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The Biota-FAPESP International Symposium on DNA Barcoding – 2009
DNA barcoding of South American mammals
Eduardo Eizirik
Lab. Biologia Genômica e Molecular, PUCRS, Brasil
Instituto Pró-Carnívoros, Brasil
Laboratory of Genomic Diversity, NIH, EUA
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
Neotropical mammals
How DNA barcodes can help the study and conservation of
Neotropical mammals:
1. Improved reliability of surveys
- Academic-oriented (e.g. geographic range refinements)
- Environmental impact assessments
2. Ecological studies
- Habitat association
- Diet
- Parasite interactions
- Monitoring of species occurrence
3. Forensics and law enforcement applications
The effort towards Large-scale DNA barcoding of
Neotropical mammals
History:
Precursor:
2005 – Beginning of the Brazilian DNA barcoding network
- 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-based biodiversity research,
genome center networks and bioinformatics advances.
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.
The effort towards Large-scale DNA barcoding of
Neotropical mammals
History:
2007 – Regional CBOL meeting in Campinas, Brazil
- Mammals emerge as a CBOL-endorsed regional priority
for DNA barcoding.
- Several members of the 2005 network confirm
participation, while additional partner institutions join.
The effort towards Large-scale DNA barcoding of
Neotropical mammals
History:
2007 – present
Activities:
1. Talks, symposia and/or planning meetings during subsequent
regional, national and international congresses:
- 2007, 2008 – Brazilian Congress of Genetics
- 2008 – Brazilian Congress of Zoology, Brazilian
Congress of Mammalogy, Regional Genetics Meeting (RS)
- 2009 – International Mammalogical Congress, Argentina
2. Funding proposals: CYTED (2007), PROSUL (2007, 2008).
PROSUL project proposal – 2008 (excerpt)
Goal:To consolidate an international network whose aim is generate, analyze and apply an integrated data base of DNA barcodes for South American mammals.
Official participants: 21 research institutions from six countries (Brazil, Uruguay, Chile, Bolivia, Peru and Venezuela).
- museum-based groups working on mammal systematics- molecular genetics laboratories
Proposed tasks:(i) Training of students from multiple countries in the use of molecular tools for biodiversity studies;(ii) Coordination meeting comprising group leaders;(iii) Reagent costs for the initial phase of data collection.
PROSUL 2008 participating institutionsBrazilPUCRS - Pontifícia Universidade Católica do Rio Grande do SulUFMG - Universidade Federal de Minas GeraisUFRGS - Universidade Federal do Rio Grande do SulUFES - Universidade Federal do Espírito SantoFZB/RS - Fundação Zoobotânica do Rio Grande do SulURI – Universidade Regional IntegradaFURB – Universidade Regional de BlumenauUFPR –Universidade Federal do ParanáUFRJ - Museu NacionalINCA - Instituto Nacional de CâncerFIOCRUZ - Fundação Oswaldo CruzUERJ - Universidade do Estado do Rio de JaneiroUSP - Instituto de BiociênciasUSP/ESALQ - Escola Superior de Agricultura Luiz de QueirozINPA - Instituto Nacional de Pesquisas da AmazôniaUFMS - Universidade Federal de Mato Grosso do SulUCB-DF - Universidade Católica de BrasíliaUFPA - Universidade Federal do ParáUFAM - Universidade Federal do Amazonas
PROSUL 2008 participating institutions
Uruguay
FC - Facultad de Ciencias (Enrique Lessa)
Chile
UC - Universidad de Chile (Angel Spotorno)
Venezuela
USB - Universidad Simon Bolivar (Marisol Aguilera)
Peru
UPCH - Universidad Peruana Cayetano Heredia (Jose R. Espinosa)
Bolivia
MNHN - Museo Nacional de Historia Natural (Julieta Vargas)
South American Network for Mammalian DNA barcoding
Regional Nodes
Brazil
1. Rio Grande do Sul – PUCRS/UFRGS
2. Espírito Santo – UFES
3. Minas Gerais – UFMG
4. Rio de Janeiro – INCA/UERJ
5. São Paulo - USP
6. Pará - UFPA
7. Goiás/Brasília - UFG
Uruguay
1. Universidad de la Republica
Carnivora
Xenarthra
Rodentia
Chiroptera
Small mammals
Xenarthra
Chiroptera
Xenarthra
Chiroptera
Rodentia
Rodentia
Primates
Primates
Species sampled so far:
Porto Alegre (PUCRS/UFRGS)Xenarthra – 5 spp.Carnivora – 23 spp. Next targets: Cetacea, Primates Rodentia – 43 spp.Cetartiodactyla – 4 spp.Chiroptera – 15 spp.Total: 90 spp (~ 600 specimens)
Belo Horizonte (UFMG)Xenarthra – 7 spp.Chiroptera – 35 spp. (> 200 specimens)
Espírito Santo (UFES)Rodentia, Didelphimorphia, Chiroptera – 85 spp. (259 specimens)
São Paulo (USP)Xenarthra – 6 spp. (149 specimens) [N. Moraes-Barros]
Next targets: Chiroptera, Rodentia [F. Martins]
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
bPbr01Pteronura brasiliensis
Martes americana
Mam02Martes americana (Neártico)
Lcn1
Lontra canadensisLontra canadensis (Neártico)
bLlo30
bLlo06
bLlo15
bLlo29
bLlo31
Lontra longicaudis
bPon56
bP13Panthera onca
Panthera tigris
Puma concolor
Lco9
Lco10Leopardus colocolo
Oge38
bLge32
Oge63
Leopardus geoffroyi
bLti97
bLge01
bLti96
Leopardus tigrinus
100
100
100
100
70
99
98
82
92
99
91
74
86
99
100
100
100
100
81
100
62
99
83
98
78
99
99
60
76
81
100
0.02
Building a
carnivore barcode
database: COI
Brazil
Bolívia
Urugua
y
Leopardus tigrinus
Leopardus colocolo
Leopardus pardalis
L
.
g
e
o
f
f
r
o
y
i
bLge28| Leopardus geoffroyi
bLge37| Leopardus geoffroyi
bLge29| Leopardus geoffroyi
bLge36| Leopardus geoffroyi
bLge43| Leopardus geoffroyi
bLg68| Leopardus geoffroyi
bLge65| Leopardus geoffroyi
bLge66| Leopardus geoffroyi
bLge57| Leopardus geoffroyi
bLge54| Leopardus geoffroyi
blge55| Leopardus geoffroyi
bLti59| Leopardus tigrinus
bLti075| Leopardus tigrinus
bLti062| Leopardus tigrinus
bLti07| Leopardus tigrinus
Lco07| Leopardus colocolo
Lpa32| Leopardus pardalis
86
99
81
85
86
100
3934
32
46
52
98
58
0.02
bPve305| Lycalopex vetulus
Pve310| Lycalopex vetulus
bPve307| Lycalopex vetulus
Pve317| Lycalopex vetulus
bPve315| Lycalopex vetulus
bPve311| Lycalopex vetulus
Pve315| Lycalopex vetulus
culp1208| Lycalopex culpaeus
culp3008| Lycalopex culpaeus
culp1606| Lycalopex culpaeus
culp2805| Lycalopex culpaeus
bPgy35| Lycalopex gymnocercus
bPgy40| Lycalopex gymnocercus
bPgy09| Lycalopex gymnocercus
s.001| Lycalopex sechurea
s.01| Lycalopex sechurea
s.002| Lycalopex sechurea
Dg19| Lycalopex griseus
Dg8coi| Lycalopex griseus
Dgr15| Lycalopex griseus
Dgr18| Lycalopex griseus
Dgr19| Lycalopex griseus
Dfu29| Lycalopex fulvipes
Dfu29.1| Lycalopex fulvipes
Df27| Lycalopex fulvipes
Dfu24| Lycalopex fulvipes
Df20| Lycalopex fulvipes
Dfu37| Lycalopex fulvipes
96
70
27
31
89
100
98
61
36
52
87
77
61
56
63
43
87
73
55
79
60
86
59
84
0.002
Lycalopex vetulus
Lycalopex culpaeus
Lycalopex
gymnocercus
Lycalopex sechurae
Lycalopex griseus
Lycalopex fulvipes
Evolutionary ecology of L. tigrinus and L. geoffroyi
Leopardus tigrinus
Leopardus geoffroyi
?
L. colocolo
Habitat use of L. tigrinus and L. geoffroyi in RS state
100 miles
N
Uruguay
Argentina
Atlantic Ocean
Gramineous SteppePark SteppeArboreal SteppeSteppical SavannahSemidecidual Stational ForestDecidual Stational ForestMixed Ombrophilous ForestDense Ombrophilous Forest
Pioneer FormationsEcological Tension Area
Dietary analysis of L. tigrinus e L. geoffroyi
using stomach contents of roadkilled animals
0
5
10
15
20
25
30
Akod
on sp
Calom
ys sp
Del
omys d
orsa
lis
Holo
chilu
s bra
silie
nsis
Mus
mus
culu
s
Olig
orym
ozys
sp
Ory
zom
ys sp
Oxym
ycteru
s sp
Rattu
s ra
ttus
Cav
ia sp
Mon
odelph
is sp
Col
umbifo
rmes
Cuc
ulifo
rmes
Gru
iform
es
Passe
riform
es
Tinam
iform
es
Sauria
Serpen
tes
Anur
a
Prey category
% o
f p
rey in
die
t
Leopardus tigrinus
Leopardus geoffroyi
CE01|Puma yagouaroundi|Ne306
CE02|Puma yagouaroundi|Ne306
OPN57|Oligoryzomys nigripes
OPN87|Oligoryzomys nigripes
OPN55|Oligoryzomys nigripes
JR332|Oligoryzomys flavescens
JR210|Oligoryzomys flavescens
JR209|Oligoryzomys flavescens
JR202|Oligoryzomys flavescens
OPN60|Oligoryzomys nigripes
JR244|Oligoryzomys flavescens
CE32|L. geoffroyi|Lgeof08
CE39|L. geoffroyi|NE312
CE47|L. tigrinus|bLti122
EU095456|Oligoryzomys fulvescens
PCE21|Deltamys kempi
CE10|L. tigrinus|NE312
CE20|L. tigrinus|bLti122
CE03|Leopardus geoffroyi|Lge076
CE04|Leopardus geoffroyi|Lge076
JR196|Sooretamys angouya
9790|Nectomys squamipes
CE61|L. tigrinus|bLti001
CE63|L. tigrinus|NE022
9735|Juliomys pictipes
9667|Juliomys pictipes
CE25|L. tigrinus|bLti079
CE65|L. tigrinus|NE022
CE05|L. geoffroyi|bLge074
CE59|L. tigrinus|bLti069
JR 405|Calomys tener
LBCE 5556|Calomys expulsus
CRB 2732|Calomys expulsus
LBCE 1547|Calomys expulsus
CE011|Leopardus geoffroyi|Ne312
LBCE 1548|Calomys expulsus
CE66|L. tigrinus|NE313
CE62|L. tigrinus|NE022
JR395|Oxymycterus nasutus
JR328|Akodon azarae
JR329|Akodon azarae
9595|Akodon montensis
PCE23|Oligoryzomys nigripes
JR 407|Akodon montensis
CE06|Leopardus geoffroyi|Ne308
6844|Akodon paranaensis
6963|Akodon paranaensis
CE09|P. yagouaroundi|NE314
JR411|Akodon paranaensis
100
100
100
96
39
100
100
89
68
45
99
65
86
80
87
99
56
100
68
85
100
59
92
100
78
78
58
99
51
100
82
55
96
99
99
43
99
99
78
93
67
42
31
20
12
11
0.02
Dietary analysis of L. tigrinus e
L. geoffroyi
using stomach contents of
roadkilled animals:
DNA barcoding of prey items
Development of molecular tools for carnivore
species identification from faecal DNA
“Molecular scatology meets DNA barcoding”
Assessment of variability in mtDNA segments
Generation of large data bases of carnivore sequences
Development of molecular tools for carnivore
species identification from faecal DNA
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
Haag et al. 2009
Identification of carnivores using short DNA segments
Goal: global standardized
saystem for carnivore
identification.
Application in ecological,
biogeographic and forensic
studies.
Ongoing tests in multiple field
sites in South America
Brazil (RS, ES, MS, MT, TO,
MG,DF), Argentina.
P.B. Chaves et al., in prep.
Identification of carnivores using short DNA segments
Ongoing surveys and ecological
studies
Testing and optimization of protocols for African carnivores:
Partnership with CCF, Namibia.
Identification of carnivores using short DNA segments
car70R Reverse Complement
Car78
bFca57
bFca53
bFca52
bFca54
Car73
bFca59
bFca55
bFca58
bFca02
bFca56
NC 001700.1| Felis catus
Fma
Fma11
57
39
25
12
21
30
52
34
97
46
70
91
18
car70R Reverse Complement
Car78
bFca57
bFca53
bFca52
bFca54
Car73
bFca59
bFca55
bFca58
bFca02bFca56
NC 001700.1| Felis catus
Fma
Fma11
Fni
Fni14
serval 3
serval 1
Lse
Lse18
AY598470.1|AY598470S01 Lynx canadensis
AH014070.1|SEG AY598470S Lynx canadensis
Car69
Cca21
Cca1
CarCaracal
Car49
car88R Reverse Complement
car93R Reverse Complement
car54copy
car47
car76R Reverse Complement
Aju
NC 005212.1| Acinonyx jubatus
Car48
AY463959.1| Acinonyx jubatus
car87R Reverse Complement
AF344830.1| Acinonyx jubatus
car89R Reverse Complement
car94R Reverse Complement
car2R Reverse Complement
Car2
Ppa286
Car8ccfAndBrazil
CarLeop
Ple185
Ple153
car84copy Reverse Complement
lionF
Cfe1
car52
NC 008450.1| Neofelis nebulosa
Vci
bAbi
Ial2
Rme
Hja
Hpa1
Pcr
Hbr1
Hhy40
Ccr34
Ccr236
Phe
Pli
NC 001602.1| Halichoerus grypus
Zca
Oro
AY377297.1| Hydrurga leptonyx
AY377296.1| Hydrurga leptonyx
NC 008425.1| Hydrurga leptonyx
Man68
AY377295.1| Ommatophoca rossii
AY377294.1| Ommatophoca rossii
Bal
Bas
AM711898.1| Spilogale putorius complete
bCar24
AB291076.1| Martes melampus
AB291075.1| Meles meles anakuma
AB291077.1| Enhydra lutris
Ist
Ssu
Car12
AY598506.1|AY598506S01 Alopex lagopus
AH014073.1|SEG AY598506S Alopex lagopus
CarBatEaredFox
carWildDog
B11and12and15
DQ480508.1| Canis lupus isolate 1 fro...
AY598494.1|AY598494S01 Canis lupus
DQ480502.1| Canis familiaris isolate ...
AH014072.1|SEG AY598494S Canis lupus
DQ480507.1| Canis lupus isolate 2 fro...
DQ480504.1| Canis lupus isolate 1 fro...
DQ480501.1| Canis familiaris isolate ...
AY656738.1| Canis familiaris isolate ...
AY729880.1| Canis familiaris
AY656737.1| Canis familiaris isolate ...
NC 002008.4| Canis lupus familiaris
DQ480491.1| Canis familiaris isolate ...
DQ480505.1| Canis lupus isolate 1 fro...
DQ480492.1| Canis familiaris isolate ...
DQ480503.1| Canis lupus isolate 1 fro...
NC 008092.1| Canis lupus
DQ480506.1| Canis lupus isolate 1 fro...
car50copy
car85R Reverse ComplementAY656739.1| Canis familiaris isolate ...
NC 008093.1| Canis latrans
DQ480511.1| Canis latrans isolate 2 f...
DQ480510.1| Canis latrans isolate 1 f...
DQ480509.1| Canis latrans isolate 1 f...
Car79
car23 copy
Car53
Car81
car74R Reverse Complement
Car71
car63R Reverse Complement
Car57
Car56
Car11
car91R Reverse Complement
Car82
car45R Reverse Complement
Car9ccf
Car64
Car68
Car15
Car80
car90R Reverse Complement
Car43
Car83
Car77
car44copy
car55copy
car62
car66
car65copy
car60copy
Car75
100
100
52
88
100
100
100
95
100
97
88
57
75
70
39
25
12
21
30
52
34
97
46
70
99
17
1
1
0
1
23
14
33
50
67
100
46
88
97
57
91
35
61
48
25
91
27
38
61
50
39
18
7
19
7
45
7
42
2
1
5
1
16
29
2
0
3
7
27
0
0
0
1
1
1
0
10
8
23
45
61
85
99
28
58
86
87
38
35
43
45
34
78
46
21
30
16
17
27
17
48
27
12
12
0,02
IUCN Cat Specialist Group
Car69
Cca21
Cca1
Caracal52
88
100
car70R Reverse Complement
Car78
bFca57
bFca53
bFca52
bFca54
Car73
bFca59
bFca55
bFca58
bFca02bFca56
NC 001700.1| Felis catus
Fma
Fma11
Fni
Fni14
serval 3
serval 1
Lse
Lse18
AY598470.1|AY598470S01 Lynx canadensis
AH014070.1|SEG AY598470S Lynx canadensis
Car69
Cca21
Cca1
CarCaracal
Car49
car88R Reverse Complement
car93R Reverse Complement
car54copy
car47
car76R Reverse Complement
Aju
NC 005212.1| Acinonyx jubatus
Car48
AY463959.1| Acinonyx jubatus
car87R Reverse Complement
AF344830.1| Acinonyx jubatus
car89R Reverse Complement
car94R Reverse Complement
car2R Reverse Complement
Car2
Ppa286
Car8ccfAndBrazil
CarLeop
Ple185
Ple153
car84copy Reverse Complement
lionF
Cfe1
car52
NC 008450.1| Neofelis nebulosa
Vci
bAbi
Ial2
Rme
Hja
Hpa1
Pcr
Hbr1
Hhy40
Ccr34
Ccr236
Phe
Pli
NC 001602.1| Halichoerus grypus
Zca
Oro
AY377297.1| Hydrurga leptonyx
AY377296.1| Hydrurga leptonyx
NC 008425.1| Hydrurga leptonyx
Man68
AY377295.1| Ommatophoca rossii
AY377294.1| Ommatophoca rossii
Bal
Bas
AM711898.1| Spilogale putorius complete
bCar24
AB291076.1| Martes melampus
AB291075.1| Meles meles anakuma
AB291077.1| Enhydra lutris
Ist
Ssu
Car12
AY598506.1|AY598506S01 Alopex lagopus
AH014073.1|SEG AY598506S Alopex lagopus
CarBatEaredFox
carWildDog
B11and12and15
DQ480508.1| Canis lupus isolate 1 fro...
AY598494.1|AY598494S01 Canis lupus
DQ480502.1| Canis familiaris isolate ...
AH014072.1|SEG AY598494S Canis lupus
DQ480507.1| Canis lupus isolate 2 fro...
DQ480504.1| Canis lupus isolate 1 fro...
DQ480501.1| Canis familiaris isolate ...
AY656738.1| Canis familiaris isolate ...
AY729880.1| Canis familiaris
AY656737.1| Canis familiaris isolate ...
NC 002008.4| Canis lupus familiaris
DQ480491.1| Canis familiaris isolate ...
DQ480505.1| Canis lupus isolate 1 fro...
DQ480492.1| Canis familiaris isolate ...
DQ480503.1| Canis lupus isolate 1 fro...
NC 008092.1| Canis lupus
DQ480506.1| Canis lupus isolate 1 fro...
car50copy
car85R Reverse ComplementAY656739.1| Canis familiaris isolate ...
NC 008093.1| Canis latrans
DQ480511.1| Canis latrans isolate 2 f...
DQ480510.1| Canis latrans isolate 1 f...
DQ480509.1| Canis latrans isolate 1 f...
Car79
car23 copy
Car53
Car81
car74R Reverse Complement
Car71
car63R Reverse Complement
Car57
Car56
Car11
car91R Reverse Complement
Car82
car45R Reverse Complement
Car9ccf
Car64
Car68
Car15
Car80
car90R Reverse Complement
Car43
Car83
Car77
car44copy
car55copy
car62
car66
car65copy
car60copy
Car75
100
100
52
88
100
100
100
95
100
97
88
57
75
70
39
25
12
21
30
52
34
97
46
70
99
17
1
1
0
1
23
14
33
50
67
100
46
88
97
57
91
35
61
48
25
91
27
38
61
50
39
18
7
19
7
45
7
42
2
1
5
1
16
29
2
0
3
7
27
0
0
0
1
1
1
0
10
8
23
45
61
85
99
28
58
86
87
38
35
43
45
34
78
46
21
30
16
17
27
17
48
27
12
12
0,02
car70R Reverse Complement
Car78
bFca57
bFca53
bFca52
bFca54
Car73
bFca59
bFca55
bFca58
bFca02bFca56
NC 001700.1| Felis catus
Fma
Fma11
Fni
Fni14
serval 3
serval 1
Lse
Lse18
AY598470.1|AY598470S01 Lynx canadensis
AH014070.1|SEG AY598470S Lynx canadensis
Car69
Cca21
Cca1
CarCaracal
Car49
car88R Reverse Complement
car93R Reverse Complement
car54copy
car47
car76R Reverse Complement
Aju
NC 005212.1| Acinonyx jubatus
Car48
AY463959.1| Acinonyx jubatus
car87R Reverse Complement
AF344830.1| Acinonyx jubatus
car89R Reverse Complement
car94R Reverse Complement
car2R Reverse Complement
Car2
Ppa286
Car8ccfAndBrazil
CarLeop
Ple185
Ple153
car84copy Reverse Complement
lionF
Cfe1
car52
NC 008450.1| Neofelis nebulosa
Vci
bAbi
Ial2
Rme
Hja
Hpa1
Pcr
Hbr1
Hhy40
Ccr34
Ccr236
Phe
Pli
NC 001602.1| Halichoerus grypus
Zca
Oro
AY377297.1| Hydrurga leptonyx
AY377296.1| Hydrurga leptonyx
NC 008425.1| Hydrurga leptonyx
Man68
AY377295.1| Ommatophoca rossii
AY377294.1| Ommatophoca rossii
Bal
Bas
AM711898.1| Spilogale putorius complete
bCar24
AB291076.1| Martes melampus
AB291075.1| Meles meles anakuma
AB291077.1| Enhydra lutris
Ist
Ssu
Car12
AY598506.1|AY598506S01 Alopex lagopus
AH014073.1|SEG AY598506S Alopex lagopus
CarBatEaredFox
carWildDog
B11and12and15
DQ480508.1| Canis lupus isolate 1 fro...
AY598494.1|AY598494S01 Canis lupus
DQ480502.1| Canis familiaris isolate ...
AH014072.1|SEG AY598494S Canis lupus
DQ480507.1| Canis lupus isolate 2 fro...
DQ480504.1| Canis lupus isolate 1 fro...
DQ480501.1| Canis familiaris isolate ...
AY656738.1| Canis familiaris isolate ...
AY729880.1| Canis familiaris
AY656737.1| Canis familiaris isolate ...
NC 002008.4| Canis lupus familiaris
DQ480491.1| Canis familiaris isolate ...
DQ480505.1| Canis lupus isolate 1 fro...
DQ480492.1| Canis familiaris isolate ...
DQ480503.1| Canis lupus isolate 1 fro...
NC 008092.1| Canis lupus
DQ480506.1| Canis lupus isolate 1 fro...
car50copy
car85R Reverse ComplementAY656739.1| Canis familiaris isolate ...
NC 008093.1| Canis latrans
DQ480511.1| Canis latrans isolate 2 f...
DQ480510.1| Canis latrans isolate 1 f...
DQ480509.1| Canis latrans isolate 1 f...
Car79
car23 copy
Car53
Car81
car74R Reverse Complement
Car71
car63R Reverse Complement
Car57
Car56
Car11
car91R Reverse Complement
Car82
car45R Reverse Complement
Car9ccf
Car64
Car68
Car15
Car80
car90R Reverse Complement
Car43
Car83
Car77
car44copy
car55copy
car62
car66
car65copy
car60copy
Car75
100
100
52
88
100
100
100
95
100
97
88
57
75
70
39
25
12
21
30
52
34
97
46
70
99
17
1
1
0
1
23
14
33
50
67
100
46
88
97
57
91
35
61
48
25
91
27
38
61
50
39
18
7
19
7
45
7
42
2
1
5
1
16
29
2
0
3
7
27
0
0
0
1
1
1
0
10
8
23
45
61
85
99
28
58
86
87
38
35
43
45
34
78
46
21
30
16
17
27
17
48
27
12
12
0,02
Car49
car88R Reverse Complement
car93R Reverse Complement
car54copy
car47
car76R Reverse Complement
Aju
NC 005212.1| Acinonyx jubatus
Car48
AY463959.1| Acinonyx jubatus
car87R Reverse Complement
AF344830.1| Acinonyx jubatus
car89R Reverse Complement
car94R Reverse Complement17
1
1
0
1
23
14
33
50
46
97
car70R Reverse Complement
Car78
bFca57
bFca53
bFca52
bFca54
Car73
bFca59
bFca55
bFca58
bFca02bFca56
NC 001700.1| Felis catus
Fma
Fma11
Fni
Fni14
serval 3
serval 1
Lse
Lse18
AY598470.1|AY598470S01 Lynx canadensis
AH014070.1|SEG AY598470S Lynx canadensis
Car69
Cca21
Cca1
CarCaracal
Car49
car88R Reverse Complement
car93R Reverse Complement
car54copy
car47
car76R Reverse Complement
Aju
NC 005212.1| Acinonyx jubatus
Car48
AY463959.1| Acinonyx jubatus
car87R Reverse Complement
AF344830.1| Acinonyx jubatus
car89R Reverse Complement
car94R Reverse Complement
car2R Reverse Complement
Car2
Ppa286
Car8ccfAndBrazil
CarLeop
Ple185
Ple153
car84copy Reverse Complement
lionF
Cfe1
car52
NC 008450.1| Neofelis nebulosa
Vci
bAbi
Ial2
Rme
Hja
Hpa1
Pcr
Hbr1
Hhy40
Ccr34
Ccr236
Phe
Pli
NC 001602.1| Halichoerus grypus
Zca
Oro
AY377297.1| Hydrurga leptonyx
AY377296.1| Hydrurga leptonyx
NC 008425.1| Hydrurga leptonyx
Man68
AY377295.1| Ommatophoca rossii
AY377294.1| Ommatophoca rossii
Bal
Bas
AM711898.1| Spilogale putorius complete
bCar24
AB291076.1| Martes melampus
AB291075.1| Meles meles anakuma
AB291077.1| Enhydra lutris
Ist
Ssu
Car12
AY598506.1|AY598506S01 Alopex lagopus
AH014073.1|SEG AY598506S Alopex lagopus
CarBatEaredFox
carWildDog
B11and12and15
DQ480508.1| Canis lupus isolate 1 fro...
AY598494.1|AY598494S01 Canis lupus
DQ480502.1| Canis familiaris isolate ...
AH014072.1|SEG AY598494S Canis lupus
DQ480507.1| Canis lupus isolate 2 fro...
DQ480504.1| Canis lupus isolate 1 fro...
DQ480501.1| Canis familiaris isolate ...
AY656738.1| Canis familiaris isolate ...
AY729880.1| Canis familiaris
AY656737.1| Canis familiaris isolate ...
NC 002008.4| Canis lupus familiaris
DQ480491.1| Canis familiaris isolate ...
DQ480505.1| Canis lupus isolate 1 fro...
DQ480492.1| Canis familiaris isolate ...
DQ480503.1| Canis lupus isolate 1 fro...
NC 008092.1| Canis lupus
DQ480506.1| Canis lupus isolate 1 fro...
car50copy
car85R Reverse ComplementAY656739.1| Canis familiaris isolate ...
NC 008093.1| Canis latrans
DQ480511.1| Canis latrans isolate 2 f...
DQ480510.1| Canis latrans isolate 1 f...
DQ480509.1| Canis latrans isolate 1 f...
Car79
car23 copy
Car53
Car81
car74R Reverse Complement
Car71
car63R Reverse Complement
Car57
Car56
Car11
car91R Reverse Complement
Car82
car45R Reverse Complement
Car9ccf
Car64
Car68
Car15
Car80
car90R Reverse Complement
Car43
Car83
Car77
car44copy
car55copy
car62
car66
car65copy
car60copy
Car75
100
100
52
88
100
100
100
95
100
97
88
57
75
70
39
25
12
21
30
52
34
97
46
70
99
17
1
1
0
1
23
14
33
50
67
100
46
88
97
57
91
35
61
48
25
91
27
38
61
50
39
18
7
19
7
45
7
42
2
1
5
1
16
29
2
0
3
7
27
0
0
0
1
1
1
0
10
8
23
45
61
85
99
28
58
86
87
38
35
43
45
34
78
46
21
30
16
17
27
17
48
27
12
12
0,02
car2R Reverse Complement
Car2
Ppa286
Car8
CarLeop
Ple185
Ple153
car84
lionF75
99
88
57
35
61
48
91
car70R Reverse Complement
Car78
bFca57
bFca53
bFca52
bFca54
Car73
bFca59
bFca55
bFca58
bFca02bFca56
NC 001700.1| Felis catus
Fma
Fma11
Fni
Fni14
serval 3
serval 1
Lse
Lse18
AY598470.1|AY598470S01 Lynx canadensis
AH014070.1|SEG AY598470S Lynx canadensis
Car69
Cca21
Cca1
CarCaracal
Car49
car88R Reverse Complement
car93R Reverse Complement
car54copy
car47
car76R Reverse Complement
Aju
NC 005212.1| Acinonyx jubatus
Car48
AY463959.1| Acinonyx jubatus
car87R Reverse Complement
AF344830.1| Acinonyx jubatus
car89R Reverse Complement
car94R Reverse Complement
car2R Reverse Complement
Car2
Ppa286
Car8ccfAndBrazil
CarLeop
Ple185
Ple153
car84copy Reverse Complement
lionF
Cfe1
car52
NC 008450.1| Neofelis nebulosa
Vci
bAbi
Ial2
Rme
Hja
Hpa1
Pcr
Hbr1
Hhy40
Ccr34
Ccr236
Phe
Pli
NC 001602.1| Halichoerus grypus
Zca
Oro
AY377297.1| Hydrurga leptonyx
AY377296.1| Hydrurga leptonyx
NC 008425.1| Hydrurga leptonyx
Man68
AY377295.1| Ommatophoca rossii
AY377294.1| Ommatophoca rossii
Bal
Bas
AM711898.1| Spilogale putorius complete
bCar24
AB291076.1| Martes melampus
AB291075.1| Meles meles anakuma
AB291077.1| Enhydra lutris
Ist
Ssu
Car12
AY598506.1|AY598506S01 Alopex lagopus
AH014073.1|SEG AY598506S Alopex lagopus
CarBatEaredFox
carWildDog
B11and12and15
DQ480508.1| Canis lupus isolate 1 fro...
AY598494.1|AY598494S01 Canis lupus
DQ480502.1| Canis familiaris isolate ...
AH014072.1|SEG AY598494S Canis lupus
DQ480507.1| Canis lupus isolate 2 fro...
DQ480504.1| Canis lupus isolate 1 fro...
DQ480501.1| Canis familiaris isolate ...
AY656738.1| Canis familiaris isolate ...
AY729880.1| Canis familiaris
AY656737.1| Canis familiaris isolate ...
NC 002008.4| Canis lupus familiaris
DQ480491.1| Canis familiaris isolate ...
DQ480505.1| Canis lupus isolate 1 fro...
DQ480492.1| Canis familiaris isolate ...
DQ480503.1| Canis lupus isolate 1 fro...
NC 008092.1| Canis lupus
DQ480506.1| Canis lupus isolate 1 fro...
car50copy
car85R Reverse ComplementAY656739.1| Canis familiaris isolate ...
NC 008093.1| Canis latrans
DQ480511.1| Canis latrans isolate 2 f...
DQ480510.1| Canis latrans isolate 1 f...
DQ480509.1| Canis latrans isolate 1 f...
Car79
car23 copy
Car53
Car81
car74R Reverse Complement
Car71
car63R Reverse Complement
Car57
Car56
Car11
car91R Reverse Complement
Car82
car45R Reverse Complement
Car9ccf
Car64
Car68
Car15
Car80
car90R Reverse Complement
Car43
Car83
Car77
car44copy
car55copy
car62
car66
car65copy
car60copy
Car75
100
100
52
88
100
100
100
95
100
97
88
57
75
70
39
25
12
21
30
52
34
97
46
70
99
17
1
1
0
1
23
14
33
50
67
100
46
88
97
57
91
35
61
48
25
91
27
38
61
50
39
18
7
19
7
45
7
42
2
1
5
1
16
29
2
0
3
7
27
0
0
0
1
1
1
0
10
8
23
45
61
85
99
28
58
86
87
38
35
43
45
34
78
46
21
30
16
17
27
17
48
27
12
12
0,02
DQ480491.1| Canis familiaris isolate ...
DQ480505.1| Canis lupus isolate 1 fro...
DQ480492.1| Canis familiaris isolate ...
DQ480503.1| Canis lupus isolate 1 fro...
NC 008092.1| Canis lupus
DQ480506.1| Canis lupus isolate 1 fro...
car50
car85R
AY656739.1| Canis familiaris isolate ...
NC 008093.1| Canis latrans
DQ480511.1| Canis latrans isolate 2 f...
DQ480510.1| Canis latrans isolate 1 f...
DQ480509.1| Canis latrans isolate 1 f...
Car79
car23
Car53
Car81
car74R
Car71
car63R
Car57
Car56
Car11
car91R
Car82
car45R
Car9ccf
Car64
Car68
Car15
Car80
car90R
Car43
Car83
Car77
car44copy
car55copy
car62
car66
car65copy
car60copy
Car75
85
99
58
86
87
43
78
Current challenges for large-scale DNA barcoding
of Neotropical mammals:
1. Samples with no vouchers (especially medium-sized and
large species).
2. Museum vouchers with no tissue samples.
3. Unsampled species.
4. Poor geographic coverage for most species.
5. Taxonomically complex taxa (need for thorough revision).
6. Lack of manpower, lack of large-scale funding.
Students
Henrique Figueiró
Marina Favarini
Fernanda Valdez
Ezequiel Fabiano
Flávia Tirelli
Cristine Trinca
Camila Jaeger
Paulo B. Chaves
Vanessa G. Graeff
Gabriel Macedo
Support: CNPq, CAPES, PUCRS
ACKNOWLEDGEMENTS:
Carnivore scat ID projects
Fernanda Michalski (Pró-Carnívoros)
Laurie Marker (CCF)
Anne Schmidt-Küntzel (CCF)
ACKNOWLEDGEMENTS:
Y. Leite, L. P. Costa, V. Fagundes, A. Ditchfield (UFES)
F. R. Santos (UFMG)
L. Müller, P. C. Estrela, T. R. O. Freitas (UFRGS)
J. S. Morgante, N. Moraes-Barros, F. M. Martins (USP)
L. R. Oliveira (UNISINOS/GEMARS)
V. Valiati (UNISINOS)
S. L. Bonatto (PUCRS)
A.R. Percequillo (ESALQ/USP)
C. R. Bonvicino, H. Seuánez (INCA)
J.A. Oliveira (Museu Nacional)
Salvatore Siciliano (FIOCRUZ)
R. Collevatti (UFG)
H. Schneider, M.I. Sampaio (UFPA)
M. A. Jardim (FZB-RS)
F. B. Peters, L. F. Machado (ULBRA)
J. Koenemann (PUCRS – Uruguaiana)
M. Bordignon (UFMS)
A.C. M. de Oliveira (UFPA)
L. Geise (UERJ)
J.I.R. Porto (INPA), I. Farias (UFAM), L. Tchaika (UEMA)
F. Braga (Museu Capão da Imbuia - PR)