DNA Barcoding and Biodiversity Conservation
Eduardo Eizirik
Centro de Biologia Genômica e Molecular, PUCRS, BrasilInstituto Pró-Carnívoros, BrasilLaboratory of Genomic Diversity, NIH, EUA
Images (partial): www.tolweb.org
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: 1.1.1. 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: 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 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.
bPgy35 bPgy06
Pgy05 Pgy02
Lycalopex gymnocercus
bPve05 bPve06 bPve04
Lycalopex vetulus
bCth208 bCth205 bCth164 bCthImperatrizMA bCth185 bCth51
Cerdocyon thous
Lobo-guaraExtr1SCL bCbr302II Lobo-guara3 Cbr05
Chrysocyon brachyurus
Aau586 Aau683 Aau687 A.australis
Aau689L-159-H04
Arctocephalus australis
Arctocephalus forsteri bPbr02 bPbr01
Pteronura brasiliensis
Martes americana Mam02
Martes americana (Neártico)
Lcn1 Lontra canadensis
Lontra canadensis (Neártico)
bLlo30 bLlo06 bLlo15 bLlo29 bLlo31
Lontra longicaudis
bPon56 bP13
Panthera onca
Panthera tigris Puma concolor
Lco9 Lco10
Leopardus colocolo
Oge38 bLge32 Oge63
Leopardus geoffroyi
bLti97 bLge01 bLti96
Leopardus tigrinus
100
100
100
100
7099
98
8292
99
91
74
86
99
100
100
100
100
81
100
6299
83
98
78
99
99
60
76
81
100
0.02
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 bpBARCODE 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.
0.02
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
100
99
DNA identification of field-collected scats – ATP6 (105 bp)
A20-consenso-574 A43-consenso-574 Felis catus
Lynx canadensis ATP6 Pco 541 Puma concolor Pco356 Puma concolor
bPon51 Panthera onca bPon24 Sangue Panthera onca bPon13 sangue Panthera onca
A34-consenso-574 A27-consenso-574 A42-consenso-574
bSve303ccrf.scf bSve305ccrf.scf
A30-consenso-574 Canis familiaris Canis lupus Clupusccrr
Clatransccrr A22-consenso-580
Cbr06ccrr Lobo-guar FAL36 fezes 0.5ul sem purif... Cbr07ccrr Lobo-guarFAL39 fezes .5ul sem purificar
100
100
8699
99
98
97
97
52
39
70
75
59
76
38
91
93
0.02
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/05
81
99
99
80
99
99
77
71
96
97
93
89
47
72
53
51
62
0.02
Rabies virus in Brazilian wild canids(P. Carnieli Jr. – Inst. Pasteur – Brazil)[control region]
Phylogeography of the crab-eating fox (Cerdocyon thous)
Northern Northern CladeClade
C14C14C4C4
C3C3C6C6
C2C2C5C5
C15C15C11C11C9C9
C10C10C17C17C21C21C16C16C13C13
C12C12C18C18
C8C8C7C7
C19C19C20C20
C1C1
C29C29C25C25C35C35
C22C22C24C24C26C26C27C27
C28C28C23C23
C30C30C33C33
C34C34C32C32
C31C31P.vetulus
P.vetulusP.vetulus
P.gymnocercusP.gymnocercus
P.gymnocercus0.005 substitutions/site0.005 substitutions/site
99/70/100/10099/70/100/100
85/ */62/5385/ */62/53
99/94/99/10099/94/99/100
Southern Southern CladeClade
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. ChavesVanessa G. GraeffTaiana Haag Ligia TchaickaTatiane C. TrigoEunice MattePaulo Prates Jr.Cristine S. TrincaDaniela CopettiManoel Rodrigues Gabriel MacedoLuana CardosoHenrique FigueiróFlávia TirelliAnelisie S. SantosAna Carolina G. Escobar
Sandro L. BonattoBrazilian DNA barcode networkOliver Ryder
Pedro Carnieli Jr.
Dênis SanaFlávio 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, PUCRS
ACKNOWLEDGEMENTS:
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