1
Appendix 1: Phylogeny
For this analysis we draw on both nuclear and mitochondrial sequences mostly obtained in our
lab (Kennedy et al., submitted; Price et al., in preparation), for 303 species of Passerine birds.
We incorporated GenBank sequences as available for mitochondrial sequences and an additional
two nuclear introns (ODC introns 6-7, GAPDH intron 11) and one protein-coding nuclear gene
(RAG-1) commonly used in avian phylogenetic studies. The complete dataset will be submitted
to GenBank in association with the papers listed above. For the purposes of this paper, we
constructed an estimate of phylogenetic relationships as follows.
Sequences were aligned using MAFFT version 6 (Katoh and Toh 2008) with
complementary manual adjustments. The mitochondrial dataset consisted of 2178 bp, after the
removal of stop codons, and the nuclear dataset consisted of a maximum of 4676 bp, when
accounting for indel variation. A time-calibrated phylogeny was constructed using BEAST
v1.6.0 (Drummond and Rambaut 2007) with data partitioned for rate variation between each
gene and mitochondrial genes were further partitioned into three codon positions. Topology was
constrained to be the same over all partitions. The most appropriate likelihood model for each
partition was determined with MrModelTest v2.0 (Nylander 2004), using the Akaike Information
Criterion (Posada and Buckley 2004). MrModelTest output suggested the GTR + Γ model for
cytochrome b and myoglobin, the GTR + Γ + I model for ND2, ODC, and RAG-1, and the HKY
+ Γ model for GAPDH. We used an uncorrelated lognormal relaxed molecular clock model for
each partition; however, cytochrome b was additionally set to evolve with a mean rate of 0.0105
according to Weir and Schluter (2008).
1
2
We used two fossils taken from Becker (1987) to time-calibrate our phylogeny and set
hard minimum age boundaries. A fossil Miocitta was used to calibrate the node between the
New-world species Cyanocorax mystacalis and Old-world Corvoidea in the genus Corvus and a
fossil Parulidae was used to calibrate the node between the Old-world species Fringilla
montifringilla and the New-world nine-primaried oscines. Fossil calibration points were set using
a uniform distribution with a minimum age of 15 and 18 Ma, respectively. Speciation was set to
occur under a birth-death process. Markov chains were run for 50,000,000 generations with trees
sampled every 1,000 generations. We used the program Tracer v1.5 (Rambaut and Drummond
2007) to ensure maximization of effective sampling sizes and optimization of parameter
estimates. We discarded 25,000 trees as burn-in and estimated posterior probabilities using the
maximum clade credibility method in TreeAnnotator v1.6.0 (Drummond and Rambaut 2007).
To assess robustness of the results to phylogenetic uncertainty, the main tests described in the
text were conducted on several additional trees sampled from the Bayesian output, with
consistent results.
The tree (in Newick format) is given below:
((((((((((((((((((Saxicola_caprata:8.05487,Saxicola_ferreus:8.05487):3.3655,(Monticola_rufiventr
is:8.00778,Monticola_cinclorhynchus:8.00778):3.41259):1.14298,((Chaimarrornis_leucocephalu
s:6.21749,Rhyacornis_fuliginosa:6.21749):3.50361,Phoenicurus_frontalis:9.72111):2.84225):0.8
4262,((Tarsiger_chrysaeus:6.14434,Tarsiger_indicus:6.14434):3.42442,(Tarsiger_hyperythrus:3.
78285,Tarsiger_rufilatus:3.78285):5.78591):3.83722):0.859507,((((((Enicurus_leschenaulti:2.88
092,Enicurus_maculatus:2.88092):5.3277,Enicurus_scouleri:8.20862):0.961852,(Enicurus_imm
aculatus:4.0522,Enicurus_schistaceus:4.0522):5.11827):3.02075,Heteroxenicus_stellatus:12.191
2):0.8942,(Cinclidium_frontale:10.6317,Myophonus_caeruleus:10.6317):2.45376):0.732621,My
iomela_leucura:13.818):0.447439):0.282991,Hodgsonius_phaenicuroides:14.5485):0.192407,((((
((Ficedula_superciliaris:2.08089,Ficedula_westermanni:2.08089):1.14429,Ficedula_sapphira:3.2
2518):6.95588,Ficedula_strophiata:10.1811):1.63945,Muscicapella_hodgsoni:11.8205):0.65124,
Ficedula_hyperythra:12.4718):1.23705,((((Brachypteryx_montana:5.30337,Brachypteryx_leuco
phrys:5.30337):0.661633,Brachypteryx_hyperythra:5.965):4.47539,Luscinia_brunnea:10.4404):
2.36518,Ficedula_tricolor:12.8056):0.903228):1.03208):1.19904,(((((Cyornis_poliogenys:4.7061
2
3
,Cyornis_rubeculoides:4.7061):3.37098,Cyornis_unicolor:8.07707):3.17157,Ficedula_monileger
:11.2486):1.02732,((Niltava_grandis:9.72445,Niltava_sundara:9.72445):0.873141,Niltava_macg
rigoriae:10.5976):1.67838):0.438783,Eumyias_thalassinus:12.7147):3.22517):1.68843,((Copsyc
hus_saularis:11.6683,Copsychus_malabaricus:11.6683):3.60794,(Muscicapa_ferruginea:3.68976
,Muscicapa_sibirica:3.68976):11.5865):2.35206):4.61742,((((Turdus_albocinctus:3.65504,(Turd
us_boulboul:2.61404,Turdus_unicolor:2.61404):1.04099):8.98677,Zoothera_citrina:12.6418):1.3
2324,(((Zoothera_monticola:8.61294,Zoothera_dauma:8.61294):2.19801,(Zoothera_mollissima:
9.5857,Zoothera_dixoni:9.5857):1.22526):2.75012,(Cochoa_viridis:4.41453,Cochoa_purpurea:4
.41453):9.14654):0.403975):3.36175,Grandala_coelicolor:17.3268):4.91897):1.49983,Gracula_r
eligiosa:23.7456):0.492901,(Cinclus_cinclus:5.34118,Cinclus_pallasii:5.34118):18.8973):5.2778
,(((Sitta_cinnamoventris:10.1365,Sitta_himalayensis:10.1365):3.06688,(Sitta_frontalis:10.1919,
Sitta_formosa:10.1919):3.01149):14.1033,(((Certhia_discolor:8.81746,Certhia_nipalensis:8.817
46):2.43921,Certhia_familiaris:11.2567):13.0006,Troglodytes_troglodytes:24.2572):3.04941):2.
20963):1.10167,((((((((((((Carpodacus_edwardsii:5.91483,Carpodacus_pulcherrimus:5.91483):1.
91411,Carpodacus_rubicilloides:7.82894):0.778491,((Carpodacus_thura:5.5243,Pyrrhospiza_pu
nicea:5.5243):1.07745,Propyrrhula_subhimachala:6.60174):2.00569):1.27592,Haematospiza_sip
ahi:9.88335):1.91815,((Loxia_curvirostra:6.53607,Carduelis_spinoides:6.53607):3.96355,Carpo
dacus_erythrinus:10.4996):1.30188):0.725413,(((Leucosticte_nemoricola:6.05242,Carpodacus_n
ipalensis:6.05242):3.80622,(Carpodacus_rubescens:7.6598,Pyrrhoplectes_epauletta:7.6598):2.19
885):1.55323,((Pyrrhula_erythaca:0.508044,Pyrrhula_erythrocephala:0.508044):4.1325,Pyrrhula
_nipalensis:4.64055):6.77132):1.11504):1.57673,((Mycerobas_affinis:6.72665,Mycerobas_mela
nozanthos:6.72665):1.20017,Mycerobas_carnipes:7.92682):6.17681):4.89195,Melophus_lathami
:18.9956):1.72886,((((Anthus_hodgsoni:6.00841,Anthus_roseatus:6.00841):6.3641,Anthus_ruful
us:12.3725):1.21758,((Motacilla_alba:0.837537,Motacilla_cinerea:0.837537):0.49377,Motacilla
_maderaspatensis:1.33131):12.2588):5.92293,Passer_rutilans:19.513):1.21143):2.67237,(((Lonc
hura_striata:4.54214,Lonchura_punctulata:4.54214):14.8837,Ploceus_benghalensis:19.4258):2.4
1235,((Prunella_strophiata:7.49961,Prunella_immaculata:7.49961):2.94408,Prunella_collaris:10.
4437):11.3944):1.55868):2.66664,((Chloropsis_hardwickii:13.8286,Chloropsis_aurifrons:13.828
6):9.66493,Irena_puella:23.4935):2.56994):1.33889,((((((((Aethopyga_nipalensis:6.88166,Aetho
pyga_gouldiae:6.88166):1.69496,Aethopyga_saturata:8.57662):2.20592,Aethopyga_siparaja:10.
7825):0.938936,Aethopyga_ignicauda:11.7215):2.71021,(Cinnyris_asiaticus:11.76,Chalcoparia_
singalensis:11.76):2.67166):3.52918,Arachnothera_longirostra:17.9609):0.917018,Arachnothera
_magna:18.8779):2.17492,(((Dicaeum_ignipectus:5.61615,Dicaeum_cruentatum:5.61615):0.665
379,Dicaeum_minullum:6.28153):6.58114,(Dicaeum_chrysorrheum:9.12713,Dicaeum_melanox
anthum:9.12713):3.73554):8.19013):6.34956):3.21562):0.0643309,Regulus_regulus:30.6823):0.
717503,((((((((((((((((((Minla_cyanouroptera:8.09724,Actinodura_nipalensis:8.09724):0.871348,
Heterophasia_annectans:8.96859):0.872723,(Actinodura_egertoni:8.36633,Minla_strigula:8.366
33):1.47498):1.36344,Minla_ignotincta:11.2047):0.868879,(Leiothrix_argentauris:4.37421,Leiot
hrix_lutea:4.37421):7.69942):0.348655,(((Heterophasia_capistrata:4.17313,Heterophasia_pulche
lla:4.17313):4.65786,Heterophasia_picaoides:8.83099):2.42455,(Liocichla_phoenicea:6.06793,L
iocichla_bugunorum:6.06793):5.18761):1.16674):3.3676,((Trochalopteron_squamatum:11.2597,
Trochalopteron_subunicolor:11.2597):1.93807,(Trochalopteron_affine:9.14654,Trochalopteron_
erythrocephalum:9.14654):4.05121):2.59213):1.18348,(((((((Dryonastes_caerulatus:4.10327,Gar
rulax_albogularis:4.10327):3.75115,Garrulax_pectoralis:7.85442):1.22646,Dryonastes_ruficollis
:9.08088):2.05201,Ianthocincla_rufogularis:11.1329):0.952215,Ianthocincla_ocellata:12.0851):1
.19842,(Garrulax_monileger:8.9968,Garrulax_leucolophus:8.9968):4.28672):2.01707,Turdoides
3
4
_striata:15.3006):1.67277):0.83847,(Grammatoptila_striata:14.9317,Cutia_nipalensis:14.9317):2
.88016):3.55702,((((Malacocincla_abbotti:13.9644,Pellorneum_ruficeps:13.9644):1.65289,(Nap
othera_epilepidota:11.6526,Rimator_malacoptilus:11.6526):3.9647):2.37982,(((Alcippe_rufogul
aris:11.2254,Alcippe_cinerea:11.2254):1.11862,Alcippe_castaneceps:12.3441):2.41035,Gampso
rhynchus_rufulus:14.7544):3.24273):1.46072,(Alcippe_nipalensis:9.94173,Pellorneum_albiventr
e:9.94173):9.51613):1.91099):0.823536,(((((((Pomatorhinus_ruficollis:3.68241,Pomatorhinus_sc
histiceps:3.68241):2.25838,Xiphirhynchus_superciliaris:5.94079):3.03774,Pomatorhinus_ferrugi
nosus:8.97853):3.20334,(Sphenocichla_humei:10.1753,Stachyris_nigriceps:10.1753):2.00661):0
.580579,Pomatorhinus_erythrogenys:12.7625):4.10647,Spelaeornis_caudatus:16.8689):0.989809
,(((Stachyris_rufifrons:6.89585,Stachyris_ruficeps:6.89585):2.41313,Stachyris_chrysaea:9.3089
8):4.53115,Macronous_gularis:13.8401):4.0186):4.33365):0.956037,((((Yuhina_gularis:7.11641,
Yuhina_occipitalis:7.11641):1.39316,(Yuhina_flavicollis:6.2594,Yuhina_bakeri:6.2594):2.2501
6):4.2036,(Zosterops_palpebrosus:11.2778,Yuhina_nigrimenta:11.2778):1.4354):1.50195,Staphi
da_castaniceps:14.2151):8.9333):1.35762,(((((((Paradoxornis_gularis:5.57405,Paradoxornis_rufi
ceps:5.57405):2.66029,Conostoma_oemodium:8.23435):0.632783,Paradoxornis_unicolor:8.867
13):3.72145,((Paradoxornis_fulvifrons:6.44329,Paradoxornis_nipalensis:6.44329):4.65437,Parad
oxornis_atrosuperciliaris:11.0977):1.49092):1.24435,(Alcippe_ludlowi:3.64072,Alcippe_vinipec
tus:3.64072):10.1922):1.60128,Alcippe_chrysotis:15.4342):3.14093,Myzornis_pyrrhoura:18.575
1):5.9309):1.83138,(((((((((Seicercus_affinis:4.75762,Seicercus_poliogenys:4.75762):0.732547,
Seicercus_burkii:5.49017):1.25863,Seicercus_whistleri:6.7488):5.08076,((Phylloscopus_reguloi
des:7.73033,Phylloscopus_xanthoschistos:7.73033):1.08301,Phylloscopus_cantator:8.81334):3.0
1622):0.469259,(Phylloscopus_magnirostris:10.4764,Phylloscopus_trochiloides:10.4764):1.8223
8):1.44719,Seicercus_castaniceps:13.746):4.20789,((Phylloscopus_affinis:12.4418,Phylloscopus
_fuligiventer:12.4418):2.56092,(Phylloscopus_chloronotus:10.9159,(Phylloscopus_pulcher:8.49
241,Phylloscopus_maculipennis:8.49241):2.4235):4.08678):2.95121):5.11674,(((((((Cettia_flavo
livacea:3.21286,Cettia_fortipes:3.21286):3.43306,Cettia_brunnescens:6.64591):2.46196,Tickelli
a_hodgsoni:9.10788):1.36989,Orthotomus_cuculatus:10.4778):3.60709,((Abroscopus_albogulari
s:8.95573,Abroscopus_schisticeps:8.95573):1.62745,Abroscopus_superciliaris:10.5832):3.50168
):1.46352,(((Cettia_brunnifrons:9.89675,Tesia_castaneocoronata:9.89675):1.34951,Cettia_major
:11.2463):0.910353,(Tesia_cyaniventer:5.35152,Tesia_olivea:5.35152):6.8051):3.39177):1.2309
8,Cettia_pallidipes:16.7794):6.29128):1.26475,((Aegithalos_concinnus:7.57574,Aegithalos_ious
chistos:7.57574):10.3019,Leptopoecile_sophiae:17.8776):6.45778):2.00203):0.409821,(((((((Pri
nia_cinereocapilla:4.00487,Prinia_rufescens:4.00487):2.66543,Prinia_hodgsonii:6.67029):2.306
61,Prinia_socialis:8.9769):4.09741,(((Prinia_crinigera:3.49215,Prinia_sylvatica:3.49215):3.7935
9,Prinia_atrogularis:7.28574):3.35686,Prinia_inornata:10.6426):2.43171):1.84104,Orthotomus_s
utorius:14.9153):2.10091,Cisticola_exilis:17.0163):9.53213,(((((Hypsipetes_mcclellandi:12.039
6,Hypsipetes_leucocephalus:12.0396):1.35118,Hemixos_flavala:13.3908):2.58386,Pycnonotus_
striatus:15.9747):3.10056,Alophoixus_flaveolus:19.0752):2.02587,(((Pycnonotus_cafer:3.85115,
Pycnonotus_leucogenys:3.85115):2.95019,Pycnonotus_jocosus:6.80134):6.11135,Pycnonotus_fl
aviventris:12.9127):8.1884):5.44729):0.198853):1.54882,(((((Bradypterus_mandelli:6.80811,Bra
dypterus_thoracicus:6.80811):3.06599,Bradypterus_luteoventris:9.8741):2.80874,Megalurus_pal
ustris:12.6828):13.0522,(Pnoepyga_pusilla:10.1735,Pnoepyga_albiventer:10.1735):15.5615):1.4
1858,(((Delichon_dasypus:1.83488,Delichon_nipalense:1.83488):8.6709,Hirundo_daurica:10.50
58):3.33947,Hirundo_rustica:13.8452):13.3084):1.14244):1.7717,(Culicicapa_ceylonensis:24.78
66,Chelidorhynx_hypoxantha:24.7866):5.28116):0.308177,((((Parus_rubidiventris:6.4887,Parus
_ater:6.4887):2.88162,Parus_dichrous:9.37033):2.25287,((Parus_major:3.68221,Parus_monticol
4
5
us:3.68221):4.82613,Parus_spilonotus:8.50833):3.11486):4.04875,((Cephalopyrus_flammiceps:
3.75546,Sylviparus_modestus:3.75546):9.37259,Melanochlora_sultanea:13.128):2.5439):14.704
):1.02387):2.23417,((((((((Corvus_corax:9.84043,Nucifraga_caryocatactes:9.84043):1.62575,(G
arrulus_glandarius:10.3279,Pica_pica:10.3279):1.13829):3.19132,(Urocissa_flavirostris:9.19408
,Cissa_chinensis:9.19408):5.46342):1.03513,(((Dendrocitta_frontalis:7.91952,Dendrocitta_form
osae:7.91952):1.91082,Dendrocitta_vagabunda:9.83034):4.09548,(Pyrrhocorax_graculus:6.0260
1,Pyrrhocorax_pyrrhocorax:6.02601):7.89981):1.76681):4.43358,(Lanius_schach:0.920737,Lani
us_tephronotus:0.920737):19.2055):0.750878,(Hypothymis_azurea:6.62481,Terpsiphone_paradi
si:6.62481):14.2523):1.13869,((((((Dicrurus_paradiseus:5.80672,Dicrurus_annectans:5.80672):1.
45595,Dicrurus_hottentottus:7.26267):1.74767,Dicrurus_remifer:9.01034):0.665952,Dicrurus_le
ucophaeus:9.67629):2.16704,Dicrurus_aeneus:11.8433):9.49448,Rhipidura_albicollis:21.3378):
0.677966):2.74472,(((((Pericrocotus_speciosus:5.71573,(Pericrocotus_brevirostris:4.33344,Peric
rocotus_ethologus:4.33344):1.38229):1.86967,Pericrocotus_solaris:7.5854):10.7262,(Coracina_
melaschistos:11.6395,Coracina_macei:11.6395):6.67207):4.20993,(((Tephrodornis_gularis:7.33
434,Hemipus_picatus:7.33434):10.6023,Aegithina_tiphia:17.9366):1.49745,Artamus_fuscus:19.
4341):3.08743):0.957002,(((((Pteruthius_flaviscapis:6.13946,Pteruthius_rufiventer:6.13946):5.9
6739,Pteruthius_melanotis:12.1069):1.44144,Pteruthius_xanthochlorus:13.5483):6.44172,Erporn
is_zantholeuca:19.99):2.2108,(((Oriolus_kundoo:3.26258,Oriolus_tenuirostris:3.26258):3.59265,
Oriolus_traillii:6.85524):2.0078,Oriolus_xanthornus:8.86304):13.3378):1.27771):1.28198):8.873
47):20.467,((Pitta_sordida:17.2282,Pitta_nipalensis:17.2282):17.9483,(Psarisomus_dalhousiae:1
8.9744,Serilophus_lunatus:18.9744):16.2021):18.9245);
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