DNA Barcoding and Biodiversity Conservation Eduardo Eizirik Centro de Biologia Gen´mica e Molecular, PUCRS, Brasil Instituto Pr³-Carn­voros, Brasil Laboratory

  • View
    214

  • Download
    0

Embed Size (px)

Text of DNA Barcoding and Biodiversity Conservation Eduardo Eizirik Centro de Biologia Gen´mica e...

  • DNA Barcoding and Biodiversity Conservation

    Eduardo Eizirik

    Centro de Biologia Genmica e Molecular, PUCRS, BrasilInstituto Pr-Carnvoros, BrasilLaboratory of Genomic Diversity, NIH, EUA

  • Images (partial): www.tolweb.orgBiodiversity:

    Species, ecosystems, evolutionary lineages, genetic diversity, cultural diversity.

    Why is it important ? Intrinsic value Practical (anthropocentric) value: Ecosystem services. Source of food, materials, substances, innovation.

  • The Biodiversity Crisis

  • TimeNo. of speciesSpecies known to sciencePresently living speciesSpecies diversity

  • The Biodiversity CrisisUrgent needs:

    - To inventory, document, map and characterize the worlds biodiversity;

    To understand and monitor current threats to this biodiversity, as well as their impacts in various contexts;

    To eliminate or limit the magnitude of these threats, and/or to minimize their impacts through conservation and management actions.

  • Applications of DNA Barcoding in Biodiversity ConservationGathering data on components of native biodiversity;1.1. Baseline data;1.2. Monitoring of biodiversity in impacted areas;

    Gathering data on threats to native biotas;- e.g. invasive species, pathogens, wildlife trafficking.

    Helping to enforce actions aimed at curbing threats to biodiversity.- e.g. wildlife forensic analyses.

  • Applications of DNA Barcoding in Biodiversity ConservationGathering data on components of native biodiversity

    1.1. Baseline data: 1.1.1. Thoroughly inventorying all of the Earths ecosystems

    Discovery of new species;Improved knowledge on geographic ranges of species.

    Analysis of diverse sources/kinds of biological specimens (including environmental samples);Close interaction with morphology-based taxonomy and reference collections;Link to in-depth studies (e.g. phylogeographic) DNA banks

  • Applications of DNA Barcoding in Biodiversity ConservationGathering data on components of native biodiversity

    1.1. Baseline data: 1.1.2. Improving knowledge on species ecology and life history

    Identification of morphologically distinct genders and life history stages;Diet (e.g. using fecal DNA);Interactions with parasites, symbionts and pathogens;Spatial and temporal patterns of species occurrence, including habitat association.

  • Applications of DNA Barcoding in Biodiversity ConservationGathering data on components of native biodiversity

    1.2. Monitoring of biodiversity in impacted areas:(i.e. almost everywhere ...)

    Surveys of species occurrence in areas suffering varying degrees and kinds of disturbance:Information on susceptibility vs. resilience of each organism;Caution with sampling procedures.

    Links to DNA barcoding efforts targeting agricultural and epidemiological (e.g. emerging diseases) aspects.

  • Applications of DNA Barcoding in Biodiversity Conservation2. Gathering data on threats to native biotas:

    Mapping and monitoring the spread of invasive species;

    Identifying vectors and reservoirs of pathogens that threaten wildlife populations (as well as addressing potential emerging diseases for humans);

    Understanding the dynamics of wildlife trafficking activities;

    DNA barcodes that also identify geographic provenance.

  • Applications of DNA Barcoding in Biodiversity Conservation3. Helping to enforce actions aimed at curbing threats to biodiversity.

    Wildlife forensic analyses: - Species-level identification (and geographic origin when possible) of confiscated materials (e.g. meat products, eggs, pelts, bones, wood, etc.);

    - Example: whale meat in Japanese and Korean markets (DNA surveillance initiative);

    Barcoding for Species Conservation (BSC) initiative (CBoL):- Bushmeat trade in Africa, international pet trade, trade in tiger parts in China, overexploitation of sharks, etc.

  • Examples of ongoing and planned research fronts in Brazil- Species identification in carnivores;

    - Fecal DNA: ecological and biogeographic studies (large-scale assessment of current geographic ranges);

    - Study on rabies virus in wild canids.

    Large-scale inventory of Brazilian biodiversity

    - Multi-center project designed in 2005 to boost taxonomic research in Brazil using the DNA barcode concept as a catalyst to integrate field collections, museum research, genome center networks and bioinformatic advances.

  • Central portion of the standard COI barcode (~400 bp)Building a carnivore barcode database: COI

  • Selection of a Carnivore-optimized mini-barcode for fecal DNA:

    COI barcode (658 bp)

    Sliding window approach;

    Data set with 45 carnivore species representing several families

  • 16 Kb12.5 KbATP6 (125 bp)Panthera NumtmtDNACOI 1560 bpBARCODE 648 bpMINI-COI (186 bp)

    Development of additional segments for carnivore non-invasive DNA barcoding:

    Special interest in identifying jaguar vs. puma scats;

    Nuclear mtDNA insertion in the genus Panthera (numt);

    Use of a segment of the ATP6 gene

  • Species identification of field-collected scats from large felids using the ATP6 segment.0.02 bPon56 (fezes Panthera onca em lcool) bPon55 (fezes de Panthera onca em DET) bPon306 (fezes de Panthera onca) bPon307 (fezes de Panthera onca) bPon56 (fezes Panthera onca - 98 mg) bPon32 (sangue de Panthera onca) bPon56 (fezes de Panthera onca em DET) P3-16 (pele de Panthera onca) bPon305 (fezes de Panthera onca) P3-2 (plos de Panthera onca) bPon56 (fezes de Panthera onca - 48 mg) bPon24 (sangue de Panthera onca) P31-1 (plos de Panthera onca) F2-636 (fezes de felino grande) Puma concolor (sangue) L.V.(fezes de felino grande) F57-1C (fezes de felino grande) F2-635 (fezes de felino grande) Felis catus10099

  • DNA identification of field-collected scats ATP6 (105 bp)

  • 10/FOX/BA/04 77/FOX/BA/05 65/FOX/BA/05 66/FOX/BA/05 35/FOX/PE/05 33/FOX/PE/05 43/FOX/PE/05 45/FOX/PE/05 38/FOX/PE/05 40/FOX/PE/05 55/FOX/PI/05 37/FOX/PE/05 28/FOX/BA/04 4/FOX/BA/04 64/FOX/BA/05 41/FOX/PE/05 Cerd bcth184 PE 46/FOX/PE/05 36/FOX/PE/05 Cerd bcth228 MA 23/FOX/PI/05 42/FOX/PE/05 44/FOX/PE/05 Cerd LG212 MT 25/FOX/PI/05 Cerd bcth198 MG 2/FOX/BA/04 Lgymno LG166 Lgymno LG45(RS) Lvetulus LG282 Lvetulus LG185 MG Lvetulus LG184 BA 26/FOX/PI/05 59/FOX/PI/05 50/DOG/PE/05 51/DOG/PE/05 48/DOG/PE/05 34/DOG/PE/05 49/DOG/PE/0581999980999977719697938947725351620.02 Rabies virus in Brazilian wild canids(P. Carnieli Jr. Inst. Pasteur Brazil)[control region]

  • Phylogeography of the crab-eating fox (Cerdocyon thous)Northern CladeC14C4C3C6C2C5C15C11C9C10C17C21C16C13C12C18C8C7C19C20C1C29C25C35C22C24C26C27C28C23C30C33C34C32C31P.vetulusP.vetulusP.vetulusP.gymnocercusP.gymnocercusP.gymnocercus0.005 substitutions/site99/70/100/10085/ */62/5399/94/99/100Southern ClademtDNA CRTchaicka et al. 2007

  • Large-scale inventorying of Brazilian biodiversity (2005) Sampling strategy15 sites:-10,000 samples/site: - fish - amphibians - reptiles (incl. birds) - mammals - spiders - Leguminosae

  • Large-scale inventorying of Brazilian biodiversity

    6 museums Involved in coordinating collection trips, curation of sampled specimens and their morphology-based analysis

    14 Centers of Molecular Biodiversity: Network of genome centers and molecular biology laboratories performing high-throughput sequencing of DNA barcodes from 150,000 samples;

    Bioinformatics tools: online management of data collection, analysis and integration (e.g. morphology, DNA barcodes, geography)

    Training activities: courses, workshops.

  • Paulo B. ChavesVanessa G. GraeffTaiana Haag Ligia TchaickaTatiane C. TrigoEunice MattePaulo Prates Jr.Cristine S. TrincaDaniela CopettiManoel Rodrigues Gabriel MacedoLuana CardosoHenrique FigueirFlvia TirelliAnelisie S. SantosAna Carolina G. EscobarSandro L. BonattoBrazilian DNA barcode networkOliver Ryder

    Pedro Carnieli Jr.

    Dnis SanaFlvio RodriguesCibele Indrusiak Ronaldo MoratoTadeu G. OliveiraLaury Cullen Jr.Rodrigo JorgeLeonardo ViannaCarlos De Angelo Mario S. Di Bitetti Support: CNPq, CAPES, FNMA/MMA, CESP, NIH-USA, PUCRSACKNOWLEDGEMENTS: