What new research can we do with a MILLION Barcode records? Paul De Barro, Stephen Cameron and Chris Hardy CSIRO Entomology Second International Barcode.

Pissodes castaneus AJ850007 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAAATAG GCG------- -T---TTTTG ACATCCTAAA GGCCCGCCGA CGG------- G--------- --GG------ ---------- ---------- Chrysomela scripta AF267436 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGTG ATTTGTCTGG TTAATTCCGA TAACGAACGA GATTCTAGCC TGCTAACTAG GCGT------ -T---TTTCG ACATCCCAAA GGCCCGCCGG TTG------- A--------- --GG------ ---------- ---------- Plegaderus cf. nitidus AY02833 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAAATAG GCGT------ TA---ATTCG ACATCTCAAA GGCCCGCCGG CCC------- G--------- --GC------ ---------- ---------- Rhynchophorus cruentatus AF389 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGC------ -T---TTTTG ACATCCTAAA GGCCCGCCGG CCG------- G--------- --CG------ ---------- ---------- Ocypus opthalmicus AJ810739 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGTG ATCTGTCAGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGT-----A CT----TTCG ACATCTCAAA GGTCG----- ---------- ---------- ---------- ---------- ---------- Galerucella nympheae AF267443 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGT------ -A---TTTCG ACATCCCAAA GGCCCGTCGG TAT------- G--------- --GA------ ---------- ---------- Microsporus sp. AF427599 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGTG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTTTGAGA ATTCAATCCG GTATCTATGA GGTGCGTGCA CGCGATCAGC TATGGGCTGA GAGAGCGCCG TCGGTGGCAT GGACCGTTGT Apotomus rufithorax AF012497 --TGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGATTG ATTTGTCTGC TTAATTGCGA TAACGAACGA GATTCTAGCC TGCTAAATAG GCGTT----- ACTTA--CCG GTATCTCGAA GATTCGCATC TCC------- --TGGTCGTT CAGCATGTTG TTCGTTGCAT GTGTGGGCGT Carabus nemoralis AF012507 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGT-----A CT---TTCCG GTATCTCGAA GGCCGACGTC TCT------- C--------- --GGGTTTCC GTTTG----- -----GCGCG Oregus aereus AF012500 GGTGGGTGGT GGTGCATG-C CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTA----A CT---TACCG GTATCTCGAA GGCTCGCGTC TCT------- C--------- --GGTTCCCG CGT-----GT TGCGTTTGCG Lancetes varius AJ318684 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAAATAG GCGTT----A CT---TTCCG GCATCCCGAA GGCTCGCGTC ACC------- C--------- --GTTCGCC- ---------- -------GGT Hydraena iberica AJ810730 GGTGCGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGATCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTT----T CT-----CCG ACATCTCAAA GGCCA----- ---------- ---------- ---------- ---------- ---------- Trechus sp. nr. chalybeus AF00 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGACCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTT----A CT---TACCG GTATCCTGAA GGCTC--GTG TCT------- T--------- --TCGTATTC TGGCGTGCAT T-TGTCG--- Dalyat mirabilis AY926478 Cara ---GGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGTTAACTAG GCGTT----A CT---TACCG GTATCTCGAA GGCTCGCGTC TCT------- C--------- --GTATTCG- ---------- ---------- Diaprepes abbreviatus AY157729 GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTA----A AA---TTTTG ACATCTTAAA GGCCCGCCGG CCG------- A--------- --CGCGGTGT GTGGCGTGCG TGCGCGGCGC Pachnaeus litus AY157730 Curcu GGTGGGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTA----A AA---TTTTG ACATCTTAAA GGCCCGCCGG CCG------- A--------- --CGCGGTGT GTGGCGTGCG TGCGCGGCGC Meonis sp. AF398722 Harpalinae ----GGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TGCTAACTAG GCGTA----A CAAAATACCG GTATCTTGAA GGCTCCGACA CTT------- G--------- --CTTTTTGA TTTCATTCAC TGCATTTCTT Moriosomus seticollis AF398721 ----GGTGGT GGTGCATGGC CGTTCTTAGT TGGTGGAGCG ATTTGTCTGG TTAATTCCGA TAACGAACGA GACTCTAGCC TACTAAATAG ACGTT----A CACT-TACCA GTATCTCGAA GGCTC--ACA TCT------- C--------- --TCGTTTAC TTT---TCAC TATATAA---

What new research can we do with a MILLION Barcode records?

Paul De Barro, Stephen Cameron and Chris Hardy

CSIRO Entomology

Second International Barcode Conference

18-20 September 2007

Ecogenomics

The new view of animal phylogeny K Halanich (2004)Ann Rev Ecol Evol Syst 35:229-256

43 Orders and>100,000 species

How do you measure biodiversity and species

interactions at this level of complexity?

“Ecogenomics”

The idea – use barcodes to...

• Generate fundamental advances in our understanding of the relationship between biodiversity and ecosystem function (BD-EF).

• Extend the existing BD-EF paradigm to explore changes in diversity across multiple trophic levels and incorporating realistic levels diversity and complexity - consider the processes of community assembly and changes in species diversity and abundance.

• Directly link this to the concept of ecosystem resilience.

• High throughput technology will enable the exploration of this on a scale that involves replication through both space and time.

• Different patches of ecosystems could be compared over time and an index applied which measures changes in the relative proportions of indigenous and exotic species.

• Over time this will enable different habitats to be monitored with changes in the number and proportion of different haplotypes providing an index of its health in response to factors such as global climate change and biological invasion.

• This data can then be used to provide a more rigorous underpinning to our understanding of relative ecosystem vulnerability.

What would the impacts be?

The science: Quantify biodiversity and understand ecosystem processes

The outputs: Produce region-specific biodiversity assessments Based on rapid & cost-effective genetic measures of the structural and

functional biodiversity

The outcomes: The adoption of the ideology and application of transformational genomic technologies as the approach of choice

By: Environmental researchers, managers, and policy and decision-makers

As: A tool of choice for prioritization and resource allocation

What would you do using barcodes?

• DNA is the world’s best parataxonomist• Treat each haplotype as if it were a

species – population/species issues ?<2%• Measure species presence/absence

before and after

- environmental shocks• Allows reverse ecology – identifying

species that are particularly liable to impacts which can be further investigated to discover why as opposed to tracking changes in species whose ecology we know and suspect might indicate something

1 2 3 4

X X X X

X X

X

X X

X X

X X

X

X X

X X

X

X

Sp A

Sp B

Affymetrix microarray

1,000,000 targets

Conventional glass microarray

5,000 targets

High throughput gadgetry

Environmental DNA microarrays (Detecting loss of species)

A B

Blank

Plec.001

Dip.001

Hym.001

D

Trach.001

Tel.001

Chlor.002

Chlor.001

C

Nem.001

Diat.002

Cil.002

Clad.001

B

Ost.002

Cylc.001

Calan.001

Rot.001

A

4321

Blank

Plec.001

Dip.001

Hym.001

D

Trach.001

Tel.001

Chlor.002

Chlor.001

C

Nem.001

Diat.002

Cil.002

Clad.001

B

Ost.002

Cylc.001

Calan.001

Rot.001

A

4321

A: Expected pattern. B: Observed pattern

Species absent

Time

Environmental DNA microarrays (Detecting loss of species)

Blank

Plec.001

Dip.001

Hym.001

D

Trach.001

Tel.001

Chlor.002

Chlor.001

C

Nem.001

Diat.002

Cil.002

Clad.001

B

Ost.002

Cylc.001

Calan.001

Rot.001

A

4321

Blank

Plec.001

Dip.001

Hym.001

D

Trach.001

Tel.001

Chlor.002

Chlor.001

C

Nem.001

Diat.002

Cil.002

Clad.001

B

Ost.002

Cylc.001

Calan.001

Rot.001

A

4321

A B

A: Expected pattern. B: Observed pattern

Additional species

Time