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

Molecular Genetic Applications Molecular Genetic Applications and Barcodingand Barcoding

Andrew LoweAndrew Lowe

State Herbarium and Bioknowledge SA, State Herbarium and Bioknowledge SA, DEHDEH

Earth & Environmental Science, University Earth & Environmental Science, University of Adelaideof Adelaide

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy?

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Well quite a lot actually Well quite a lot actually

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Well quite a lot actually Well quite a lot actually Provided robust independent Provided robust independent

phylogenies to chart systematic and phylogenies to chart systematic and evolutionary relationshipsevolutionary relationships

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Well quite a lot actually Well quite a lot actually Provided robust independent Provided robust independent

phylogenies to chart systematic and phylogenies to chart systematic and evolutionary relationshipsevolutionary relationships

Allowed integration of fossil data Allowed integration of fossil data with molecular clock methods for with molecular clock methods for date of divergence estimationdate of divergence estimation

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Well quite a lot actually Well quite a lot actually Provided robust independent Provided robust independent

phylogenies to chart systematic and phylogenies to chart systematic and evolutionary relationshipsevolutionary relationships

Allowed integration of fossil data with Allowed integration of fossil data with molecular clock methods for date of molecular clock methods for date of divergence estimationdivergence estimation

Range of species and population level Range of species and population level tools:tools:

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Well quite a lot actually Well quite a lot actually Provided robust independent phylogenies Provided robust independent phylogenies

to chart systematic and evolutionary to chart systematic and evolutionary relationshipsrelationships

Allowed integration of fossil data with Allowed integration of fossil data with molecular clock methods for date of molecular clock methods for date of divergence estimationdivergence estimation

Range of species and population level Range of species and population level tools:tools: Speciation, hybridisation and phylogeographySpeciation, hybridisation and phylogeography Population genetics, gene flow, genetic Population genetics, gene flow, genetic

cohesion cohesion

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Have these methods made traditional Have these methods made traditional

morphological taxonomy redundant?morphological taxonomy redundant?

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Have these methods made traditional Have these methods made traditional

morphological taxonomy redundant?morphological taxonomy redundant? No – allowed new paradigm for testing No – allowed new paradigm for testing

trait evolution in relation to trait evolution in relation to phylogenetic constraints and phylogenetic constraints and environmental change:environmental change:

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Have these methods made traditional Have these methods made traditional

morphological taxonomy redundant?morphological taxonomy redundant? No – allowed new paradigm for testing No – allowed new paradigm for testing

trait evolution in relation to trait evolution in relation to phylogenetic constraints and phylogenetic constraints and environmental change:environmental change: Trait evolution and adaptationTrait evolution and adaptation Coevolution and ecological dependence Coevolution and ecological dependence Vicariance vs long distance dispersal Vicariance vs long distance dispersal Radiation and extinctionsRadiation and extinctions

Whatever has molecular Whatever has molecular genetics done for genetics done for

taxonomy?taxonomy? Have these methods made traditional Have these methods made traditional

morphological taxonomy redundant?morphological taxonomy redundant? No – allowed new paradigm for testing No – allowed new paradigm for testing

trait evolution in relation to phylogenetic trait evolution in relation to phylogenetic constraints and environmental change:constraints and environmental change: Trait evolution and adaptationTrait evolution and adaptation Coevolution and ecological dependence Coevolution and ecological dependence Vicariance vs long distance dispersal Vicariance vs long distance dispersal Radiation and extinctionsRadiation and extinctions

Potentially never had it so good with so Potentially never had it so good with so many useful and integrative tools at our many useful and integrative tools at our disposal?disposal?

Barcoding, what is it?Barcoding, what is it?

New spectra of the horizonNew spectra of the horizon

Barcoding, what is it?Barcoding, what is it?

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

Barcoding, what is it?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 Use DNA markers to provide rapid

estimation of species identity and estimation of species identity and diversitydiversity

Barcoding, what is it?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 Use DNA markers to provide rapid

estimation of species identity and estimation of species identity and diversitydiversity

Companies interested in developing Companies interested in developing handheld devices to provide field handheld devices to provide field identity and species identity and species description/information for rapid description/information for rapid assessmentassessment

Barcoding, the threatBarcoding, the threat

Is it a threat to taxonomy?Is it a threat to taxonomy?

Barcoding, the threatBarcoding, the threat

Is it a threat to taxonomy?Is it a threat to taxonomy?

Scenario 1Scenario 1 Army of untrained environmental Army of untrained environmental

consultants descending on our consultants descending on our ecosystems armed only with the ecosystems armed only with the information held in hand held information held in hand held devices devices

Barcoding, the threatBarcoding, the threat

Is it a threat to taxonomy?Is it a threat to taxonomy?

Scenario 1Scenario 1 Army of untrained environmental Army of untrained environmental

consultants descending on our consultants descending on our ecosystems armed only with the ecosystems armed only with the information held in hand held devices information held in hand held devices

Taxonomists made unemployed as all Taxonomists made unemployed as all species DNA information captured on species DNA information captured on data systemsdata systems

Barcoding, the threatBarcoding, the threat

Is it a threat to taxonomy?Is it a threat to taxonomy?

Scenario 1Scenario 1 Army of untrained environmental Army of untrained environmental

consultants descending on our ecosystems consultants descending on our ecosystems armed only with the information held in armed only with the information held in hand held devices hand held devices

Taxonomists made unemployed as all Taxonomists made unemployed as all species DNA information captured on data species DNA information captured on data systemssystems

Art of taxonomy lost to future generationsArt of taxonomy lost to future generations

Barcoding, the Barcoding, the opportunityopportunity Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Scenario 2Scenario 2

Barcoding, the Barcoding, the opportunityopportunity Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Scenario 2Scenario 2 Allows rapid assessment of difficult Allows rapid assessment of difficult

groups, grasses, algae, bacteria, groups, grasses, algae, bacteria, fungi – part of tool kitfungi – part of tool kit

Barcoding, the Barcoding, the opportunityopportunity Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Scenario 2Scenario 2 Allows rapid assessment of difficult Allows rapid assessment of difficult

groups, grasses, algae, bacteria, groups, grasses, algae, bacteria, fungi – part of tool kitfungi – part of tool kit

New funding – environmental New funding – environmental assessment assessment

Barcoding, the Barcoding, the opportunityopportunity Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Scenario 2Scenario 2 Allows rapid assessment of difficult Allows rapid assessment of difficult

groups, grasses, algae, bacteria, fungi – groups, grasses, algae, bacteria, fungi – part of tool kitpart of tool kit

New funding – environmental New funding – environmental assessment assessment

Funding for species characterisation, Funding for species characterisation, particularly to document breadth of particularly to document breadth of variation within species variation within species Use archived specimens Use archived specimens Phylogeny, systematics, taxonomyPhylogeny, systematics, taxonomy

Barcoding, the Barcoding, the opportunityopportunity Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Scenario 2Scenario 2 Allows rapid assessment of difficult groups, Allows rapid assessment of difficult groups,

grasses, algae, bacteria, fungi – part of tool grasses, algae, bacteria, fungi – part of tool kitkit

New funding – environmental assessment New funding – environmental assessment Funding for species characterisation, Funding for species characterisation,

particularly to document breadth of variation particularly to document breadth of variation within species within species Use archived specimens Use archived specimens Phylogeny, systematics, taxonomyPhylogeny, systematics, taxonomy

Taxonomists integral to barcode Taxonomists integral to barcode developmentdevelopment

Barcoding, the Barcoding, the opportunityopportunity

Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Other opportunitiesOther opportunities New phylogenetic distance metrics New phylogenetic distance metrics

and species identity measures based and species identity measures based on DNA informationon DNA information

Barcoding, the Barcoding, the opportunityopportunity

Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Other opportunitiesOther opportunities New phylogenetic distance metrics and New phylogenetic distance metrics and

species identity measures based on DNA species identity measures based on DNA informationinformation

Access to previously non-analyzable Access to previously non-analyzable material or poorly characterised systemsmaterial or poorly characterised systems Stygofauna – barcoding and DNA chip Stygofauna – barcoding and DNA chip

technologiestechnologies Sediment cores and other ancient DNA Sediment cores and other ancient DNA

materialsmaterials

Barcoding, the Barcoding, the opportunityopportunity

Is it an opportunity for taxonomy?Is it an opportunity for taxonomy?

Other opportunitiesOther opportunities New phylogenetic distance metrics and species New phylogenetic distance metrics and species

identity measures based on DNA informationidentity measures based on DNA information Access to previously non-analyzable material or Access to previously non-analyzable material or

poorly characterised systemspoorly characterised systems Stygofauna – barcoding and DNA chip technologiesStygofauna – barcoding and DNA chip technologies Sediment cores and other ancient DNA materialsSediment cores and other ancient DNA materials

Promotes importance of taxonomy to track Promotes importance of taxonomy to track changechange

Barcoding, how do we Barcoding, how do we prepareprepare

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

Barcoding, how do we Barcoding, how do we prepareprepare

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

Integrate specimen data and DNA Integrate specimen data and DNA banks (Atlas)banks (Atlas)

Barcoding, how do we Barcoding, how do we prepareprepare

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

Integrate specimen data and DNA Integrate specimen data and DNA banks (Atlas)banks (Atlas)

Online information system for Online information system for barcodes (Genbank)barcodes (Genbank)

Barcoding, how do we Barcoding, how do we prepareprepare

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

Integrate specimen data and DNA Integrate specimen data and DNA banks (Atlas)banks (Atlas)

Online information system for Online information system for barcodes (Genbank)barcodes (Genbank)

Muster and prepare Australia’s Muster and prepare Australia’s taxonomic community to meet the taxonomic community to meet the challenge (group, meetings)challenge (group, meetings)

Barcoding, how do we Barcoding, how do we prepareprepare

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

Integrate specimen data and DNA banks Integrate specimen data and DNA banks (Atlas)(Atlas)

Online information system for barcodes Online information system for barcodes (Genbank)(Genbank)

Muster and prepare Australia’s taxonomic Muster and prepare Australia’s taxonomic community to meet the challenge (group, community to meet the challenge (group, meetings)meetings)

Form strategic international alliancesForm strategic international alliances COBOL, Genome Canada – Australian ChapterCOBOL, Genome Canada – Australian Chapter

Barcoding, how do we Barcoding, how do we prepareprepare

If it is an opportunity, what do we need to do?If it is an opportunity, what do we need to do? Integrate specimen data and DNA banks Integrate specimen data and DNA banks

(Atlas)(Atlas) Online information system for barcodes Online information system for barcodes

(Genbank)(Genbank) Muster and prepare Australia’s taxonomic Muster and prepare Australia’s taxonomic

community to meet the challenge (group, community to meet the challenge (group, meetings)meetings)

Form strategic international alliancesForm strategic international alliances COBOL, Genome Canada – Australian ChapterCOBOL, Genome Canada – Australian Chapter

Fund barcoding as component of taxonomyFund barcoding as component of taxonomy