Molecular taxonomy in
Neotropical Passeriformes
Fabrício R. Santos
Associate Professor
Dep. de Biologia Geral, ICB
Universidade Federal de Minas Gerais
Belo Horizonte, MG, Brazil
Megadiversity
Mexico450
Colombia456
China499
Indonesia515
Brazil524
Mammals
Brazil468
Indonesia511
Colombia520
Mexico717
Australia755
Reptiles
China274
Mexico284
Ecuador402
Brazil517
Colombia 583
Amphibians
Australia25 000
Mexico26 000
China30 000
Colombia45 000
Brazil55 000
Vascular plants
Country and species numbersGroup
Venezuela1308
Ecuador1435
Brazil1573
Peru1705
Colombia1721
Birds
10 % of 1.4 million known species
Brazilian Amazon
Biodiversity hotspots
Atlantic Rain Forest
Cerrado
(Brazilian savanna)
Taxonomic difficulties
• Many species are largely distributed and fragmented;
• Phylogeographic studies indicate existence of many intraspecific divergent clades, even for species with samples limited geographically;
• Majority of species are still to be formally described;
• Collections are poor sources of vouchers, with few exceptions;
• A large investment is needed for new and representative samplings.
Molecular identification of known spp
All 260 known species of North-American birds
Bird Genetics in the lab
• Population Genetics
• Phylogeography
• Systematics and
phylogeny
• Reproductive behavior
• Molecular taxonomy
Molecular Methodology
Extraction,
storage, catalog
Tissue/specimen
collection
PCR
Sequencing data
MegaBACE
Data Analysis
mtDNA
D-Loop
ND5
H-strand
ND4
ND4L
ND3COIII
L-strand
ND6
ND2
ND1
COII
Small ribosomal RNA
Large ribosomal RNA
ATPase subunit 8
ATPase subunit 6
Cytochrome b
COICOI
COI sequences
• Divergent individuals chosen for COI
sequencing after phylogeographic inspection.
• High quality sequence data (510-800 bp):
large PCR amplicons as template,
two independent PCR products,
double strand sequencing,
careful edition of consensus sequences
based on phred/phrap/consed.
Molecular taxonomy in Thamnophilidae
Passeriformes; Suboscines
Inter x intraspecific diversity of COI sequences in Thamnophilidae
II
III IV
IT. caerulescens
T. ambiguus / T. pelzelni
0
1
2
3
4
5
6
7
8
9
10
11
12
0 1 2 3 4 5 6 7 8 9 10 11 12
Maximum intraspecific divergence(%)
Min
imum
inte
rspe
cific
dive
rge
nce
(%)
II
III IV
I
0
1
2
3
4
5
6
7
8
9
10
11
12
0 1 2 3 4 5 6 7 8 9 10 11 12
Maximum intraspecific divergence(%)
Min
imum
inte
rspe
cific
dive
rge
nce
(%)
B0665B0663
B0655B0653
B0654B0656B0369
B0367B0368
B0609B0647
B0317B0329B0326
B0658B0644B0657
B0677B0678
B0646B0291B0292
B0290B0680
B0643B0660
B0281B0285B1189
B1301B1188
B1296B1186B1303
B0525B0524
B0515B0511
B0513B0528
B0535B0562
B1148B1147B1150
99
99
99
99
90
99
99
99
99
99
99
99
99
99
99
91
99
99
99
82
90
D. ochropyga
D. ferruginea
R. ardesiaca
D. squamata
B0335
P. leucoptera
M. loricata
T. major
D. plumbeus
F. serrana
D. mentalis
H. atricapillus
S. cristatus
T. doliatus
T. caerulescens
T. ambiguus
T. pelzelni
Phylogeneticanalysis of COI sequences in Thamnophilidae
Thamnophilus caerulescens Thamnophilus ambiguusThamnophilus pelzelniThamnophilus doliatusHerpsilochmus atricapillusSakesphorus cristatusDsythamnus_mentalisDsythamnus plumbeusDrymophila ochropygaDrymophila ferrugineaDrymophila squamataMyrmeciza loricataRhopornis ardesiacaPyriglena leucopteraFormicivora serranaTaraba major
11111122222222222333333444 001123500344801345566779001569011
2451769253681928436
CACAAAACAACAAACCCAACAAAGCCCATAAAA .................G.T...A......... ....G..............T...A....C.... ............G.....GT...A.T.C..... .TT.............T..A.C.A.A...C... T..................AG..ATA....... .....GG............A...A.A......G .G.........G..T....A..GA.A....... ..............A....A...A.A....... ..............T..C.A...A.AA...... ........G..........G...A.AT...... ............C......A...A.A....... ..............T....A...T.AT...T.. .........G.........A...T.A.....G. .......T.....GT....A...A.AT...... ...G......T....T...A...A.A.......
Autapomorphic sites in ThamnophilidaeSynapomorphic in each species
Character basedbarcodes 16 spp
COI variable positions
0000000
58149564710650
Molecular taxonomy in Neotropical Passeriformes
• A broad geographic sampling should be priority;
• Details of population structure and phylogeography should be used, particularly for species with large geographic distribution, or likely susceptible to sympatric substructuring due to sexual selection etc;
• High quality sequences should be used to provide a more discriminating power;
• These studies should be accomplished closely by other taxonomists, as many more taxa are expected to be found.
Colaborators
• Miguel A. Marini and team - UnB;• Marcos Rodrigues and team - UFMG;• Cristina Miyaki and team - USP;• Marcelo Ferreira Vasconcelos;• Lucas Carrara and team – UFMG.
Team
DanielaEloísa
Sibelle Anderson, Juliana e Camila
Support
PG Ciência Animal - UFMG
Top Related