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Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
Andrew Lowe - Plants Plenary
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Andrew Lowe - Plants Plenary

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DNA Barcoding for Rapid Biodiversity Inventory, Conservation Prioritisation, and control of illegal Logging

DNA Barcoding for Rapid Biodiversity Inventory, Conservation Prioritisation, and control of illegal Logging

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  • 1. DNA barcoding forRapid Biodiversity Inventory, Conservation Prioritisation,and Control of Illegal Logging Andrew Lowe,Craig Costion, Hugh Cross, Bernd Degen Darren Crayn, Jonathan Geach
  • 2. • Barcoding Australian wet tropics trees – rapid biodiversity inventory – conservation prioritisation – biogeographic understanding• Barcoding Australian plants and soils – Terrestrial Ecosystem Research Network – biodiversity surveillance and monitoring• Barcoding and DNA fingerprinting tropical timber species for control of illegal logging
  • 3. Costion et al. (2011) Plant DNA barcodes can accurately estimate species richness in poorly known floras. PLoS ONE: In press Why barcode plants in the tropics? • High percentage of flora is undescribed • Fertile material for accurate field ID’s • Rapid habitat loss, increasing threats • Rapid biodiversity assessments needed DNA barcoding can help
  • 4. Australia’s ever-wet tropical rainforest Lockerbie Scrub McIlwraith/Iron Ranges Wet Tropics BARCODING PROGRESS Wet tropics has 2,144 vascular plants 1,200-1,400 species w/ at least 1 barcode 500 species – have 2-3 replicate barcodes 40% - 50%
  • 5. Cambium extraction• Rapid and easy tissue collection for DNA extraction• DNA from cambium shown to be less hampered by defensive chemicals in leaves (Colpaert et al 2005)
  • 6. Sample allCostion et al. (2011) PLoS ONE: In press E1 individuals present E15 then contruct F05 F44 distance trees E2 99 F11 E10 F22 • Can we use DNA – 31 F41 F54 F20 barcodes to estimate 33 F67 F26 99 F36 the diversity of an area 99 F45 F53 where species are 23 99 F09 F35 F03 unknown? 38 40 E17 F66 63 F28 99 F01 F02 E9 F40Discriminate Species: Assessing accuracy of F19 99 F27barcoding loci to discriminate species F48 26 F51 vs. F38 82 F rbcL57 R A08 F52Estimate Species: Using plant DNA barcodes 36 F56 E3to estimate species richness 98 44 F29 F07 98 50 F17 F60 99 F68 37 99 F69
  • 7. Costion et al. (2011) PLoS ONE: In press Distance tree of DNA samples Identities confirmed
  • 8. Costion et al. (2011) PLoS ONE: In press• No gain in in discrimination accuracy by adding matK• Estimation accuracy decreases with matK With addition of 3rd locus trnH psbA discrimination accuracy remains same ~ 70% Estimation accuracy increases to 89%
  • 9. Costion et al. (2011) PLoS ONE: In press 89% accuracy of species ID with rbcL & trnH psbA combination Biodiversity assessments possible! ~ poorly known areas ~ tree saplings/seedlings ~ high canopy ~ roots or other cryptic samples
  • 10. Using barcode data to assess phylogenetic diversity Where are the hotspots of evolutionary history? Plot Network of 250Costion, C. (PhD Thesis) 0.1 hectare plots
  • 11. All angiosperm genera supertree – largest phylogeny of a tropical bioregion to date (660 species)Costion, C. (PhD Thesis)
  • 12. Costion, C. (PhD Thesis) Rainforest stability indexPD Genus Richness Hilbert et. al (2007)
  • 13. Phylogenetic Diversity (PD)/ Genus Richness (GR) PD v GR at different spatial resolutions 18 16 14 12 10PD 8 6 4 2 0 0 100 200 300 400 500 GR GR0.1 vs PD0.1 GR0.065 vs PD0.065 However, when affects GR0.125 vs PD0.125 GR0.25 vs PD0.25 of GR are removed through regression a biogeographic pattern emergesCostion, C. (PhD Thesis)
  • 14. Indomalayan lineages higher frequency in lowlands. Areas with higher PD than expected can be explained by higher proportion of non-Australian (Gondwanan) elements present. Extant rainforest 70 Ancient GondwanaIndomalayan lineages 60 Laurasian Richness 50 40 30 20 10 Uplands 0 0 200 400 600 800 1000 1200 1400 1600 1800 elevation Gondwanan lineages Elevation (m) Lowlands Indomalayan lineagesCostion, C. (PhD Thesis)
  • 15. Australian Centre for Evolutionary Biology and Biodiversity The Terrestrial Ecosystem Research Network $45M Research Infrastructure Facility for Australia The objectives of TERN are to: • network for terrestrial ecosystem research; • Coordinate national observation networks; • Improved access to observational data; • Identify future needs for research.Slide 16 Life Impact The University of Adelaide
  • 16. Australian Centre for Evolutionary Biology and BiodiversitySlide 17 Life Impact The University of Adelaide
  • 17. Australian Centre for Evolutionary Biology and Biodiversity Rangelands Forestry plot network plots Forestry Forestry plots plotsMulti-scale Plot activities-AusPlots Slide 18 Forestry University of Adelaide Life Impact The plots
  • 18. Australian Centre for Evolutionary Biology and Biodiversity NATT CSIRO plots transect SWATT TREND transect transect AlpineMulti-scale Plot activities plots-AusPlots-Long Term Ecological Research Slide 19 Forestry University of Adelaide Life Impact TheNetwork plots
  • 19. Australian Centre for Evolutionary Biology and BiodiversityMulti-scale Plot activities-AusPlots-Long Term Ecological Research Network Slide 20 Life Impact The University of Adelaide-Supersites
  • 20. Data collection and distribution: Ecoinformatics facility Australian Centre for Evolutionary Biology and Biodiversity Multi-Scale Plot Network Soils Coasts AusCover OzFlux AusPlots Plot networks Supersites EcoinformaticsSlide 21 Life Impact The University of Adelaide Scaling/Modelling ACEAS TERN Portal
  • 21. AusPlotsCentre for Evolutionary Biology and Biodiversity AustralianContinental stratification to group bioregions to establish biodiversitymonitoring plots Rangelands plot network Forestry plots Slide 22 Life Impact The University of Adelaide
  • 22. Australian Centre for Evolutionary Biology and BiodiversityAusPlots – site methodology1,000 (approx) permanent biodiversity survey plots being established across the Australian ContinentCombine traditional and cutting edge techniques – modular– baseline surveys of vegetation and soil diversity and structure– collect leaf and soil samples for analysis • Taxonomy, carbon, nutrients, isotopes, • DNA barcoding, phylogeography, genomics– Photo points, image interpretation and remote sensing cal/val. Slide 23 Life Impact The University of Adelaide
  • 23. Australian Centre for Evolutionary Biology and BiodiversityLong term ecological research network NATT CSIRO plots transect SWATT TREND transect Lindenmayer transect and NSW plots Alpine plotsSlide 24 Life Impact The University of Adelaide
  • 24. TREND Australian Centre for Evolutionary Biology and Biodiversity TRENDTransect for Environmental monitoring and Decision making How to inform ecosystem management decisions in a variable and changing climate: Access historical information on change Establish monitoring program to track change Use ‘space as a proxy time’ for predicted changes Model predictions of changes and compare Slide 25 Life Impact The University of Adelaide
  • 25. Temperature gradients Australian Centre for Evolutionary Biology and Biodiversity Rainfall gradientsSlide 26 Life Impact The University of Adelaide
  • 26. Australian Centre for Evolutionary Biology and BiodiversitySlide 27 Life Impact The University of Adelaide
  • 27. Australian Centre for Evolutionary Biology and BiodiversityPlot-based information – flora, veg structure, soils - field & remote sensed Slide 28 Life Impact The University of Adelaide
  • 28. Australian Centre for Evolutionary Biology and Biodiversity Plot-based DNA analysis DNA barcoding to understand taxonomy, phylogenetic diversity, community composition and turnover (IBOL)Dick and Kress (2009) Slide 29 Life Impact The University of Adelaide
  • 29. Australian Centre for Evolutionary Biology and Biodiversity Plot-based DNA analysis DNA barcoding to understand taxonomy, phylogenetic diversity, community composition and turnover (IBOL) Genomic analysis to examine soil communities (metabarcoding, amplicon COX, RBCL, ITS) and plant gene expression changes along selection pressures (ARC, BGI, BPA)Slide 30 Life Impact The University of Adelaide Callistemon teretifolius (2009) Dick and Kress
  • 30. VERIFYING TIMBER SOURCES
  • 31. Range of levels of DNA discrimination DNA Fingerprinting  Individual log tracking – Verify integrity of supply chain Phylogeography  Regional origin – Verify country source DNA barcoding  Species origin – Verify species
  • 32. Application to date Individual log tracking with Certisource With funding support from the International Tropical Timber Organisation  PrimaryLowe et al., 2010
  • 33. Application to date Individual log tracking with Certisource With funding support from the International Tropical Timber Organisation  Primary At concession 2627 logs sampledLowe et al., 2010
  • 34. Application to date Individual log tracking with Certisource With funding support from the International Tropical Timber Organisation  Primary At concession At saw mill 2627 logs sampled 32 logs randomly sampledLowe et al., 2010
  • 35. Application to date Individual log tracking with Certisource With funding support from the International Tropical Timber Organisation  Matched back Primary At concession At saw mill 2627 logs sampled 32 logs randomly sampledLowe et al., 2010
  • 36. Timber TrackingForest and sawmill samples profiled with 14 microsatellitesExample Test 1 Test 2Forest sample 236, 238 240,248Sawmill sample 236, 238 238,246 No. loci match? Substitution?Sample 1 6 exact 1 in 50 millionLowe et al., 2010
  • 37. Timber TrackingForest and sawmill samples profiled with 14 microsatellitesExample Test 1 Test 2Forest sample 236, 238 240,248Sawmill sample 236, 238 238,246 No. loci match? Substitution?Sample 1 6 exact 1 in 50 millionOf 32 samples, 27 exact match, 5 did not amplifyProbability of substitution very lowLowe et al., 2010
  • 38. Range of levels of DNA discrimination DNA Fingerprinting  Individual log tracking – Verify integrity of supply chain Phylogeography  Regional origin – Verify country source DNA barcoding  Species origin – Verify species
  • 39. Checking country of origin Mahogany Score for Guatemala: 100% 33 populations 2038 trees genotyped Degen et al, subm. Score for Bolivia: 98.7%Practical test with 20 mahogany wood samples of Germantimber trader + 11 wood samples from South America
  • 40. Checking region of originMerbau – valuable timber treeIntsia bijugaSingapore and New GuineaIntsia palembanicaSabah and Papua>1000 individuals screened6 chloroplast loci
  • 41. Checking region of originMerbau – valuable timber treeIntsia bijugaSingapore and New GuineaIntsia palembanicaSabah and Papua>1000 individuals screened6 chloroplast loci
  • 42. Range of levels of DNA discrimination DNA Fingerprinting  Individual log tracking – Verify integrity of supply chain Phylogeography  Regional origin – Verify country source DNA barcoding  Species origin – Verify species
  • 43. Checking species identity Mahogany Specific projects with focus on CITES protected tree species => vTI + University of Hamburg (Aki Höltken and Elisabeth Magel) Swietenia macrophylla S. mahagoniApproach:• sequencing of cpDNA- Swietenia macrophylla fragments• searching for SNPs• new primer design for short PCR amplification products (< 350 bp)
  • 44. New project in Africa Seven target countriesSource: http://africamap.harvard.edu/Center for Geographic Analysis Species identity Country of origin Chain of custody 45
  • 45. DNA extraction from wood DNA + other compounds Wood contains many secondary compounds that affect success of DNA extraction and PCR Including: cellulose, lignin, hemicellulose, resins, waxes, trace elements
  • 46. DNA extraction from wood Boundaries of possibility Composite Raw Sawn Solid wood Ancient wood products Pulp andtimber timber product (Mary Rose) (veneer, ply) paper Technology frontierIntact DNA Highly degraded DNA
  • 47. Acknowledgements• Wet tropics barcoding – Australian Tropical Herbarium, James Cook University, TRIN, CSIRO, – Craig Costion, Darren Crayn, Gary Sankowsky, Andrew Ford, Dan Metcalfe, Will Edwards, James Richardson, Hugh Cross• TERN/TREND – Jeff Foulkes, Ben Sparrow, Andrew White, Nikki Thurgate, – Greg Guerin, Hugh Cross, Ed Biffin, Kimberly McCallum• Illegal logging – von Thunen Institute, Double Helix Tracking Technologies – Bernd Degen, Hugh Cross, Aki Höltken, Darren Thomas, Jonathan Geach

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