DNA Barcoding and Biodiversity Conservation Eduardo Eizirik Centro de Biologia Genômica e Molecular, PUCRS, Brasil Instituto Pró-Carnívoros, Brasil Laboratory.

Slides:

Advertisements

Similar presentations

- Unit VI - IAS Specimen Collection, Identification, and Preservation Rebecca M. Westbrooks Randy G. Westbrooks Steven Manning Global Invasive Species.

Advertisements

The Discovery Corridor Concept and its Applicability January 13/14, 2004 workshop St. Andrews Biological Station, St. Andrews, N.B.

Massachusetts Division of Fisheries & Wildlife Pam Landry, MassWildlife Education Coordinator Photos by Bill.

Development of a Comprehensive Wildlife Conservation Strategy for Georgia Georgia Department of Natural Resources Wildlife Resources Division.

Corals and sea anemones on line: a functioning biodiversity database D. G. Fautin R. W. Buddemeier University of Kansas: Department of Ecology and Evolutionary.

Catalogue of Life, Reading, UK, 29 March 2007 Consortium for the Barcode of Life (CBOL): Linking Molecules to the Catalogue of Life David E. Schindel,

DNA Barcodes: Linking GenBank records to Museum Specimens David E. Schindel, Executive Secretary, CBOL Robert Hanner, University of Guelph.

Wildlife Learning Objectives Birds, Mammals, Amphibians and Reptiles Species Identification: Identify wildlife species common to NS and the.

The Challenge of Scale: Is Biodiversity Big Science? Woody Turner Biodiversity & Ecological Forecasting Team Meeting University of Maryland May 1, 2008.

Data Analysis Working Group, DIMACS, 26 Sept 2005 DNA Barcoding and the Consortium for the Barcode of Life David E. Schindel, Executive Secretary National.

SinBIOTA 2.0: Planning a New Generation Environmental Information System Prof. Carlos A. Joly & Prof.João Meidanis University of Campinas & Scylla Bioinformatics.

Population Ecology in Conservation and Management What brings about declines? How do we identify and deal with causes?

BIOSAFETY CONCERNS IN THE CONTEXT OF BIOTECHNOLOGY. Presentation for Training Workshop for Regional Advisors Bangkok, Thailand May 2006.

Interaction of Invasive Plants with Environment and Other Biota Eric Dibble Bill James Susan Wilde.

S PECIAL G UEST. Florida Museum of Natural History Douglas Jones UF Biodiversity Initiative.

Evolutionary Genomics and the Museum: Enhancing insight into evolutionary processes using museum collections An Introduction to AIM-UP! – Advancing the.

Biodiversity and Climate Change

Biodiversity and Conservation Created by Beckie Granatstein, B.A., BSc., MSc.

Way Forward Resources: –Sense of urgency, willingness to collaborate –Species richness –Unevenly distributed expertise, collections; some strengths –Workforce.

University of Puerto Rico, Río Piedras Campus Funded by National Science Foundation and the University of Puerto Rico NSF-HRD ( ); NSF.

Principles of Conservation Biology BIOL Biodiversity.

Drivers for a PRAGMA Biodiversity Science Expedition Reed Beaman Florida Museum of Natural History University of Florida.

Data Requirements for Field Release and Monitoring Jon Knight Imperial College London

Environmental Science

Richard White Biodiversity Data. Outline Biodiversity: what is it? – Definitions: is biodiversity: A resource? Something which can be measured? How to.

DNA Barcoding – Southern African Experience Michelle van der Bank.

DNA Barcoding Amy Driskell Laboratories of Analytical Biology

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

RAPID ASSESSMENT PROGRAM (RAP) Terrestrial Ecosystems Freshwater Ecosystems Marine Ecosystems.

Scott Miller – SANBI, 7 April 2006 Overview of DNA Barcoding and the Barcode of Life Initiative Scott E. Miller, Chair, CBOL Executive Committee National.

Census of Marine Life, Amsterdam – 16 May 2006 The Protocol Chain for DNA Barcoding Projects.

Eastern Bearded-dragon (Pogona barbata) – Toowoomba, Australia © Arthur D. Chapman Principles of Data Quality Australian Biodiversity Information Services.

Adaptation of Biodiversity to Climate Change in southern Africa CSIR, National Botanical Institute, University of Pretoria & Kruger National Park.

Prepared for the 3rd SBB telecon 20 Mar 2012 Michele Walters, BI-01 task coordinator.

Planning for Arctic GIS and Geographic Information Infrastructure Sponsored by the Arctic Research Support and Logistics Program 30 October 2003 Seattle,

© GEO Secretariat GEO Ecosystem task and GEO BON Carlos Padovani, Brazil Georgios Sarantakos, GEO Secretariat Beijing, China April 21, 2013 GEO Ecosystem.

Progress since the February 2005 London DNA Barcode of Life Conference Scott Miller, Chair Consortium for the Barcode of Life Smithsonian Institution.

Aspects for Improving the ABBI Patricia Escalante Instituto de Biología UNAM AOU-Collections Committee member.

Muthama Muasya University of Cape Town Application of DNA barcoding in plant taxonomy, Eastern Africa Experience.

FISH SPECIES IDENTIFICATION AND BIODIVERSIFICATION IN ENUGU METROPOLIS RIVER BY DNA BACODING PRESENTED BY Chioma Nwakanma (PhD) Michael Okpara University.

Characterization, Inventory and Monitoring of trends in indigenous livestock Dr. E. D. Ilatsia D. N. Kamiti 23-Oct-15Animal Breeding and Genomics Group1.

Consortium for the Barcode of Life

Diversity of Living Things 1.1: Biodiversity. Biodiversity Number and variety of species and ecosystems on Earth By the end of 2010, 1.7 million species.

DNA Barcoding and the Consortium for the Barcode of Life Katie Ferrell, Project Manager National Museum of Natural History Smithsonian Institution

Conservation planning strategies at the landscape scale.

1 Biodiversity. 2 BIODIVERSITY Includes a variety of factors  Genetic Diversity – genetic variability within a species  Species Diversity – variety.

Linking Barcode Data to Multiple Users David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution

AREAS OF CONSERVATION EMPHASIS ACE-II Photos courtesy of USFWS National Image Library Melanie Gogol-Prokurat California Department of Fish and Wildlife.

Context: The Strategic Plan for Establishing the Network Integrated Biocollections Alliance Judith E. Skog, Office of the Assistant Director, Biological.

Evolution of Biodiversity

CEPDEC-TZ Training course: Digitisation of Biodiversity Information 13th – 17th July 2009 Dar es Salaam, Tanzania GLOBAL BIODIVERSITY INFORMATION FACILITY.

Research Problem In one sentence, describe the problem that is the focus of your classroom research project about student learning: There is a growing.

Dmytro Kryvokhyzha. United Nations Conference on the Human Environment, Stockholm 1972 United Nations Conference on Environment and Development, Rio de.

Conservation Biology and Restorative Ecology. What matters most in an ecosystem: BIODIVERSITY Genetic diversity Species diversity Ecosystem diversity.

INTRODUCTION Use of DNA data in determining phylogenetic relationships is well established. DNA barcode approach to use.

Conserving Europe’s plant genetic resources for use now and in the future PGR Forum European crop wild relative diversity assessment and conservation forum.

Emerging Threats Program Text The Emerging Pandemic Threats Program.

Introduction to Environment. Environment : from the French word ‘environner ‘- to encircle or surround Whatever is around us constitutes our Environment.

State Standards Biotechnology. Understand how biotechnology is used to affect living organisms. Summarize aspects of biotechnology including: Specific.

Inventory & Monitoring Program U.S. National Wildlife Refuge System Natural Resources Program Center National Office USFWS U.S. Fish & Wildlife Service.

Sustaining Wild Species

Geographic Information Systems (GIS) and the Conservation and Use of Plant Genetic Resources Summary of

IUCN and Biodiversity Assessment

Volume 23, Issue 24, Pages (December 2013)

7.b Marine alien species on EASIN

Expert group on management of Natura 2000

Micro- to Macro-system Integration

Presentation transcript:

DNA Barcoding and Biodiversity Conservation Eduardo Eizirik Centro de Biologia Genômica e Molecular, PUCRS, Brasil Instituto Pró-Carnívoros, Brasil Laboratory of Genomic Diversity, NIH, EUA

Images (partial): Biodiversity: - 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

Time No. of species Species known to science Presently living species Species diversity

The Biodiversity Crisis Urgent needs: - To inventory, document, map and characterize the world´s 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 Conservation 1.Gathering data on components of native biodiversity; 1.1. Baseline data; 1.2. Monitoring of biodiversity in impacted areas; 2.Gathering data on threats to native biotas; - e.g. invasive species, pathogens, wildlife trafficking. 3.Helping to enforce actions aimed at curbing threats to biodiversity. - e.g. wildlife forensic analyses.

Applications of DNA Barcoding in Biodiversity Conservation 1.Gathering data on components of native biodiversity 1.1. Baseline data: Thoroughly inventorying all of the Earth’s 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 Conservation 1.Gathering data on components of native biodiversity 1.1. Baseline data: 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 Conservation 1.Gathering 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 Conservation 2. 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 Conservation 3. 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 Kb 12.5 Kb ATP6 (125 bp) Panthera Numt mtDNA COI 1560 bp BARCODE 648 bp MINI-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 bPon56 (fezes Panthera onca em álcool) 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 (pêlos de Panthera onca) bPon56 (fezes de Panthera onca - 48 mg) bPon24 (sangue de Panthera onca) P31-1 (pêlos 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 catus

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/ Rabies virus in Brazilian wild canids (P. Carnieli Jr. – Inst. Pasteur – Brazil) [control region]

Phylogeography of the crab-eating fox (Cerdocyon thous) Northern Clade C14 C4 C3 C6 C2 C5 C15 C11 C9 C10 C17 C21 C16 C13 C12 C18 C8 C7 C19 C20 C1 C29 C25 C35 C22 C24 C26 C27 C28 C23 C30 C33 C34 C32 C31 P.vetulus P.gymnocercus substitutions/site 99/70/100/100 85/ */62/53 99/94/99/100 Southern Clade mtDNA CR Tchaicka et al. 2007

Large-scale inventorying of Brazilian biodiversity (2005) Sampling strategy 15 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. Chaves Vanessa G. Graeff Taiana Haag Ligia Tchaicka Tatiane C. Trigo Eunice Matte Paulo Prates Jr. Cristine S. Trinca Daniela Copetti Manoel Rodrigues Gabriel Macedo Luana Cardoso Henrique Figueiró Flávia Tirelli Anelisie S. Santos Ana Carolina G. Escobar Sandro L. Bonatto Brazilian DNA barcode network Oliver Ryder Pedro Carnieli Jr. Dênis Sana Flávio Rodrigues Cibele Indrusiak Ronaldo Morato Tadeu G. Oliveira Laury Cullen Jr. Rodrigo Jorge Leonardo Vianna Carlos De Angelo Mario S. Di Bitetti Support: CNPq, CAPES, FNMA/MMA, CESP, NIH-USA, PUCRS ACKNOWLEDGEMENTS: