

Well quite a lot actually Well quite a lot actually

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

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

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

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

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

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

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

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

Barcoding, what is it? New spectra of the horizon New spectra of the horizon

Barcoding, what is it? What is it and what does it offer? What is it and what does it offer?

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

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

Barcoding, the threat Is it a threat to taxonomy? Is it a threat to taxonomy?

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

Barcoding, the threat Is it a threat to taxonomy? 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 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 Taxonomists made unemployed as all species DNA information captured on data systems

Barcoding, the threat Is it a threat to taxonomy? 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 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 Taxonomists made unemployed as all species DNA information captured on data systems Art of taxonomy lost to future generations Art of taxonomy lost to future generations

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

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

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

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

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

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

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

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

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

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

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

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

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

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