What new research can we do with a MILLION by ocv22853

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									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?
                                               1   2   3   4
• DNA is the world’s best parataxonomist
                                               X   X   X   X   Sp A
• Treat each haplotype as if it were a
   species – population/species issues ?<2%    X       X
• Measure species presence/absence             X
   before and after
                                                   X   X
  - environmental shocks
• Allows reverse ecology – identifying         X   X
   species that are particularly liable to
                                               X   X
   impacts which can be further investigated
   to discover why as opposed to tracking      X               Sp B
   changes in species whose ecology we
                                               X       X
   know and suspect might indicate
   something                                   X       X

                                                   X

                                                   X
High throughput gadgetry

 Conventional glass           Affymetrix
     microarray               microarray
   5,000 targets           1,000,000 targets
Environmental DNA microarrays
(Detecting loss of species)

                                           Time
                 A                                      B
        1            2          3          4

 A   Rot.001     Calan.001   Cylc.001   Ost.002
                                   
                                   
                                   
                                   
                                   

 B   Clad.001     Cil.002    Diat.002   Nem.001
                                    
                                    
                                    
                                    
                                    

 C   Chlor.001   Chlor.002   Tel.001    Trach.001
                                     
                                     
                                     
                                     
                                     

 D   Hym.001      Dip.001    Plec.001    Blank
                                    
                                    
                                    
                                    
                                    

A: Expected pattern. B: Observed pattern

                                                    Species absent
Environmental DNA microarrays
(Detecting loss of species)

                                          Time
                A                                           B
       1            2          3          4

A   Rot.001     Calan.001   Cylc.001   Ost.002
                                  
                                  
                                  
                                  
                                  

B   Clad.001     Cil.002    Diat.002   Nem.001
                                   
                                   
                                   
                                   
                                   

C   Chlor.001   Chlor.002   Tel.001    Trach.001
                                    
                                    
                                    
                                    
                                    

D   Hym.001      Dip.001    Plec.001    Blank
                                   
                                   
                                   
                                   
                                   

A: Expected pattern. B: Observed pattern

                                                   Additional species

								
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