SUPPORTING INFORMATION
Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveals constant and cryptic diversification in an old
radiation of rain forest understorey specialists
Fernando M. d’Horta, Andrés M. Cuervo, Camila C. Ribas, Robb T. Brumfield, Cristina Y. Miyaki
Journal of Biogeography
Appendix S1 Tissue samples analysed, taxa, collection number and localities. The subspecies were assigned based on the morphology
and/or geographic origin of the specimens.
Species
Sclerurus albigularis
Subespecies
No.
Institution1
Locality
Country
kempffi
A1
LSUMZ-B18322
Velasco, PN Noel Kempf Mercado, Santa Cruz
Bolivia
kempffi
A1
LSUMZ-B18400
Velasco, PN Noel Kempf Mercado, Santa Cruz
Bolivia
kempffi
A2
FMNH 389834
Cachoeira Nazaré, Rondônia
Brazil
kempffi
A3*
LGEMA 491
Aripuanã, Mato Grosso
Brazil
kempffi
A4
LGEMA 13673
Gaúcha do Norte, Mato Grosso
Brazil
Sclerurus scansor
Sclerurus caudacutus
albicollis
A5
LSUMZ-B38492
Chuchial, ca. 37 km SE Samaipata, Santa Cruz
Bolivia
zamorae (?)
A6
LSUMZ-B1974
Puellas, km 44 on Villa Rica - Pto Bermudez highway, Pasco
Peru
albicollis
A7
LSUMZ-B21203
Ridge E junction of Rios Tavaro-Guacamayo, Puno
Peru
albicollis
A8*
MPEG 58881
ESEC Rio Acre, Acre
Brazil
zamorae
A9
LSUMZ-B27738
ca. 77 km WNW Contamana, Loreto
Peru
zamorae
A10
LSUMZ-B40608
ca. 86 km SE Suanjui on E bank of upper rio Pauya, Loreto
Peru
zamorae
A11*
LSUMZ-B5412
20 km by road NE Tarapoto on road to Yurimagu, San Martín
Peru
cearensis
S1*
LGEMA 10481
Sítio Sinimbu, Mulungu, Serra de Baturité, Ceará
Brazil
cearensis
S2
LGEMA 10460
Itatira, Serra do Machado, Ceará
Brazil
scansor
S3*
LGEMA 926
Morro Grande, São Paulo
Brazil
scansor
S3
LGEMA 821
Morro Grande, São Paulo
Brazil
scansor
S4
LGEMA 1138
Juquitiba, São Paulo
Brazil
scansor
S5
LGEMA 13672
Estação Ecológica Bananal, São Paulo
Brazil
scansor
S6
FMNH 395418
Boraceia, São Paulo
Brazil
scansor
S7*
LGEMA 13678
PE Vila Velha, Paraná
Brazil
scansor
S8
LSUMZ-B25912
Cord. Caaguazu, 7.5 km E from San Carlos
Paraguay
scansor
S9
LGEMA 1577
Nucleo Curucutu, PE Serra do Mar, São Paulo
Brazil
scansor
S10
LGEMA 2188
Rancho Queimado, Santa Catarina
Brazil
scansor
S11
LGEMA 2178
Colonia Cerrito, Arroio do Padre/Pelotas, Rio Grande do Sul
Brazil
scansor
S12
LGEMA 13675
Urtigueira, Paraná
Brazil
caudacutus
C1*
USNM-B11751
10 km SSE Gunn’s Landing
Guyana
brunneus
C2*
INPA A210
RDS Amanã, Comunidade Nova Canaã
Brazil
brunneus
C3
LSUMZ-B7101
5 km N Amazonas, 85 km NE Iquitos
Peru
brunneus
C4
ANSP 2659
5 km SO de Taisha
Ecuador
brunneus
C5
LSUMZ-B40207
ca. 86 km SE Suanjui on E bank of upper rio Pauya
Peru
brunneus
C6*
INPA A344
ca. 45 km SW Porto Velho, left bank of Madeira River
Brazil
brunneus
C6
INPA A351
ca. 45 km SW Porto Velho, left bank of Madeira River
Brazil
brunneus
C7
INPA A189
ca. 20 km N Abunã, left bank of Madeira River
Brazil
Sclerurus guatemalensis
Sclerurus mexicanus
brunneus
C8
FMNH 398007
Quebrada Aguas Calientes, 2.75 km E Shintuya, Alto Madre de Dios
Peru
brunneus
C9
LSUMZ-B9654
Nicolás Suarez, ca. 12 km by road S Cobija, ca. 8 km W on road to Mueden 325m
Bolivia
brunneus
C10
LSUMZ-B10601
W bank of Rio Shesha, ca. 65 km ENE Pucallpa, 300m
Peru
brunneus
C11
LGEMA xxx
Estação Ecológica Mojica Nava, Rondônia
Brazil
brunneus
C12
LSUMZ-B4653
S Rio Amazonas, ca. 10 km SSW mouth Rio Napo on E bank Quebrada Vainilla, 100 m
Peru
brunneus
C12
LSUMZ-B4744
S Rio Amazonas, ca. 10 km SSW mouth Rio Napo on E bank Quebrada Vainilla, 100 m
Peru
brunneus
C13
LSUMZ-B11249
SE slope Cerro Tahuayo, ca km EBE Pucallpa
Peru
pallidus
C14
MPEG 55401
Altamira, Ilha da Taboca, Rio Xingu, Pará
Brazil
pallidus
C15*
FMNH 391349
Serra dos Carajas, Pará
Brazil
pallidus
C16
MPEG 55661
Vitoria do Xingu, Marg Esquerda, Rio Xingu, Pará
Brazil
pallidus
C17*
USNM-B6945
Altamira, 52 km SSW, E Bank Rio Xingu
Brazil
pallidus
C18
MPEG 57610
Manicore, Rod Estanho km 126, Amazonas
Brazil
pallidus
C19
FMNH 389835
Cachoeira Nazare, W bank Jiparana River, Rondônia
Brazil
pallidus
C19
FMNH 389836
Cachoeira Nazare, W bank Jiparana River, Rondônia
Brazil
pallidus
C20*
INPA A539
Igarapé Extremo, 135 km S Novo Aripuanã , m. dir. Rio Aripuanã,
Brazil
pallidus
C21
MPEG 56657
Igarape Mutum, Juruti, Pará
Brazil
guatemalensis
G1
LSUMZ-B18076
guatemalensis
G2
LSUMZ-B8771
Forestry Camp (Salamanca)
Belize
guatemalensis
G3*
LSUMZ-B60659
Atlántida Department
Honduras
guatemalensis
G4
USNM-B309
Isla San Cristobal, Bocatorito
Panama
salvini
G5
LSUMZ-B26538
17 km by road NW Gamboa, Rio Agua Salud, Colón
Panama
salvini
G6
LSUMZ-B46563
Rancho Frio, ca. 10 km S El Real, Darien
Panama
salvini
G7*
LSUMZ-B1393
ca. 9 km NW Cana on slopes of Cerro Pirré, Darien
Panama
mexicanus
M1*
MBM 10649
Santa Maria de Jesus, Quetzaltenango
Guatemala
mexicanus
M1
MBM 10648
Santa Maria de Jesus, Quetzaltenango
Guatemala
pullus
M2
LSUMZ-B1366
ca. 9 km NW Cana on slopes Cerro Pirre, Darien, 1400 m
Panama
pullus
M3
USNM-B 5363
Los Planes, Chiriquí
Panama
pullus
M4
MBM 14943
Santa Fé, Veraguas
Panama
Mexico
pullus
M5
LSUMZ-B72105
Turrique, Reserva El Copal, Cartago
Costa Rica
pullus
M6
LSUMZ-B16042
4 km SE Virgen del Socorro, Heredia
Costa Rica
pullus
M7
LSUMZ-B35755
Cartago
Costa Rica
pullus
M8*
LSUMZ-B35770
11 km SW Pejibaye
Costa Rica
obscurior
M9*
LSUMZ-B11742
El Placer, Esmeraldas, 670 m
Ecuador
obscurior
M10
ANSP 2410
20 km NNW of Alto Tambo, Esmeraldas, 225 m
Ecuador
obscurior
M9
LSUMZ-B11813
El Placer, Esmeraldas, 670 m
Ecuador
andinus
M11
IAvH-BT 115
PNN Tamá, Toledo, Norte de Santander, 1200 m
Colombia
andinus
M12
COP-AMC1270
P.N. Chorro El Indio, Táchira, 1100 m.
Venezuela
andinus
M13
IAvH-BT 2455
La Cumbre, cuenca alta del río Bitaco, Valle del Cauca, 2000 m
Colombia
andinus
M13
IAvH-BT 2444
La Cumbre, cuenca alta del río Bitaco, Valle del Cauca, 2000 m
Colombia
andinus
M14*
LSUMZ-B12146
Mindo, Pichincha, 1500 m
Ecuador
?
M15
LSUMZ-B9565
Nicolas Suarez, 12 km by road S of Cobija
Bolívia
?
M16*
INPA A339
ca. 45 km SW Porto Velho, left bank of Madeira River
Brazil
?
M17
LSUMZ-B36721
Reserva Biologica Rio Ouro Preto
Brazil
?
M18
MPEG 58883
ESEC Rio Acre, Acre
Brazil
?
M19*
USNM-B6958
Altamira, Pará
Brazil
?
M20
MPEG A8398
Ourilandia do Norte, Pará
Brazil
?
M21
MPEG 55654
Senador Jose Porfirio, Marg Direita, Rio Xingu, Pará
Brazil
macconnelli
M22
LSUMZ-B20395
Manaus, km 34 ZF-3, Faz. Esteio
Brazil
macconnelli
M23
USNM-B5155
Rio Waruma
Guyana
macconnelli
M24*
AMNH ROP108
Rio Carapo; Guaiquimi
Venezuela
peruvianus
M25*
LSUMZ-B58406
Curva Alegre, Puno, 1100 m.
Peru
peruvianus
M26
FMNH 433369
Consuelo, 15.9 km SW Pilcopata
Peru
peruvianus
M27
FMNH 321714
Tono
Peru
peruvianus
M28
LSUMZ-B6765
27 km by road N Rio Quiquibey
Bolívia
peruvianus
M29
LSUMZ-B5452
20 km by road NE Tarapoto on road to Yurimagu.,San Martín, 1050 m
Peru
peruvianus
M30*
LSUMZ-B6980
5 km N Amazonas, 85 km NE Iquitos
Peru
Sclerurus rufigularis
peruvianus
M31
ANSP 4454
Panguri; ca. 12 km NE San Francisco del Vergel, Zamora-Chinchipe
Ecuador
peruvianus
M32
ANSP 4877
Pasohurco, Km 57 on Hollin-Loreto road, Napo
Ecuador
peruvianus
M33
LSUMZ-B28035
ca. 77 km WNW Contamana, Loreto, 1000 m.
Peru
rufigularis
R1*
MPEG 55658
Senador Jose Porfirio, Marg Direita, Rio Xingu, Pará
Brazil
rufigularis
R2
LSUMZ-B4595
S Rio Amazonas, ca. 10 km SSW mouth Rio Napo on E bank Quebrada Vainilla, 100 m
Peru
rufigularis
R3*
INPA A193
ca. 20 km N Abunã
Brazil
rufigularis
R3
INPA A261
ca. 20 km N Abunã, marg. direita do Rio Madeira
Brazil
rufigularis
R4
MPEG 57611
Manicore, Rod Estanho km 126, Amazonas
Brazil
rufigularis
R5
MPEG 56658
Igarape Mutum, Juruti, Pará
Brazil
rufigularis
R6*
LSUMZ-B14896
Serrania de Huanchaca, 25 km a SE de Catarata
Bolívia
rufigularis
R7
LSUMZ-B31381
ca. 90 km E Vila Nova
Brazil
rufigularis
R8
LSUMZ-B12691
Velasco, W BANK Rio Paucerna, 4 km upstream
Bolívia
rufigularis
R9
LGEMA 494
Aripuana, Mato Grosso
Brazil
brunnescens
R10
LGEMA 9920
Rio Quiuini, Barcelos, Amazonas
Brazil
brunnescens
R11
ANSP 5798
14 km N Tigre Playa
Ecuador
brunnescens
R12
LSUMZ-B42747
ca. 54 km NNW da foz do rio Morona, margem oeste
Peru
brunnescens
R13
LSUMZ-B2738
1 km N Rio Napo, 157 km by river NNE Iquitos
Peru
brunnescens
R14*
IAvH-BT 418
Serranía del Chiribiquete, Río Mesay, Caquetá
Colombia
brunnescens
R14
IAvH-BT 400
Serranía del Chiribiquete, Río Mesay, Caquetá
Colombia
brunnescens
R15
AMNH RWD17095
Rio Mawarinumo, Amazonas
Venezuela
brunnescens
R16
LSUMZ-B4418
Lower Rio Napo region, E bank Rio Yanayacu
Peru
brunnescens
R17
LSUMZ-B7122
5 km N Amazonas, 85 km NE Iquitos
Peru
brunnescens
R18
IAvH-BT 519
Serranía del Chiribiquete, Río Sararamano, Caquetá
Colombia
brunnescens
R19
INPA A720
ESEC Juami-Japurá; m dir do Rio Japurá; médio Rio Juami, ca 157 km W Japurá
Brazil
furfurosus
R20
LSUMZ-B20396
Manaus, km 34 ZF-3, Faz. Esteio
Brazil
fulvigularis
R21*
USNM-B5161
Essequibo
Guyana
fulvigularis
R22
AMNH ROP274
40 KM E Tumarenco by road
Venezuela
fulvigularis
R23
LSUMZ-B65761
Distrikt Sipaliwini, Leli Gebergte
Suriname
fulvigularis
R24
USNM-B10830
Montanhas Acari, lado N
Guiana
fulvigularis
R25
ANSP 5603
5 km N Rockstone, E bank Essequibo River
Guyana
Geositta poeciloptera
Outgroup LSUMZ-B13975
-
-
Geositta tenuirostris
Outgroup LSUMZ-B103927
-
-
Xenops minutus
Outgroup LSUMZ-B11948
Lepidocolaptes
angustirostris
Outgroup
Upucerthia albigula
Outgroup
1
LGEMA – Laboratório de Genética e Evolução de Aves da Universidade de São Paulo; MPEG – Museu Paraense Emílio Goeldi; INPA -
Instituto de Pesquisas Amazônicas; FMNH – Field Museum of Natural History; AMNH – American Museum of Natural History; ANSP Academy of Natural Sciences of Philadelphia; IAvH-BT – Banco de Tejidos, Instituto Alexander von Humboldt; COP: Colección
Ornitológica Phelps; USNM – National Museum of Natural History, Smithsonian Institution; LSUMZ – Museum of Natural Science,
Louisiana State University; MBM – Barrick Museum of Natural History, University of Nevada at Las Vegas. * Samples used to estimate
the timing of diversification events.
Appendix S2 Procedures of DNA extraction, amplification, sequencing and alignment.
Genomic DNA was extracted from tissue samples using a phenol-chloroform protocol
(Bruford et al., 1992) or a DNeasy tissue kit (Qiagen, Valencia, CA, USA), following
the manufacturer’s protocol. Primers for amplification were Fib7U and Fib7L for Fib7
(Prychitko & Moore, 1997), L14841 (Kocher et al., 1989) and H16065 (Cracraft &
Helm-Bychowski, 1993) for cyt b, L5215 (Hackett, 1996), LMet and H6313 (Sorenson
et al.,1999) for ND2, and L10755 and H11151 for ND3 (Chesser, 1999). Internal
sequencing primers for Fib7 were 413U (Chesser, 2004) and 453LSclerurus (5'GTACTTTACAACTGAGCTCCA-3'), developed for this study; for cyt b were P5L and
H658 (Irestedt et al., 2002), and for ND2 were L5758 and H5766 (Sorenson et al.,
1999). Amplifications were performed in 25 µL reactions as described in Brumfield et
al. (2007) or in 10 µL reactions containing 0.8 mM dNTP, 1 mM of each primer, 0.5 U
Taq polymerase (Pharmacia), buffer 1X (Pharmacia), and 1 m (~10 ng) of template
DNA. Locus-specific annealing temperatures were 54 °C, 54 °C, 59 °C and 54 °C for
Fib7, cyt b, ND2 and ND3, respectively. The thermocycling conditions were as follows:
an initial denaturation at 95 °C for 2–5 min, followed by 35–40 cycles of denaturation at
95 °C for 1–2 min, annealing at 54–59 °C for 30 s, extension at 72 °C for 40 s, and a
final extension step at 72 °C for 5 min. Amplicons were visualized by electrophoresis in
1% agarose gel and purified using 20% polyethylene glycol. Both strands of purified
amplicons were cycle-sequenced using Big Dye Terminator kit 3.1 (Applied
Biosystems, Foster City, CA, USA), purified with Sephadex (G-50 fine), and sequenced
on either an ABI 377 Automated Sequencer or an ABI 3100 Genetic Analyzer (Applied
Biosystems). Sequences were inspected, edited, and aligned using CodonCode Aligner
(CodonCode Corporation) and the algorithm Clustal X (Thompson et al., 1997).
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the beta-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves:
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Appendix S3 Mean pairwise (p)-distances between and within species of Sclerurus leaftossers based on 2408 bp of mtDNA (below the diagonal)
and 914 bp Fib7 (above the diagonal). Sclerurus mexicanus values are divided into two groups: the South American lineages combined (SA) and
the Central American clade (CA).
Sclerurus taxa
1. albigularis
2. caudacutus
3. guatemalensis
4. mexicanus (SA)
5. mexicanus (CA)
6. rufigularis
7. scansor
n
mtDNA
12
24
7
27
9
27
13
Fib7
12
21
7
23
9
22
13
1
0.10
0.09
0.15
0.14
0.13
0.03
2
0.01
0.06
0.14
0.14
0.15
0.11
3
0.01
0.00
0.15
0.13
0.14
0.10
Mean p-distance
Interspecific
4
5
6
0.02
0.02
0.02
0.01
0.01
0.01
0.02
0.02
0.02
0.01
0.01
0.12
0.00
0.10
0.09
0.16
0.15
0.14
7
0.00
0.01
0.01
0.02
0.02
0.03
Intraspecific
mtDNA
Fib7
0.02
0.00
0.02
0.00
0.02
0.00
0.04
0.00
0.02
0.00
0.02
0.00
0.01
0.00