ncomms12709-s1

Full text

Basal oscines Corvides
Passerides
Core-Passerides
Muscicapida
Petroicida
Eupetida
Melanocharitida
Cnemophilida
Passerida
Sylviida
Corvoidea
Malaconotoidea
Orioloidea
0.01
Leptocoma sperata
Oxylabes madagascariensis
Aegithina lafresnayei
Ploceus cucullatus
Modulatrix stictigula
Erythrocercus mccallii
Menura novaehollandiae
Climacteris melanurus
Paradisaea minor
Rhagologus leucostigma
Picathartes gymnocephalus
Mohoua albicilla
Hyliota flavigaster
Lamprolia victoriae
Dulus dominicus
Fringilla montifringilla
Ptilorrhoa leucosticta
Machaerirhynchus nigripectus
Philesturnus carunculatus
Regulus regulus
Eulacestoma nigropectus
Corvus corax
Lanius excubitor
Sturnus vulgaris
Eremophila alpestris
Nicator chloris
Oedistoma iliolophus
Timalia pileata
Vireo solitarius
Toxorhamphus novaeguineae
Bleda syndactylus
Peucedramus taeniatus
Certhia americana
Coracina tenuirostris
Pardalotus striatus
Chelidorhynx hypoxanthus
Bombycilla garrulus
Orthonyx temminckii
Melanocharis versteri
Cinclus pallasii
Chloropsis sonnerati
Motacilla alba
Psaltriparus minimus
Estrilda melpoda
Sitta europaea
Foulehaio carunculatus
Abroscopus albogularis
Falcunculus frontatus
Struthidea cinerea
Prunella fulvescens
Passer domesticus
Orthotomus castaneiceps
Irena puella
Acrocephalus orientalis
Hylia prasina
Monarcha takatsukasae
Timeliopsis fulvigula
Cormobates leucophaea
Panurus biarmicus
Pycnonotus jocosus
Parus major
Eopsaltria griseogularis
Oreoica gutturalis
Pomatostomus superciliosus
Cinclosoma punctatum
Psophodes occidentalis
Vidua regia
Hirundo rustica
Artamus cinereus
Oreocharis arfaki
Pteruthius flaviscapis
Acanthorhynchus tenuirostris
Aegithalos concinnus
Donacobius atricapilla
Promerops gurneyi
Culicicapa ceylonensis
Tesia cyaniventer
Rhipidura javanica
Malurus alboscapulatus
Daphoenositta chrysoptera
Progne subis
Ptilonorhynchus violaceus
Phylloscopus trochilus
Meliphaga montana
Locustella lanceolata
Pnoepyga pusilla
Macrosphenus flavicans
Pericrocotus divaricatus
Cisticola anonymus
Cnemophilus loriae
Microeca papuana
Ailuroedus buccoides
Remiz coronatus
Chaetops aurantius
Seicercus montis
Loboparadisea sericea
Petroica multicolor
Troglodytes troglodytes
Sylvia nana
Oriolus chinensis
Muscicapa striata
Pachycephala vitiensis
Prionops plumatus
Sylvietta virens
Supplementary Figure 1. Maximum likelihood tree from the incomplete matrix. Numbers by nodes
indicate ML bootstrap support/posterior probability from Bayesian analysis. Unlabelled nodes
have support of 100/1.0. Circled node indicates the lone discrepancy in concatenated analyses
(see text). Sub-clades of Corvides are shown at the superfamily level, whereas Passerides
subclades are shown at the parvorder level (see Supplementary Discussion for details).
<50/0.99
<50/0.99
<50/0.99 <50/0.99
<50/0.99
<50/0.99
94/1.0
86/1.0
71/1.0
80/1.0
97/1.0
78/1.0
77/1.0
98/1.0
91/1.0
79/1.0
97/1.0
Supplementary Figures

“Basal
Oscines”
Corvides Passerides
Supplementary Figure 2. Phylogenetic relationships among oscines estimated using concatenation (maximum likelihood estimation
with RAxML, left) and coalescent approaches (SVDquartets, right). Bootstrap support values are 100% unless otherwise indicated
by numbers below nodes. Red branches indicate conflicting relationships that are highly supported (bootstrap proportion ≥ 70%)
in both approaches; blue branches indicate conflicting relationships that are not highly supported by one of the approaches.
Taxa involved in conflicting relationships are highlighted in brown.
48
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77
Pnoepyga
Furnarius
Microeca
Promerops
Macrosphenus
Modulatrix
Orthonyx
Pachycephala
Vireo
Eopsaltria
Ptilorrhoa
Melanocharis
Philesturnus
Fringilla
Hydrornis
Malurus
Certhia
Mohoua
Picathartes
Timeliopsis
Erythrocercus
Abroscopus
Cinclus
Nicator
Petroica
Sylvia
Sylvietta
Timalia
Dulus
Seicercus
Eulacestoma
Rhipidura
Hirundo
Troglodytes
Irena
Prunella
Hylia
Pomatostomus
Climacteris
Aegithina
Ploceus
Muscicapa
Leptocoma
Culicicapa
Eremophila
Falcunculus
Orthotomus
Cnemophilus
Motacilla
Cisticola
Oxylabes
Lamprolia
Chaetops
Psaltriparus
Pardalotus
Passer
Machaerirhynchus
Oreocharis
Peucedramus
Oreoica
Hyliota
Chloropsis
Cormobates
Chelidorhynx
Corvus
Sturnus
Oriolus
Parus
Monarcha
Loboparadisea
Paradisaea
Regulus
Tesia
Menura
Remiz
Pteruthius
Locustella
Toxorhamphus
Meliphaga
Pycnonotus
Donacobius
Lanius
Vidua
Progne
Coracina
Struthidea
Phylloscopus
Rhagologus
Prionops
Sitta
Bleda
Ailuroedus
Estrilda
Pericrocotus
Panurus
Cinclosoma
Oedistoma
Ptilonorhynchus
Daphoenositta
Psophodes
Artamu s
Foulehaio
Acanthorhynchus
Bombycilla
Acrocephalus
Aegithalos
Daphoenositta
Macrosphenus
Donacobius
Chaetops
Acanthorhynchus
Rhagologus
Panurus
Bombycilla
Psaltriparus
Chloropsis
Loboparadisea
Paradisaea
Pteruthius
Struthidea
Petroica
Eulacestoma
Aegithina
Cinclosoma
Oxylabes
Artamu s
Parus
Vidua
Ploceus
Timeliopsis
Leptocoma
Malurus
Pardalotus
Modulatrix
Rhipidura
Pomatostomus
Peucedramus
Pnoepyga
Picathartes
Pachycephala
Hyliota
Bleda
Oriolus
Falcunculus
Eopsaltria
Cinclus
Orthonyx
Vireo
Timalia
Furnarius
Melanocharis
Orthotomus
Seicercus
Acrocephalus
Prionops
Mohoua
Menura
Troglodytes
Tesia
Monarcha
Sylvietta
Certhia
Hylia
Locustella
Prunella
Cnemophilus
Regulus
Eremophila
Dulus
Foulehaio
Abroscopus
Irena
Pycnonotus
Psophodes
Corvus
Estrilda
Lanius
Toxorhamphus
Cisticola
Phylloscopus
Motacilla
Oreocharis
Machaerirhynchus
Promerops
Passer
Aegithalos
Remiz
Muscicapa
Ptilonorhynchus
Sylvia
Erythrocercus
Sitta
Philesturnus
Meliphaga
Pericrocotus
Cormobates
Hydrornis
Culicicapa
Microeca
Sturnus
Climacteris
Nicator
Lamprolia
Oedistoma
Progne
Hirundo
Oreoica
Fringilla
Coracina
Chelidorhynx
Ailuroedus
Ptilorrhoa
99
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99
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99
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99
98
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78
98

Supplementary Figure 3. Results of gene-tree based coalescent methods. Bootstrap percentages shown by nodes. Nodes with 100% bootstrap support are
unlabeled; nodes with less than 50% support collapsed. Highlighted genera indicate samples with short contig lengths as discussed in text. Colored bars indicate
basal oscines (green), Corvides (orange), and Passerides (blue).
Regulus
Sturnus
Cnemophilus
Orthotomus
Struthidea
Chloropsis
Eopsaltria
Passer
Aegithalos
Prionops
Meliphaga
Rhagologus
Cormobates
Eulacestoma
Coracina
Orthonyx
Pnoepyga
Pachycephala
Vireo
Microeca
Modulatrix
Hirundo
Hyliota
Pteruthius
Bleda
Pardalotus
Cisticola
Peucedramus
Macrosphenus
Chelidorhynx
Petroica
Abroscopus
Cinclosoma
Cinclus
Falcunculus
Lamprolia
Eremophila
Estrilda
Fringilla
Vidua
Menura
Sylvietta
Picathartes
Dulus
Pericrocotus
Rhipidura
Aegithina
Toxorhamphus
Leptocoma
Seicercus
Donacobius
Oreocharis
Oxylabes
Parus
Panurus
Remiz
Chaetops
Sitta
Corvus
Ailuroedus
Hylia
Psaltriparus
Pomatostomus
Philesturnus
Melanocharis
Irena
Muscicapa
Machaerirhynchus
Acanthorhynchus
Oreoica
Lanius
Prunella
Bombycilla
Tesia
Acrocephalus
Timeliopsis
Mohoua
Pycnonotus
Malurus
Phylloscopus
Culicicapa
Climacteris
Ptilonorhynchus
Sylvia
Promerops
Artamus
Foulehaio
Nicator
Troglodytes
Paradisaea
Oriolus
Monarcha
Loboparadisea
Locustella
Erythrocercus
Motacilla
Daphoenositta
Progne
Timalia
Certhia
Oedistoma
Ptilorrhoa
Psophodes
Ploceus
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95
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99
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78 97
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90
70
689793
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99
99
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99
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50
Hirundo
Struthidea
Sylvietta
Passer
Cisticola
Bombycilla
Monarcha
Pnoepyga
Tesia
Abroscopus
Nicator
Pteruthius
Picathartes
Ptilorrhoa
Modulatrix
Psophodes
Rhagologus
Microeca
Machaerirhynchus
Menura
Climacteris
Philesturnus
Irena
Fringilla
Orthonyx
Oreocharis
Remiz
Oedistoma
Eulacestoma
Toxorhamphus
Cnemophilus
Coracina
Artamus
Timalia
Timeliopsis
Regulus
Estrilda
Cinclus
Chelidorhynx
Foulehaio
Troglodytes
Mohoua
Corvus
Muscicapa
Daphoenositta
Progne
Orthotomus
Oxylabes
Prionops
Cormobates
Sitta
Eopsaltria
Parus
Falcunculus
Malurus
Phylloscopus
Ailuroedus
Meliphaga
Promerops
Chloropsis
Panurus
Pycnonotus
Ptilonorhynchus
Motacilla
Pachycephala
Petroica
Prunella
Oreoica
Pardalotus
Leptocoma
Peucedramus
Ploceus
Sylvia
Pomatostomus
Loboparadisea
Lanius
Pericrocotus
Donacobius
Lamprolia
Eremophila
Vidua
Chaetops
Vireo
Melanocharis
Paradisaea
Bleda
Seicercus
Acrocephalus
Certhia
Oriolus
Psaltriparus
Macrosphenus
Locustella
Erythrocercus
Aegithalos
Dulus
Culicicapa
Cinclosoma
Hyliota
Rhipidura
Acanthorhynchus
Aegithina
Sturnus
Hylia
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96
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97 58
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95
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96 98
69
STEAC ASTRAL MPEST
Machaerirhynchus
Rhagologus
Oxylabes
Aegithalos
Pomatostomus
Orthotomus
Lamprolia
Dulus
Leptocoma
Struthidea
Eopsaltria
Locustella
Prionops
Corvus
Oedistoma
Modulatrix
Eremophila
Lanius
Psophodes
Fringilla
Culicicapa
Coracina
Prunella
Oreocharis
Irena
Ploceus
Timalia
Motacilla
Pericrocotus
Cormobates
Artamus
Sturnus
Malurus
Chaetops
Orthonyx
Pnoepyga
Hyliota
Pardalotus
Mohoua
Erythrocercus
Peucedramus
Climacteris
Certhia
Falcunculus
Vidua
Passer
Phylloscopus
Sylvietta
Chelidorhynx
Ptilonorhynchus
Oreoica
Tesia
Hylia
Oriolus
Ptilorrhoa
Sylvia
Menura
Foulehaio
Seicercus
Daphoenositta
Psaltriparus
Timeliopsis
Rhipidura
Donacobius
Bleda
Ailuroedus
Paradisaea
Chloropsis
Sitta
Progne
Vireo
Hirundo
Promerops
Muscicapa
Aegithina
Melanocharis
Toxorhamphus
Macrosphenus
Pteruthius
Parus
Bombycilla
Microeca
Cnemophilus
Pachycephala
Cisticola
Remiz
Cinclosoma
Cinclus
Abroscopus
Philesturnus
Panurus
Eulacestoma
Monarcha
Acrocephalus
Loboparadisea
Acanthorhynchus
Petroica
Picathartes
Meliphaga
Pycnonotus
Troglodytes
Regulus
Estrilda
Nicator
62
65
91
50
91
74
90
87
96
97
95
94
83
69
72
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88
69
94
71
97
98
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94
51
54
63
55
84
91
53
89 77
Oedistoma
Estrilda
Ailuroedus
Locustella
Oxylabes
Eulacestoma
Falcunculus
Fringilla
Cinclus
Seicercus
Parus
Promerops
Timeliopsis
Motacilla
Passer
Corvus
Hirundo
Sylvietta
Vireo
Daphoenositta
Monarcha
Picathartes
Rhipidura
Melanocharis
Climacteris
Pomatostomus
Modulatrix
Machaerirhynchus
Aegithalos
Orthotomus
Abroscopus
Muscicapa
Certhia
Acrocephalus
Chelidorhynx
Oreoica
Troglodytes
Chaetops
Chloropsis
Sitta
Cormobates
Oreocharis
Petroica
Microeca
Cisticola
Ptilonorhynchus
Pachycephala
Pnoepyga
Meliphaga
Artamus
Menura
Lamprolia
Phylloscopus
Culicicapa
Pycnonotus
Ptilorrhoa
Hylia
Bleda
Oriolus
Tesia
Progne
Donacobius
Prunella
Pericrocotus
Aegithina
Sylvia
Nicator
Pardalotus
Cinclosoma
Remiz
Timalia
Peucedramus
Dulus
Erythrocercus
Toxorhamphus
Panurus
Acanthorhynchus
Sturnus
Rhagologus
Philesturnus
Bombycilla
Coracina
Foulehaio
Eremophila
Pteruthius
Orthonyx
Malurus
Eopsaltria
Macrosphenus
Psophodes
Paradisaea
Hyliota
Struthidea
Lanius
Prionops
Ploceus
Mohoua
Loboparadisea
Irena
Vidua
Regulus
Leptocoma
Cnemophilus
Psaltriparus
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70
91
64
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78
98
66
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59
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82
93
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78
86
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98
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52
51
STAR

Lanius
Lamprolia
Rhipidura
Struthidea
Monarcha
Corvus
Paradisaea
1
1
1
1
1
0.62
Aegithina
Artamus
Prionops
Rhagologus
Machaerirhynchus
0.57
1
1
1
Rhipidura
Lamprolia
Struthidea
Lanius
Monarcha
Corvus
Paradisaea
1
1
0.6
1
0.98
1
Artamus
Machaerirhynchus
Prionops
Rhagologus
Aegithina
0.98
1
1
Lanius
Struthidea
Lamprolia
Corvus
Monarcha
Paradisaea
Rhipidura
1
1
0.64
1
1
1
Prionops
Rhagologus
Aegithina
Artamus
Machaerirhynchus
0.99
1
1
Corvus
Lanius
Struthidea
Monarcha
Lamprolia
Rhipidura
Paradisaea
0.99
0.64
1
1
1
0.98
Lamprolia
Rhipidura
Monarcha
Corvus
Struthidea
Paradisaea
Lanius
1
0.53
1
0.99
1
0.98
Rhagologus
Prionops
Aegithina
Machaerirhynchus
Artamus
1
1
1
0.59
Machaerirhynchus
Prionops
Rhagologus
Aegithina
Artamus
1
1
1
0.51
Lamprolia
Lanius
Paradisaea
Corvus
Rhipidura
Monarcha
Struthidea
0.96
0.99
1
0.7
1
0.53
Prionops
Rhagologus
Artamus
Machaerirhynchus
Aegithina
1
1
1
Machaerirhynchus
Rhagologus
Prionops
Artamus
Aegithina
1
1
1
Paradisaea
Rhipidura
Struthidea
Corvus
Lamprolia
Lanius
Monarcha
1
0.88
1
1
0.64
1
Lanius
Lamprolia
Monarcha
Rhipidura
Struthidea
Paradisaea
Corvus
1
1
0.99
0.59
1
0.99
Artamus
Rhagologus
Prionops
Aegithina
Machaerirhynchus
1
1
1
STEAC
STAR
MPEST
ASTRAL
TrimmedFull dataFull data Trimmed
Supplemental Figure 4. Results of GCM analyses with experimental trimming of select sequences to mimic short
contigs. Each clade includes analyses of the full data (left) and with one sample (underlined or boxed) trimmed to
the same contig lengths as those of Mohoua (the shortest contigs in our data set). In each case, the trimmed
sample moved to a position closer to the root with high support.

48
98
27
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86
36
79
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80
71
30
31
97
78
94
47
77
Pnoepyga
Furnarius
Microeca
Promerops
Macrosphenus
Modulatrix
Orthonyx
Pachycephala
Vireo
Eopsaltria
Ptilorrhoa
Melanocharis
Philesturnus
Fringilla
Hydrornis
Malurus
Certhia
Mohoua
Picathartes
Timeliopsis
Erythrocercus
Abroscopus
Cinclus
Nicator
Petroica
Sylvia
Sylvietta
Timalia
Dulus
Seicercus
Eulacestoma
Rhipidura
Hirundo
Troglodytes
Irena
Prunella
Hylia
Pomatostomus
Climacteris
Aegithina
Ploceus
Muscicapa
Leptocoma
Culicicapa
Eremophila
Falcunculus
Orthotomus
Cnemophilus
Motacilla
Cisticola
Oxylabes
Lamprolia
Chaetops
Psaltriparus
Pardalotus
Passer
Machaerirhynchus
Oreocharis
Peucedramus
Oreoica
Hyliota
Chloropsis
Cormobates
Chelidorhynx
Corvus
Sturnus
Oriolus
Parus
Monarcha
Loboparadisea
Paradisaea
Regulus
Tesia
Menura
Remiz
Pteruthius
Locustella
Toxorhamphus
Meliphaga
Pycnonotus
Donacobius
Lanius
Vidua
Progne
Coracina
Struthidea
Phylloscopus
Rhagologus
Prionops
Sitta
Bleda
Ailuroedus
Estrilda
Pericrocotus
Panurus
Cinclosoma
Oedistoma
Ptilonorhynchus
Daphoenositta
Psophodes
Artamus
Foulehaio
Acanthorhynchus
Bombycilla
Acrocephalus
Aegithalos
Cormobates
Corvus
Acrocephalus
Daphoenositta
Ptilonorhynchus
Orthonyx
Troglodytes
Pycnonotus
Bleda
Modulatrix
Motacilla
Erythrocercus
Regulus
Irena
Paradisaea
Chloropsis
Pardalotus
Culicicapa
Monarcha
Vidua
Peucedramus
Sylvietta
Passer
Promerops
Leptocoma
Aegithina
Cisticola
Mohoua
Loboparadisea
Nicator
Orthotomus
Dulus
Macrosphenus
Picathartes
Cnemophilus
Psophodes
Timeliopsis
Coracina
Hydrornis
Donacobius
Pteruthius
Melanocharis
Sylvia
Pericrocotus
Progne
Climacteris
Ailuroedus
Prunella
Remiz
Abroscopus
Hylia
Microeca
Ploceus
Fringilla
Aegithalos
Lanius
Chaetops
Rhipidura
Parus
Acanthorhynchus
Eremophila
Sturnus
Eopsaltria
Eulacestoma
Pomatostomus
Ptilorrhoa
Panurus
Artamus
Bombycilla
Vireo
Timalia
Certhia
Oxylabes
Pachycephala
Struthidea
Prionops
Lamprolia
Toxorhamphus
Meliphaga
Pnoepyga
Chelidorhynx
Phylloscopus
Locustella
Foulehaio
Oreoica
Oedistoma
Hirundo
Sitta
Oriolus
Tesia
Menura
Estrilda
Cinclosoma
Psaltriparus
Seicercus
Petroica
Cinclus
Falcunculus
Furnarius
Machaerirhynchus
Rhagologus
Philesturnus
Oreocharis
Malurus
Hyliota
Muscicapa
87
91
88
74
94
97
88
88
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86
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84
66
97
60
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95
74
54
66
87
57
Corvides “Basal
Oscines”
Passerides
Supplementary Figure. 5. Phylogenetic relationships among oscines estimated using concatenation (maximum likelihood estimation
with RAxML, left) from this study and from Jetz et al.10 (consensus of 1000 trees with subset of taxa chosen to match this
study using the Hackett et al. 2008 backbone, right). Bootstrap support values (on our tree) and Bayesian posterior probabilities
(on Jetz et al. 2012 tree) are 100% unless otherwise indicated by numbers below nodes. Red branches indicate conflicting
relationships that are highly supported in both studies; blue branches indicate conflicting relationships that are not highly
supported in one of the studies.

Corvides
“Basal
Oscines” Passerides
C
AC
C
AC
AC
AC
C
ABCD
ABCD
ABCD
ABCD
AC
AC
AC
A
ACDEF
EH
B
AC
A
AC
AC
C
ABCDE
ABCDEFH
A
E
EG
A
ABCDE
A
EFI
EF
ABCDE
A
ACDEFI
ACD
C
ACDEFGHI
ADEFGH
A
A
A
A
A
B
EF
EF
ABC
AC
ACD
DGH
DGH
EGH
ACDEFGHI
ACDEFGHI
GH
EGH
GH
EFGH
F
F
ACDEFI
E
E
G
EFI
F
ACDEFI
H
EFH
EFGH
ACDEFGHI
F
EF
EF
EFGH
FGH
H
ACDEFGHI
F
F
F
ACDEFI
ACDEFI
I
ABCDEFHI
G
ACDEFHI
DE
ABCDEFGHI
ABCDEFGHI
EFI
EFI
EFGH
DEF
ADEFH
ADEFH
F
EGH
EGH
F
DEFH
DEFH
Menura novaehollandiae
Cormobates leucophaea
Climacteris melanurus
Ptilonorhynchus violaceus
Ailuroedus buccoides
Malurus alboscapulatus
Pardalotus striatus
Acanthorhynchus tenuirostris
Timeliopsis fulvigula
Foulehaio carunculatus
Meliphaga montana
Orthonyx temminckii
Pomatostomus superciliosus
Cinclosoma punctatum
Ptilorrhoa leucosticta
Coracina tenuirostris
Pericrocotus divaricatus
Mohoua albicilla
Daphoenositta chrysoptera
Eulacestoma nigropectus
Psophodes occidentalis
Oreoica gutturalis
Falcunculus frontatus
Pachycephala vitiensis
Oriolus chinensis
Oreocharis arfaki
Pteruthius flaviscapis
Vireo solitarius
Machaerirhynchus nigripectus
Artamus cinereus
Rhagologus leucostigma
Prionops plumatus
Aegithina lafresnayei
Rhipidura javanica
Lamprolia victoriae
Monarcha takatsukasae
Paradisaea minor
Struthidea cinerea
Corvus corax
Lanius excubitor
Loboparadisea sericea
Cnemophilus loriae
Melanocharis versteri
Toxorhamphus novaeguineae
Oedistoma iliolophus
Philesturnus carunculatus
Picathartes gymnocephalus
Chaetops aurantius
Petroica multicolor
Eopsaltria griseogularis
Microeca papuana
Bombycilla garrulus
Dulus dominicus
Cinclus pallasii
Muscicapa striata
Sturnus vulgaris
Regulus regulus
Sitta europea
Troglodytes troglodytes
Certhia americana
Promerops gurneyi
Modulatrix stictigula
Leptocoma sperata
Irena puella
Chloropsis sonnerati
Peucedramus taeniatus
Ploceus cucullatus
Vidua regia
Estrilda melpoda
Prunella fulvescens
Passer domesticus
Fringilla montifringilla
Motacilla alba
Hyliota flavigaster
Culicicapa ceylonensis
Chelidorhynx hypoxanthus
Parus major
Remiz coronatus
Panurus biarmicus
Eremophila alpestris
Nicator chloris
Macrosphenus flavicans
Sylvietta virens
Orthotomus castaneiceps
Cisticola anonymus
Oxylabes madagascariensis
Locustella lanceolata
Donacobius atricapilla
Acrocephalus orientalis
Pnoepyga pusilla
Progne subis
Hirundo rustica
Bleda syndactylus
Pycnonotus jocosus
Sylvia nana
Timalia pileata
Phylloscopus trochilus
Seicercus montis
Hylia prasina
Psaltriparus minimus
Aegithalos concinnus
Erythrocercus mccallii
Tesia cyaniventer
Abroscopus albogularis
40 30 20 10 0 Ma
Supplementary Figure 6. Ancestral range estimation with BioGeoBEARS using alternative tree
derived from calibrations from Prum et al. 2015. Analysis was performed with full distribution of
clades under DEC+J model with New Guinea ancestral area not allowed before 15 Ma. Biogeo-
graphic areas: New Guinea [A], New Zealand [B], Australia [C], Wallacea [D], S and SE Asia
[including Philippines; E], sub-Saharan Africa [F], New World [G], Palearctic [including N. Africa;
H], and, Madagascar [I]. Bars indicate 95% highest posterior density of node date estimates.
50
C
C
C
C
C
C
C
C
CCA
C
C
C
C
C
C
CE
C
C
C
C
C
CC
C
C
CE
C
C
CCE
C
C
C
C
CCE
C
A
C
CC
C
C
C
E
CC
E
E
H
EH
H
HH
HHH
E
F
E
E
E
H
H
FF
HHH
F
FF
F
F
F
H
F
F
F
F
DEFI
E
EE
E
E
E
DEFHI
F
F
F
F
F
EF
F
F
H
FE

Corvides
“Basal
Oscines” Passerides
30 20 10 0 Ma
Supplementary Figure 7. Ancestral range estimation with BioGeoBEARS using full distribution of
clades under DEC+J model with no area constraint. Biogeographic areas: New Guinea [A],
New Zealand [B], Australia [C], Wallacea [D], S and SE Asia [including Philippines; E],
sub-Saharan Africa [F], New World [G], Palearctic [including N. Africa; H], and, Madagascar [I].
Menura novaehollandiae
Cormobates leucophaea
Climacteris melanurus
Ptilonorhynchus violaceus
Ailuroedus buccoides
Malurus alboscapulatus
Pardalotus striatus
Acanthorhynchus tenuirostris
Timeliopsis fulvigula
Foulehaio carunculatus
Meliphaga montana
Orthonyx temminckii
Pomatostomus superciliosus
Cinclosoma punctatum
Ptilorrhoa leucosticta
Coracina tenuirostris
Pericrocotus divaricatus
Mohoua albicilla
Daphoenositta chrysoptera
Eulacestoma nigropectus
Psophodes occidentalis
Oreoica gutturalis
Falcunculus frontatus
Pachycephala vitiensis
Oriolus chinensis
Oreocharis arfaki
Pteruthius flaviscapis
Vireo solitarius
Machaerirhynchus nigripectus
Artamus cinereus
Rhagologus leucostigma
Prionops plumatus
Aegithina lafresnayei
Rhipidura javanica
Lamprolia victoriae
Monarcha takatsukasae
Paradisaea minor
Struthidea cinerea
Corvus corax
Lanius excubitor
Loboparadisea sericea
Cnemophilus loriae
Melanocharis versteri
Toxorhamphus novaeguineae
Oedistoma iliolophus
Philesturnus carunculatus
Picathartes gymnocephalus
Chaetops aurantius
Petroica multicolor
Eopsaltria griseogularis
Microeca papuana
Bombycilla garrulus
Dulus dominicus
Cinclus pallasii
Muscicapa striata
Sturnus vulgaris
Regulus regulus
Sitta europea
Troglodytes troglodytes
Certhia americana
Promerops gurneyi
Modulatrix stictigula
Leptocoma sperata
Irena puella
Chloropsis sonnerati
Peucedramus taeniatus
Ploceus cucullatus
Vidua regia
Estrilda melpoda
Prunella fulvescens
Passer domesticus
Fringilla montifringilla
Motacilla alba
Hyliota flavigaster
Culicicapa ceylonensis
Chelidorhynx hypoxanthus
Parus major
Remiz coronatus
Panurus biarmicus
Eremophila alpestris
Nicator chloris
Macrosphenus flavicans
Sylvietta virens
Orthotomus castaneiceps
Cisticola anonymus
Oxylabes madagascariensis
Locustella lanceolata
Donacobius atricapilla
Acrocephalus orientalis
Pnoepyga pusilla
Progne subis
Hirundo rustica
Bleda syndactylus
Pycnonotus jocosus
Sylvia nana
Timalia pileata
Phylloscopus trochilus
Seicercus montis
Hylia prasina
Psaltriparus minimus
Aegithalos concinnus
Erythrocercus mccallii
Tesia cyaniventer
Abroscopus albogularis
C
C
C
C
C
C
C
C
CCC
A
A
A
A
A
A
AE
A
A
A
A
A
AC
A
A
AE
A
A
AAE
A
A
A
A
CA
A
A
A
AA
B
F
F
F
AA
F
F
G
G
G
GG
GGG
F
F
F
F
E
F
F
FF
HHH
F
FF
F
F
F
FH
F
F
F
F
F
F
II
F
F
F
ABCDEFGHI
F
F
F
F
F
F
F
F
E
FF
C
AC
C
AC
AC
AC
C
ABCD
ABCD
ABCD
ABCD
AC
AC
AC
A
ACDEF
EH
B
AC
A
AC
AC
C
ABCDE
ABCDEFH
A
E
EG
A
ABCDE
A
EFI
EF
ABCDE
A
ACDEFI
ACD
C
ACDEFGHI
ADEFGH
A
A
A
A
A
B
EF
EF
ABC
AC
ACD
DGH
DGH
EGH
ACDEFGHI
ACDEFGHI
GH
EGH
GH
EFGH
F
F
ACDEFI
E
E
G
EFI
F
ACDEFI
H
EFH
EFGH
ACDEFGHI
F
EF
EF
EFGH
FGH
H
ACDEFGHI
F
F
F
ACDEFI
ACDEFI
I
ABCDEFHI
G
ACDEFHI
DE
ABCDEFGHI
ABCDEFGHI
EFI
EFI
EFGH
DEF
ADEFH
ADEFH
F
EGH
EGH
F
DEFH
DEFH

Corvides
“Basal
Oscines” Passerides
30 20 10 0 Ma
Supplementary Figure 8. Ancestral range estimation with BioGeoBEARS using full distribution of
clades under DIVALIKE+J model with New Guinea ancestral range not allowed before 15 Ma.
Biogeographic areas: New Guinea [A], New Zealand [B], Australia [C], Wallacea [D], S and SE
Asia [including Philippines; E], sub-Saharan Africa [F], New World [G], Palearctic [including
N. Africa; H], and, Madagascar [I].
Menura novaehollandiae
Cormobates leucophaea
Climacteris melanurus
Ptilonorhynchus violaceus
Ailuroedus buccoides
Malurus alboscapulatus
Pardalotus striatus
Acanthorhynchus tenuirostris
Timeliopsis fulvigula
Foulehaio carunculatus
Meliphaga montana
Orthonyx temminckii
Pomatostomus superciliosus
Cinclosoma punctatum
Ptilorrhoa leucosticta
Coracina tenuirostris
Pericrocotus divaricatus
Mohoua albicilla
Daphoenositta chrysoptera
Eulacestoma nigropectus
Psophodes occidentalis
Oreoica gutturalis
Falcunculus frontatus
Pachycephala vitiensis
Oriolus chinensis
Oreocharis arfaki
Pteruthius flaviscapis
Vireo solitarius
Machaerirhynchus nigripectus
Artamus cinereus
Rhagologus leucostigma
Prionops plumatus
Aegithina lafresnayei
Rhipidura javanica
Lamprolia victoriae
Monarcha takatsukasae
Paradisaea minor
Struthidea cinerea
Corvus corax
Lanius excubitor
Loboparadisea sericea
Cnemophilus loriae
Melanocharis versteri
Toxorhamphus novaeguineae
Oedistoma iliolophus
Philesturnus carunculatus
Picathartes gymnocephalus
Chaetops aurantius
Petroica multicolor
Eopsaltria griseogularis
Microeca papuana
Bombycilla garrulus
Dulus dominicus
Cinclus pallasii
Muscicapa striata
Sturnus vulgaris
Regulus regulus
Sitta europea
Troglodytes troglodytes
Certhia americana
Promerops gurneyi
Modulatrix stictigula
Nectarinia sperata
Irena puella
Chloropsis sonnerati
Peucedramus taeniatus
Ploceus cucullatus
Vidua regia
Estrilda melpoda
Prunella fulvescens
Passer domesticus
Fringilla montifringilla
Motacilla alba
Hyliota flavigaster
Culicicapa ceylonensis
Chelidorhynx hypoxanthus
Parus major
Remiz coronatus
Panurus biarmicus
Eremophila alpestris
Nicator chloris
Macrosphenus flavicans
Sylvietta virens
Orthotomus castaneiceps
Cisticola anonymus
Oxylabes madagascariensis
Locustella lanceolata
Donacobius atricapilla
Acrocephalus orientalis
Pnoepyga pusilla
Progne subis
Hirundo rustica
Bleda syndactylus
Pycnonotus jocosus
Sylvia nana
Timalia pileata
Phylloscopus trochilus
Seicercus montis
Hylia prasina
Psaltriparus minimus
Aegithalos concinnus
Erythrocercus mccallii
Tesia cyaniventer
Abroscopus albogularis
C
C
C
C
C
C
C
C
CCC
C
C
C
C
C
C
CE
C
C
C
C
C
CC
C
C
CE
C
C
CCE
C
C
C
C
CE
C
A
C
CC
C
E
E
E
CC
E
E
H
DEGH
H
HH
HHG
E
F
E
E
E
H
H
FF
HHH
F
FF
F
H
F
H
F
F
F
F
ACDEFI
E
E
EH
E
E
E
ABCDEFGHI
F
F
F
F
F
E
F
F
H
FF
C
AC
C
AC
AC
AC
C
ABCD
ABCD
ABCD
ABCD
AC
AC
AC
A
ACDEF
EH
B
AC
A
AC
AC
C
ABCDE
ABCDEFH
A
E
EG
A
ABCDE
A
EFI
EF
ABCDE
A
ACDEFI
ACD
C
ACDEFGHI
ADEFGH
A
A
A
A
A
B
EF
EF
ABC
AC
ACD
DGH
DGH
EGH
ACDEFGHI
ACDEFGHI
GH
EGH
GH
EFGH
F
F
ACDEFI
E
E
G
EFI
F
ACDEFI
H
EFH
EFGH
ACDEFGHI
F
EF
EF
EFGH
FGH
H
ACDEFGHI
F
F
F
ACDEFI
ACDEFI
I
ABCDEFHI
G
ACDEFHI
DE
ABCDEFGHI
ABCDEFGHI
EFI
EFI
EFGH
DEF
ADEFH
ADEFH
F
EGH
EGH
F
DEFH
DEFH

Corvides
“Basal
Oscines” Passerides
30 20 10 0 Ma
Supplementary Figure 9. Ancestral range estimation with BioGeoBEARS using full distribution of
cladesunder BAYAREALIKE+J model with New Guinea ancestral range not allowed before 15
Ma. Biogeographic areas: New Guinea [A], New Zealand [B], Australia [C], Wallacea [D],
S and SE Asia [including Philippines; E], sub-Saharan Africa [F], New World [G], Palearctic
[including N. Africa; H], and, Madagascar [I]
Menura novaehollandiae
Cormobates leucophaea
Climacteris melanurus
Ptilonorhynchus violaceus
Ailuroedus buccoides
Malurus alboscapulatus
Pardalotus striatus
Acanthorhynchus tenuirostris
Timeliopsis fulvigula
Foulehaio carunculatus
Meliphaga montana
Orthonyx temminckii
Pomatostomus superciliosus
Cinclosoma punctatum
Ptilorrhoa leucosticta
Coracina tenuirostris
Pericrocotus divaricatus
Mohoua albicilla
Daphoenositta chrysoptera
Eulacestoma nigropectus
Psophodes occidentalis
Oreoica gutturalis
Falcunculus frontatus
Pachycephala vitiensis
Oriolus chinensis
Oreocharis arfaki
Pteruthius flaviscapis
Vireo solitarius
Machaerirhynchus nigripectus
Artamus cinereus
Rhagologus leucostigma
Prionops plumatus
Aegithina lafresnayei
Rhipidura javanica
Lamprolia victoriae
Monarcha takatsukasae
Paradisaea minor
Struthidea cinerea
Corvus corax
Lanius excubitor
Loboparadisea sericea
Cnemophilus loriae
Melanocharis versteri
Toxorhamphus novaeguineae
Oedistoma iliolophus
Philesturnus carunculatus
Picathartes gymnocephalus
Chaetops aurantius
Petroica multicolor
Eopsaltria griseogularis
Microeca papuana
Bombycilla garrulus
Dulus dominicus
Cinclus pallasii
Muscicapa striata
Sturnus vulgaris
Regulus regulus
Sitta europea
Troglodytes troglodytes
Certhia americana
Promerops gurneyi
Modulatrix stictigula
Leptocoma sperata
Irena puella
Chloropsis sonnerati
Peucedramus taeniatus
Ploceus cucullatus
Vidua regia
Estrilda melpoda
Prunella fulvescens
Passer domesticus
Fringilla montifringilla
Motacilla alba
Hyliota flavigaster
Culicicapa ceylonensis
Chelidorhynx hypoxanthus
Parus major
Remiz coronatus
Panurus biarmicus
Eremophila alpestris
Nicator chloris
Macrosphenus flavicans
Sylvietta virens
Orthotomus castaneiceps
Cisticola anonymus
Oxylabes madagascariensis
Locustella lanceolata
Donacobius atricapilla
Acrocephalus orientalis
Pnoepyga pusilla
Progne subis
Hirundo rustica
Bleda syndactylus
Pycnonotus jocosus
Sylvia nana
Timalia pileata
Phylloscopus trochilus
Seicercus montis
Hylia prasina
Psaltriparus minimus
Aegithalos concinnus
Erythrocercus mccallii
Tesia cyaniventer
Abroscopus albogularis
C
C
C
C
C
C
C
C
ABCD
ABCD ABCD
C
C
C
C
C
C
CE
C
C
C
C
C
CC
C
C
CE
C
C
CCE
C
C
C
C
CDEH
C
A
C
CC
C
E
E
E
CC
E
E
GH
EGH
GH
EGH
CEGH
GH GH GH
E
F
E
E
E
H
H
FF
HEH EFH
F
FF
F
FH
F
H
F
F
F
EF
ACDEFI
EF
EFH
EFH
EF
EF
EF
ABCDEFGHI
EF
EF
EFI
EF
EF
DEFH
EF
EF
EGH
FEFH
C
AC
C
AC
AC
AC
C
ABCD
ABCD
ABCD
ABCD
AC
AC
AC
A
ACDEF
EH
B
AC
A
AC
AC
C
ABCDE
ABCDEFH
A
E
EG
A
ABCDE
A
EFI
EF
ABCDE
A
ACDEFI
ACD
C
ACDEFGHI
ADEFGH
A
A
A
A
A
B
EF
EF
ABC
AC
ACD
DGH
DGH
EGH
ACDEFGHI
ACDEFGHI
GH
EGH
GH
EFGH
F
F
ACDEFI
E
E
G
EFI
F
ACDEFI
H
EFH
EFGH
ACDEFGHI
F
EF
EF
EFGH
FGH
H
ACDEFGHI
F
F
F
ACDEFI
ACDEFI
I
ABCDEFHI
G
ACDEFHI
DE
ABCDEFGHI
ABCDEFGHI
EFI
EFI
EFGH
DEF
ADEFH
ADEFH
F
EGH
EGH
F
DEFH
DEFH

Corvides
“Basal
Oscines” Passerides
30 20 10 0 Ma
Supplementary Figure 10. Ancestral range estimation with BioGeoBEARS using inferred origin
of clades under DEC+J model with New Guinea ancestral range not allowed before 15 Ma.
Biogeographic areas: New Guinea [A], New Zealand [B], Australia [C], Wallacea [D],
S and SE Asia [including Philippines; E], sub-Saharan Africa [F], New World [G], Palearctic
[including N. Africa; H], and, Madagascar [I].
Menura novaehollandiae
Cormobates leucophaea
Climacteris melanurus
Ptilonorhynchus violaceus
Ailuroedus buccoides
Malurus alboscapulatus
Pardalotus striatus
Acanthorhynchus tenuirostris
Timeliopsis fulvigula
Foulehaio carunculatus
Meliphaga montana
Orthonyx temminckii
Pomatostomus superciliosus
Cinclosoma punctatum
Ptilorrhoa leucosticta
Coracina tenuirostris
Pericrocotus divaricatus
Mohoua albicilla
Daphoenositta chrysoptera
Eulacestoma nigropectus
Psophodes occidentalis
Oreoica gutturalis
Falcunculus frontatus
Pachycephala vitiensis
Oriolus chinensis
Oreocharis arfaki
Pteruthius flaviscapis
Vireo solitarius
Machaerirhynchus nigripectus
Artamus cinereus
Rhagologus leucostigma
Prionops plumatus
Aegithina lafresnayei
Rhipidura javanica
Lamprolia victoriae
Monarcha takatsukasae
Paradisaea minor
Struthidea cinerea
Corvus corax
Lanius excubitor
Loboparadisea sericea
Cnemophilus loriae
Melanocharis versteri
Toxorhamphus novaeguineae
Oedistoma iliolophus
Philesturnus carunculatus
Picathartes gymnocephalus
Chaetops aurantius
Petroica multicolor
Eopsaltria griseogularis
Microeca papuana
Bombycilla garrulus
Dulus dominicus
Cinclus pallasii
Muscicapa striata
Sturnus vulgaris
Regulus regulus
Sitta europea
Troglodytes troglodytes
Certhia americana
Promerops gurneyi
Modulatrix stictigula
Leptocoma sperata
Irena puella
Chloropsis sonnerati
Peucedramus taeniatus
Ploceus cucullatus
Vidua regia
Estrilda melpoda
Prunella fulvescens
Passer domesticus
Fringilla montifringilla
Motacilla alba
Hyliota flavigaster
Culicicapa ceylonensis
Chelidorhynx hypoxanthus
Parus major
Remiz coronatus
Panurus biarmicus
Eremophila alpestris
Nicator chloris
Macrosphenus flavicans
Sylvietta virens
Orthotomus castaneiceps
Cisticola anonymus
Oxylabes madagascariensis
Locustella lanceolata
Donacobius atricapilla
Acrocephalus orientalis
Pnoepyga pusilla
Progne subis
Hirundo rustica
Bleda syndactylus
Pycnonotus jocosus
Sylvia nana
Timalia pileata
Phylloscopus trochilus
Seicercus montis
Hylia prasina
Psaltriparus minimus
Aegithalos concinnus
Erythrocercus mccallii
Tesia cyaniventer
Abroscopus albogularis
C
C
C
C
C
C
C
C
CCC
C
C
C
C
C
C
C
C
C
C
C
C
CC
C
C
CE
C
C
CCE
C
C
C
C
CE
C
A
C
CC
C
E
C
E
CC
E
E
H
EH
H
HH
HHH
E
F
E
E
E
H
H
FF
HHH
F
FF
F
F
F
H
F
F
F
F
F
F
FH
F
F
F
EF
F
E
F
E
F
E
F
F
H
FE
C
AC
C
AC
AC
C
C
AC
AC
AC
AC
C
AC
AC
A
AC
E
B
AC
A
AC
AC
C
AC
ACE
A
E
EG
A
AC
A
EFI
EF
AC
A
ACEF
A
C
EH
EFH
A
A
A
A
A
B
EF
EF
A
A
A
DGH
DGH
H
EFH
EFGH
H
EH
G
H
F
F
E
E
E
G
F
F
ACDEF
H
H
H
FH
F
EF
EF
E
FGH
H
FH
F
F
F
EFI
EFI
I
EH
G
FHI
E
EF
EF
EF
EF
EFGH
E
EH
EH
F
H
H
F
E
E

Oedistoma
Remiz
Culicicapa
Timalia
Toxorhamphus
Mohoua
Oreoica
Fringilla
Falcunculus
Meliphaga
Eopsaltria
Timeliopsis
Eremophila
Irena
Cormobates
Psaltriparus
Acrocephalus
Petroica
Motacilla
Melanocharis
Locustella
Acanthorhynchus
Pardalotus
Struthidea
Foulehaio
Leptocoma
Pericrocotus
Pomatostomus
Pachycephala
Cinclus
Tesia
Muscicapa
Certhia
Promerops
Oreocharis
Modulatrix
Chelidorhynx
Aegithalos
Oriolus
Ailuroedus
Bombycilla
Progne
Cnemophilus
Seicercus
Panurus
Daphoenositta
Machaerirhynchus
Erythrocercus
Artamu s
Rhipidura
Passer
Aegithina
Loboparadisea
Ploceus
Rhagologus
Prionops
Prunella
Sylvietta
Menura
Corvus
Hylia
Paradisaea
Lamprolia
Bleda
Sitta
Sylvia
Sturnus
Phylloscopus
Estrilda
Climacteris
Cisticola
Ptilonorhynchus
Oxylabes
Cinclosoma
Picathartes
Nicator
Monarcha
Lanius
Ptilorrhoa
Macrosphenus
Dulus
Coracina
Orthonyx
Pycnonotus
Vireo
Abroscopus
Eulacestoma
Malurus
Hyliota
Philesturnus
Peucedramus
Microeca
Psophodes
Regulus
Donacobius
Pnoepyga
Hirundo
Chaetops
Troglodytes
Vidua
Orthotomus
Parus
Pteruthius
Chloropsis
48
15
79
69
96
65
56
81
82
58
69
70
73
85
81
53
94
a) b)
Machaerirhynchus
Peucedramus
Hylia
Remiz
Timeliopsis
Oreocharis
Menura
Passer
Rhipidura
Falcunculus
Fringilla
Pomatostomus
Ploceus
Melanocharis
Promerops
Oedistoma
Cinclosoma
Nicator
Eopsaltria
Malurus
Hirundo
Cormobates
Daphoenositta
Erythrocercus
Troglodytes
Artamu s
Acanthorhynchus
Pteruthius
Ptilonorhynchus
Ailuroedus
Foulehaio
Bombycilla
Corvus
Chaetops
Orthotomus
Hyliota
Acrocephalus
Lamprolia
Regulus
Eremophila
Oriolus
Pericrocotus
Prionops
Microeca
Sylvia
Petroica
Dulus
Sturnus
Chloropsis
Cnemophilus
Seicercus
Culicicapa
Psophodes
Modulatrix
Meliphaga
Vireo
Orthonyx
Bleda
Lanius
Picathartes
Macrosphenus
Pardalotus
Leptocoma
Aegithalos
Oxylabes
Cisticola
Eulacestoma
Progne
Panurus
Oreoica
Tesia
Irena
Coracina
Philesturnus
Donacobius
Abroscopus
Struthidea
Chelidorhynx
Ptilorrhoa
Timalia
Prunella
Cinclus
Toxorhamphus
Muscicapa
Estrilda
Certhia
Pycnonotus
Loboparadisea
Phylloscopus
Sylvietta
Psaltriparus
Monarcha
Pachycephala
Vidua
Paradisaea
Pnoepyga
Climacteris
Parus
Sitta
Aegithina
Locustella
Mohoua
Motacilla
Rhagologus
60
98
70
83
75
96
99
81
79
77
36
87 99
98
79
97
60
98
99
Supplementary Figure 11. Phylogenetic relationships among oscines estimated using maximum likelihood with RAxML represented
as cladograms based on: a) 3839 UCE loci that do not overlap with chicken protein-coding genes, and b) the incomplete matrix
coded as purines and pyrimidines. Bootstrap support values are 100% unless otherwise indicated by numbers below nodes.
Red branches indicate conflicting relationships that are highly supported in both the tree and the maximum likelihood topology
inferred from the incomplete matrix (Supp. Fig. 1); blue branches indicate conflicting relationships that are not well-supported in
either the tree or the maximum likelihood tree inferred from the incomplete matrix (Supp. Fig. 1).

Supplementary Tables
Supplementary Table 1. Ancestral area estimation comparison. Results of
ancestral area estimation with BioGEOBEARS under alternative area coding schemes,
area constraints, and biogeographic models. Log likelihoods (LnL), parameter estimates
(d = dispersal rate; e = extinction rate; j = jump/founder-event speciation rate), and the
Akaike Information Criterion (AIC) are shown. In all comparisons, models featuring the
+j parameter were a better fit according to AIC.
Area coding
Area
constraint
Biogeographic
Model
LnL
No. of
Para-
meters
d
e
j
AIC
Clade full
distribution
None
DEC
-544.2919993
2
0.131400384
0.123329809
-
1092.583999
Clade full
distribution
None
DEC+J
-528.6732971
3
0.103637963
1.00E-12
0.01688541
1063.346594
Clade full
distribution
None
DIVALIKE
-565.4029502
2
0.120182614
0.277078875
-
1134.8059
Clade full
distribution
None
DIVALIKE+J
-532.5746137
3
0.108907772
1.00E-12
0.014450084
1071.149227
Clade full
distribution
None
BAYAREALIKE
-483.3219584
2
0.047713772
0.249787512
-
970.6439169
Clade full
distribution
None
BAYAREALIKE
+J
-466.3552156
3
0.051700667
0.091138618
0.011785616
938.7104312
Clade origin
None
DEC
-391.1692546
2
0.048852868
0.054179743
-
786.3385091
Clade origin
None
DEC+J
-362.2800311
3
0.037835844
1.00E-12
0.023833139
730.5600623
Clade origin
None
DIVALIKE
-397.4694434
2
0.053317122
0.043459414
-
798.9388868
Clade origin
None
DIVALIKE+J
-365.4133237
3
0.039545752
1.00E-12
0.021181363
736.8266475
Clade origin
None
BAYAREALIKE
-334.5106556
2
0.014200099
0.370286656
-
673.0213113
Clade origin
None
BAYAREALIKE
+J
-323.6850372
3
0.016332134
0.150878001
0.015600018
653.3700744
Clade full
distribution
NG not
allowed until
15 Ma
DEC
-506.2907659
2
0.711457737
0.644555593
-
1016.581532
Clade full
distribution
NG not
allowed until
15 Ma
DEC+J
-474.4742296
3
0.445973451
0.125331802
0.070592683
954.9484593
Clade full
distribution
NG not
allowed until
15 Ma
DIVALIKE
-535.3374764
2
0.721592752
0.926748808
-
1074.674953
Clade full
distribution
NG not
allowed until
15 Ma
DIVALIKE+J
-472.961273
3
0.455220043
0.114379615
0.066278442
951.9225459
Clade full
distribution
NG not
allowed until
15 Ma
BAYAREALIKE
-464.1330838
2
0.349147347
0.271151328
-
932.2661675
Clade full
distribution
NG not
allowed until
15 Ma
BAYAREALIKE
+J
-444.5458335
3
0.327167665
0.103364073
0.07203709
895.0916669
Clade origin
NG not
allowed until
15 Ma
DEC
-402.6531624
2
0.125853091
0.061071544
-
809.3063248
Clade origin
NG not
allowed until
15 Ma
DEC+J
-367.3593074
3
0.167763972
0.126837421
0.084607027
740.7186148
Clade origin
NG not
allowed until
15 Ma
DIVALIKE
-424.3742855
2
0.128864809
0.417048461
-
852.748571
Clade origin
NG not
allowed until
15 Ma
DIVALIKE+J
-368.433838
3
0.171331409
0.119036592
0.076647814
742.8676761
Clade origin
NG not
allowed until
15 Ma
BAYAREALIKE
-378.6732271
2
0.141160997
0.440416295
-
761.3464543
Clade origin
NG not
allowed until
15 Ma
BAYAREALIKE
+J
-355.7460358
3
0.132838557
0.125571944
0.082020975
717.4920716

Supplementary Discussion
Comparison of analytical methods
For ML analysis, a posteriori calculation of autoMRE indicated that bootstrapping
converged after 50 replicates. In Bayesian analyses, the average standard deviation of
split frequencies (ASDSF) dropped below 0.01 quickly (<< 1 million generations) and
remained at this level until runs were terminated (after a minimum of 5 million
generations with ASDSF below 0.01). After adjusting run settings (see Methods), chains
swapped frequently (adjacent chains ~0.2–0.5), but topology proposals were rarely
accepted (< 0.01). Likelihood values from four independent runs plateaued quickly and
stabilized in the same range. All potential scale reduction factor (PSRF) values were
close to one (0.99 < PSRF > 1.01) and all effective sample size values were greater
than 200. Rapid convergence among independent runs and the rarity of successful
topology proposals were likely caused by the strong phylogenetic signal from such a
large matrix. We removed the first 25% of generations as burn-in and summarized the
remaining runs in a majority rule consensus tree.
Analyses of the incomplete matrix (ML, Bayesian, and SVDquartets) produced highly
concordant results, and most nodes received strong support (Supplementary Figs. 1–2).
Only a single node differed between ML and Bayesian analyses (Supplementary Fig. 1;
see below). The species tree estimated by SVDquartets matched that of the
concatenated analyses more closely than gene tree-based coalescent methods (GCM;
Supplementary Fig. 2). Most conflicts between SVDquartets and concatenated
methods involved nodes with low support in one or both methods. However, the
relationships of three taxa (Paradisaea, Artamus, and Regulus) were strongly supported
and differed from ML/Bayesian inference. All three of these relationships involved short
internodes. Other discrepancies recovered in SVDQuartets, such as the placement of
Mohoua and Daphoenositta, were weakly supported. Notably, relationships of major
clades and deep lineages were congruent between SVDQuartets and concatenation
methods.
Maximum likelihood analysis of the complete matrix produced a phylogeny mostly
consistent with ML analysis of the incomplete matrix. As might be expected considering
the amount of data in each matrix (4155 loci in the incomplete matrix vs. 515 loci in the
complete matrix), some nodal support was lower with the complete matrix. However,
two relationships with low or marginal support in the analysis of the incomplete matrix
were resolved differently, but with higher support, with the complete matrix. The
relationships of Psophodes and Eulacestoma were unresolved with the incomplete
matrix, but these genera were inferred as sister taxa with 85% bootstrap support with

the complete matrix. Analysis of the complete matrix resulted in Regulus as sister to
the clade comprising Sitta, Troglodytes, and Certhia with 71% bootstrap support.
Conversely, analysis of the complete matrix resulted in Regulus as sister to
Dulus+Bombycilla with 85% bootstrap support. SVDQuartets analysis produced a third,
moderately supported relationship for Regulus (Supplementary Fig. 2). Thus, the
relationships of Regulus are best considered unresolved. The last discrepancy between
analysis of the complete and incomplete matrices involved a trio of genera (Locustella,
Donacobius, and Oxylabes) that produced conflicting relationships in all analyses (see
below).
ML analysis of the 3839 loci that did not contain protein-coding sequences recovered a
topology identical to that obtained when we included all loci with the exception of three
nodes that were not well-supported (Supplementary Fig. 11a). Likewise, we obtained a
similar topology from the “RY-coded” analysis as in our original analyses with the
exception of 5 nodes, 3 of which were not well-supported (Supplementary Fig. 11b). In
these two additional analyses, the minor conflicts do not affect our biogeographic
conclusions.
Gene tree-based coalescent methods (GCMs) produced species trees with much lower
support than concatenated methods and SVDquartets (Supplementary Fig. 3). We note
two important patterns in the species-tree results of GCMs – strong conflict among
species tree methods and a spurious, but predictable, placement of taxa that had
shorter average sequence lengths. For example, the placement of Mohoua differed
markedly between concatenated analyses and GCMs. Whereas concatenated
analyses yielded strong support for Daphoenositta and Mohoua as sister taxa and
embedded well within the Corvides, all GCMs placed Mohoua in a more basal position
as sister to the Corvides, sister to the Passerides, or even sister to the
Corvides+Passerides. DNA for Mohoua was extracted from the toepad of a museum
study skin, rather than from fresh tissue which we used for all the other species.
Although we recovered many UCE loci from the toe pad extraction, the sequences were
notably shorter than those from other samples (Supplementary Data 1). Samples
derived from fresh tissue that had shorter average locus lengths (e.g. Eulacestoma,
Modulatrix, and Macrosphenus) also had anomalous placements in species trees
(Supplementary Fig. 3). We hypothesized that missing data was causing this
discrepancy in phylogenetic placement, so we artificially shortened the sequences of
other taxa that had strong relationships in both concatenated and species-tree analyses
(Python code by C Oliveros). Shorter sequences had no effect on concatenated
analyses, but they substantially altered results in summary species tree methods; taxa
with shortened sequences were inferred to originate earlier in their clade, or even sister
to the whole clade (Supplementary Fig. 4). All disagreement between concatenated

and GCM analyses involved A) sequence length disparity, B) weakly-supported nodes,
or C) conflict among summary-species tree methods. Because none of the
concatenated results were unambiguously contradicted by GCM analyses, for the
remainder of the paper, we refer to the concatenated results.
All analyses produced conflicting results regarding the relationships among a trio of
taxa: Locustella lanceolata, Donacobius atricapillus, and Oxylabes madagascariensis
(Supplementary Figs. 1–3). Maximum likelihood analysis of the concatenated,
incomplete matrix produced strong support for Oxylabes as sister to the other two
species, whereas Bayesian and SVDQuartets analysis of the same matrix, and ML
analysis of the complete matrix, produced strong support for Locustella as sister to the
other two species. This discrepancy was the only difference between Bayesian and ML
analysis of the incomplete matrix. Three of the four GCMs (STAR, STEAC, and
ASTRAL) produced strong support for the third possible topology, with Donacobius
sister to the other two species (Supplementary Fig. 3). The fourth GCM (MP-EST)
recovered a sister relationship between Locustella and Oxylabes, but Donacobius was
more distantly related to the pair. Previous studies with greater taxon sampling within
these groups, but using fewer loci, produced a variety of moderately supported results.
Oliveros et al.1 found Donacobius sister to Locustellidae+Bernieridae (our GCM results),
whereas Alström et al.2 and Johansson et al.3 recovered Locustellidae sister to
Donacobius+Bernieridae (our Bayesian and SVDquartets results). Notably, the results
in Alström et al.2 were only supported by one of the five loci examined.
Discussion of phylogenetic relationships
Below, we restrict our discussion of phylogenetic relationships to the concatenated
results (Fig. 2, Supplementary Fig. 1), except where noted. We use higher level
classification names of Cracraft4 unless noted otherwise.
Our results at the base of the oscine phylogeny largely mirror previous studies5,6 with
Menuridae (Menura), Climacteridae+Ptilonorhynchidae (Cormobates, Climacteris,
Ptilonorhynchus, and Ailuroedus), and Meliphagoidea (Malurus, Pardalotus,
Acanthorhynchus, Timeliopsis, Foulehaio, and Meliphaga) branching in succession.
Claramunt and Cracraft7 recovered a novel relationship within Meliphagoidea, with
Meliphaga sister to Malurus+Pardalotus, but that is contradicted by our results and
other studies5,8. We find strong support for the sister pair of Orthonyx and
Pomatostomus as sister to the remainder of the oscines, in agreement with Claramunt
and Cracraft7. Previous studies have often recovered Orthonyx and Pomatostomus
branching sequentially5,9, whereas others have found the sister relationship we
recovered6,10–12. The next branch subtends a well-supported split into two large clades:

the Corvides and Passerides. Basal relationships within these two clades differ from all
previous studies.
Infraorder Corvides. The Corvides are subtended by a long branch and strongly
supported as monophyletic. At the base of the Corvides we recover strong support for
the sister pairing of Cinclosoma and Ptilorrhoa as sister to all other Corvides. Previous
studies have found Cinclosoma and/or Ptilorrhoa embedded well within the Corvides5,9–
12, except for Selvatti et al.6, which found the same relationship as the current study.
Claramunt and Cracraft7 recovered a very different arrangement of taxa at the base of
Corvides, with several putative passeridan lineages (e.g., Picathartidae,
Melanocharitidae, and Philesturnus) branching sequentially from the base of the clade.
The remaining Corvides are composed of five main clades separated by extremely short
internodes. These short internodes likely caused the disparate relationships within
Corvides among ours and previous studies. We found strong support for the sequential
branching of Campephagidae (Coracina+Pericrocotus), then Mohoua+Daphoenositta,
and three large clades. The campephagids, Mohoua, and Daphoenositta have
previously been placed in a variety of relationships in the Corvides. For example,
Aggerbeck et al.11 and Jønsson et al.12 found Mohoua sister to all other Corvides, but
not sister to Daphoenositta, which was embedded in a subclade within the Corvides.
Selvatti et al.6 placed these genera far apart in different subclades of the Corvides,
Jønsson et al.9 placed them both in unresolved positions at the base of the Corvides,
and Jetz et al.10 placed them embedded within different parts of the Corvides, but with
equivocal support. Claramunt and Cracraft7 found Mohoua and Daphoenositta sister to
Melanocharis and Vireo, respectively, which our results place far apart in the oscine
radiation.
We find strong support for three large clades in Corvides: a novel clade we call
superfamily Orioloidea, the whistlers and allies; Malaconotoidea, the shrike-like birds;
and Corvoidea, the crows and allies (Supplementary Fig. 1). We recover Eulacestoma,
Psophodes, Oreoica, Falcunculus, Pachycephala, Oriolus, Oreocharis, Pteruthius, and
Vireo in a strongly supported clade from Bayesian, maximum likelihood, and
SVDQuartets analyses (Supplementary Figs. 1–2). Malaconotoidea and Corvoidea are
subtended by long internodes, whereas the Orioloidea have an extremely short basal
branch and many short internodes within the clade. Aggerbeck et al.11 also found
support for three clades within their “Core-Corvoidea,” however, their placement of
several lineages differed from our results. For example, they found Campephagidae
(Coracina) was sister to the rest of the shrike-like birds (their clade Y), but we found
strong support for the placement of Campephagidae outside the Malaconotoidea.
Aggerbeck et al.11 also found support for a clade similar to our Orioloidea (their clade
X), but with additional taxa inside (e.g., Cinclosoma and Daphoenositta) that strongly
conflict with our results. Jønsson et al.9 recovered a weakly-supported clade comprising

fewer members than our Orioloidea. Instead, they found equivocal support at the base
of their “Core-Corvoidea” for taxa such as Eulacestoma, Oreocharis, and Psophodes.
The Corvides topology of Jetz et al.10 differs dramatically from our study
(Supplementary Fig. 5). For example, they recovered a clade of mostly Corvides taxa
that also contained taxa such as Callaeidae (Philesturnus), Cnemophilidae, and
Melanocharitidae, which we recovered as basal Passerides (see below). Furthermore,
none of our major Corvides clades (e.g., Orioloidea, Malaconotoidea, and Corvoidea)
are supported by Jetz et al.10 Instead, they recovered taxa within our Orioloidea
(Supplementary Fig. 1) scattered throughout their Corvides clade (Supplementary Fig.
5).
Infraorder Passerides. The Passerides form a clade comprising approximately one-third
of extant avian diversity, and relationships within this clade are notoriously difficult to
resolve5,6,13. Several lineages branch sequentially from the base of Passerides. These
lineages have all been lumped into a grouping called “transitional oscines” by previous
authors6,9,11 and include, Cnemophilidae (Loboparadisea+Cnemophilus),
Melanocharitidae (Melanocharis, Toxorhamphus, and Oedistoma), and Callaeidae
(Philesturnus). Our results support an expanded Passerides that includes these
aforementioned basal lineages because this clade is well supported across all analytical
methods. We follow the parvorder names of Cracraft4 to identify seven higher-level
clades within the Passerides (Supplementary Fig 1), Cnemophilida, Melanocharitida,
Eupetida, Petroicida, Muscicapida, Passerida, Sylviida. We sampled only one genus
from Callaeidae (Philesturnus), so we refrain from identifying a parvorder for this group.
The next branch subtends a clade comprising sister taxa Picathartidae+Chaetopidae
(Parvorder Eupetida), which is sister to Parvorder Petroicida (Petroica, Eopsaltria, and
Microeca). Our finding of Eupetida sister to Petroicida is unique among recent studies5–
7,9–11.
The next clade is subtended by a long branch and comprises the major groups of
Passerides: Parvorders Muscicapida, Passerida, and Sylviida; the latter is sister to
Muscicapida+Passerida. This clade is informally referred to as the “Core-Passerides”
(Fig. 1, Supplementary Fig. 1). Muscicapida contains four successive sister lineages:
Superfamilies Bombycilloidea (Bombycilla and Dulus), Muscicapoidea (Cinclus,
Muscicapa, and Sturnus), Reguloidea (Regulus) and Certhioidea (Sitta, Troglodytes,
and Certhia), but see above for discussion of alternative placements of Regulus within
Muscicapida.
The first branch within Passerida subtends two African lineages, Promeropidae
(Promerops)+Arcanatoridae (Modulatrix). The Nectarinidae (Leptocoma) are sister to a
pair of SE Asian families, Irenidae (Irena) and Chloropseidae (Chloropsis). The
remainder of this clade comprises what Cracraft4 called “‘core’ passeridans,” which

includes the monotypic Peucedramidae (Peucedramus) through Fringilla+Motacilla.
Peucedramus is the earliest diverging lineage, followed by a diverse clade of Old World
taxa comprising ploceid weavers and viduid and estrildid finches—Ploceoidea, sensu
Cracraft4. This clade is sister to a clade composed of Prunellidae (Prunella), Passeridae
(Passer), Fringillidae (Fringilla), and Motacillidae (Motacilla).
Parvorder Sylviida is the third major clade of Passerides. The first branch subtends a
novel sister relationship: Hyliotidae (Hyliota)+Stenostiridae (Culicicapa and
Chelidorhynx). Previous studies placed Hyliota as an unresolved lineage near the base
of the Passerides3,14. Analysis of full mitochondrial genomes15 found moderate support
for a sister relationship between Hyliota and Poecile, but total sampling was sparse and
Stenostiridae was not sampled. The next series of sequentially sister lineages are
represented by a clade of Paridae (Parus)+Remizidae (Remiz), followed by Panuridae
(Panurus)+Alaudidae (Eremophila); the latter clade is referred to as Superfamily
Alaudoidea by Cracraft4. The next two branches represent African radiations:
Nicatoridae (Nicator) followed by Panuridae (Panurus)+Alaudidae (Eremophila); the
latter clade is referred to by Cracraft4 as Superfamily Alaudoidea. Remaining lineages in
Sylviida have received considerable attention with little consensus of branching
pattern13. Here, we found high support for many relationships; however, short
internodes left some relationships along the backbone equivocal. For example,
relationships among four lineages were equivocal, including branches subtending 1)
Cisticolidae (Cisticola and Orthotomus); 2) Bernieridae (Oxylabes), Locustellidae
(Locustella), and Donacobiidae (Donacobius), but see above for alternative topologies
in this clade; 3) Acrocephalidae (Acrocephalus) and Pnoepygidae (Pnoepyga); and 4)
Hirundinidae (Progne and Hirundo). Finally, a large and diverse clade was recovered.
Within this clade, we found support for a major split between Pycnonotidae (Bleda and
Pycnonotus), Timaliidae and allies (Timalia), and Sylviidae (Sylvia) from Phylloscopidae
(Phylloscopus and Seicercus), Hyliidae (Hylia), Aegithalidae (Psaltriparus and
Aegithalos), Erythrocercidae (Erythrocercus) and Cettiidae (Tesia and Abroscopus).
Jetz et al.10 used a hybrid super-tree/super-matrix approach with topological constraints
to reconstruct a phylogeny of all bird species, which subsequently formed the
phylogenetic basis of several influential analyses of bird evolution16–20. Because Jetz et
al.10 included all bird species, our results can be compared directly to their phylogeny.
We computed a consensus tree from 1,000 trees with the “Hackett” constraints
downloaded from birdtree.org/subsets, limiting the species to those we included in our
analysis (Supplementary Fig. 5). Many strongly supported differences are apparent at
all levels of the oscine phylogeny, especially in Corvides, placement of transitional
Oscine lineages, and basal relationships in Passerides. To quantify concordance
between the two trees, we calculated the normalized Robinson-Foulds metric21 in Paup,
ver. 4.0a14622, with a result of 0.438. This value means that ~44% of the bipartitions

found in the two trees are unique to only one of the trees. This large discrepancy likely
relates to the disparate approaches of the two studies. Jetz et al.10 analyzed a large,
sparse super-matrix from relatively few markers whereas we analyzed a massive
character matrix for a limited number of samples.
Discussion of divergence time estimates
Dates derived from the Jarvis et al.23 secondary calibrations (Fig. 1) differed slightly
from those produced with the Prum et al.24 secondary calibrations (Supplementary Fig.
6), but 95% highest posterior density intervals broadly overlapped. For example, we
inferred the base of the Corvides as 21.9 Ma (CI: 19.8–24.0 Ma) with the Jarvis et al.23
calibrations, but 24.3 Ma (CI: 20.8–28.2 Ma) with the Prum et al.24 calibrations.
Important to our discussion of biogeographic history, the two methods broadly agree
about the timeframe of oscine diversification. Although we inferred some nodes as
latest Oligocene with the Prum calibrations, compared to earliest Miocene with the
Jarvis calibrations, the earliest inferred dispersal events out of Australasia cluster
around the initial uplift of Wallacea with both sets of calibrations.
We compared these results to oft-cited rates of mitochondrial DNA evolution in birds.
Sequence capture techniques produce reads from non-target regions such as the
mitochondrial genome. We assembled mitochondrial genomes from cleaned reads
using the program ARC (https://ibest.github.io/ARC/) using the mitochondrial genome of
Vidua chalybeata (GenBank AF090341) as a reference. We aligned contigs of
mitochondrial genomes to the annotated reference genome using Geneious ver. 6.1.2.
From these alignments, we extracted gene sequences of NADH subunit 2 (ND2) and
cytochrome b (cytb) for each individual. We estimated rates of mitochondrial evolution
in ND2 and cytb using the calibrated ultrametric UCE topology in BEAST 2.225. We
selected a separate uncorrelated lognormal relaxed clock for each gene. We partitioned
each mitochondrial gene by codon position, and for each partition, we selected the
GTR+G model and estimated base frequencies. We executed two independent 1x108
generation MCMC runs, each sampled every 1x105 generations. We removed the first
25% of posterior samples as burnin, and we assessed MCMC convergence and
stationarity in Tracer ver. 1.626. For each gene, we then calculated the mean
substitution rate estimate and its 95% highest posterior density interval from the post-
burnin posterior distribution.
Using our topology and time estimates, we recovered a divergence rate of 2.3% per
million years for cytochrome b (CI 2.20%–2.42%) and 3.2% per million years for ND2
(CI 3.08%–3.34%). These estimates are faster than the 2% average rate cited for birds

but fall well within the range of rates estimated empirically from a variety of avian
taxa27,28.
Discussion of ancestral range estimates
We focus discussion of biogeographic results on four important clades: all Oscines, the
Corvides, the Passerides, and the Core-Passerides. Ancestral range estimates for
these clades using their full distribution or their inferred origin produced almost identical
results. Model selection with AIC indicated that the DEC-LIKE+j model was a better fit
than DEC-LIKE, and therefore we present results of reconstructions using full clade
distributions and the DEC-LIKE+j model (Fig. 2, but see examples under different
modeling choices Supplementary Figs. 7–10).
Given the DEC-LIKE+j model, biogeographic analyses estimated the ancestral range of
all oscines as Australia. An Australian origin of oscines has been consistently recovered
in other studies as well5,9,11. The estimated ancestral ranges of Corvides and
Passerides varied mainly depending on whether the 15 Ma constraint on New Guinea
was used. Without the constraint, the ranges of both nodes were estimated to be New
Guinea. However, when a New Guinea range prior to 15 Ma was disallowed, the ranges
of both nodes were reconstructed as Australia (Fig. 1). A New Guinea origin for these
clades have been found by other authors9,11 but their results rely on two important,
albeit questionable, assumptions. First, these studies assume an older age for these
nodes (~30–45 Ma), which appears to be too old based on more recent and
independent estimates of the timing of avian diversification23,24. The second
assumption is that small, ephemeral proto-Papuan islands existed and were biologically
relevant for ancestral range estimation. Our study is the first to estimate an Australian
ancestral range for these two clades, which we believe is a more plausible alternative to
the proto-Papuan origin hypothesis for these groups because of its consistency with
paleogeographic reconstructions and the oscine fossil record (see below). Origin of the
core-Passerides, the first major oscine clade to radiate outside of Australasia, also
depended on presence or absence of the 15 Ma New Guinea constraint. With New
Guinea constrained, we inferred a SE Asian origin of the core-Passerides, followed by a
rapid radiation and multiple dispersals into the Palaearctic and sub-Saharan Africa.
Without a constraint, the origin of this clade was reconstructed as sub-Saharan Africa.
Using alternate models (Supplementary Table 1), biogeographic reconstructions were
similar to those inferred with the DEC-LIKE+j model. Identical to results from the DEC-
LIKE+j model (Fig. 1), DIVA-LIKE+j (S7) and BAYAREA-LIKE+j (S8) models with New
Guinea emergence constrained also inferred Australian origin of oscines, Corvides, and
Passerides, as well as the SE Asian origin of Core-Passerides. The only substantial
differences between models were found when analyses allowed emergence of New

Guinea prior to 15 Ma, when the BAYAREALIKE and BAYAREALIKE+J models yielded
Australia+New Guinea or Australia+New Guinea+S and SE Asia for Oscines, Corvides,
and Passerides. However, these models assume all cladogenesis occurs within, rather
than between designated areas, an unrealistic assumption likely violated in songbirds.
Paleogeography of Wallacea and Australasia
Wallacea comprises a composite geological landscape that assembled within a
boundary zone of extensive tectonic convergence between the Australian, Pacific, and
Eurasian plates. As such, the geotectonic history of this ecoregion is exceptionally
complex, with virtually all known surface and mantle processes locally active during the
Cenozoic29–31. Although knowledge and understanding of this regional geodynamic
complexity is far from complete, recent advances in resolving the broad-scale geological
assembly of Wallacea has provided an important spatio-temporal framework for testing
biogeographic hypotheses and exploring the potential role of this insular system in
linking Australasian biotas with Southeast Asia and beyond32.
Australia’s separation from Antarctica was largely complete by the Late Cretaceous, yet
these East Gondwanan fragments remained in close proximity well into the
Paleogene33. Tectonics in this region shifted dramatically in the Late Eocene (~45 Ma)
as seafloor spreading ended in the Tasman and Coral Seas but accelerated along the
Southeast Indian Ridge (SIR), starting Australia’s rapid progression north towards its
present-day position34. This, in turn, led to subduction of oceanic lithosphere at the Java
trench, which continued throughout the Oligocene, steadily reducing the vast expanse
of open ocean between Australasia and Sundaland29. During this period, emergent land
within Wallacea was limited to portions of West Sulawesi and a volcanic arc of small
isolated islands to the east that remained separated from the Australian continental
margin by a deep-sea passage spanning hundreds of kilometers.
Extensive land formation in Wallacea was initiated in the Early Miocene (~ 23 Ma) due
to tectonic collision between proto-Sulawesi fragments and the Sula spur, an Australian
continental promontory extending northwest from the Bird’s Head region of present-day
New Guinea30,31. Continued convergence at this collisional boundary resulted in
widespread island formation and orogenic uplift in portions of Sulawesi, providing the
first links between Australasia and Sundaland, albeit in the form of island chains and not
a continuous land bridge. This increased connectivity was short-lived however, and by
15 Ma subduction rollback in the region caused much of the newly formed land to
subside, decreasing land area across Wallacea29,30,32. Consequently, the most likely
window for dispersal from Australia to SE Asia spanned roughly 23–15 Ma. This

reduction of land area during the Miocene may explain the absence of relictual oscine
lineages in Wallacea that would lend support for such a colonization history.
As subsidence continued in Wallacea and extensional deformation began fragmenting
the Sula spur into the Banda embayment during the mid-Miocene, bulldozing of pre-
collisional complexes along the Australian and Pacific tectonic boundary promoted the
development of small subaerial islands in the vicinity of present-day New Guinea
around 15 Ma35,36. Considerable debate and uncertainty remain with respect to the
timing and geotectonic processes that drove New Guinea’s rapid and complex
orogenesis, but paleogeographic models generally agree that only ephemeral, low-lying
islands and carbonate platforms existed in the region until uplift of the Central Dividing
Ranges (CDR) began in the Late Miocene35 or Pliocene37, with the possible exception
of limited early uplift in the Papuan Peninsula during the Oligocene35,36. The latter
hypothesis for an early Papuan Peninsula orogeny appears exceedingly unlikely, as
there is no biogeographic evidence to support such an early terrestrial history in the
region38. van Ufford’s36 model for development of the CDRs suggests uplift initiated
around 12 Ma due to under-thrusting of Australian continental basement and bulldozing
of passive-margin strata, followed by early stage collisional orogenesis at about 8 Ma
that gave rise to much of the extensive New Guinea highlands by 5 Ma. This hypothesis
differs substantially from that of Hill and Hall37, who posit that New Guinea remained
largely submerged until about 5 Ma, when a shift in tectonic motions initiated
convergence between the Australian and Pacific plates, leading to rapid uplift of the
fold-and-thrust montane belt that comprises the CDRs. Despite the profound
differences between these competing tectonic models, it is now clear that New Guinea’s
remarkably recent geological development and rapid orogeny largely precludes the
island from playing a significant role in early Oscine diversification and dispersal out of
Australia.
Paleontological context
Although the oscine fossil record is sparse, and few taxa are placed phylogenetically,
our timeframe and biogeographic hypothesis for oscine diversification agrees broadly
with Mayr’s39 review of paleontological constraints on passerine evolution. Our data
indicate that crown oscine lineages first reached Asia at the Oligocene-Miocene
transition and dispersed worldwide shortly thereafter. The earliest oscine fossils from
the northern hemisphere are from late Oligocene Europe40,41, but they have not been
identified as either crown or stem lineages. The earliest passerine fossils from Africa42
and the New World43,44 are from the Miocene.

Paleoecology and evolution of the Australasian mesic biota
We propose that oscine songbirds initially diversified in isolation on the Australian plate,
with dispersive elements subsequently colonizing Southeast Asia and other regions of
the globe in the Early Miocene when tectonic collision and uplift in Wallacea produced
newly emergent islands that enabled biotic interchange between Australasia and
Sundaland. Although unconstrained biogeographic reconstructions indicate that many
of these early oscine lineages originated in New Guinea (Supplementary Fig. S7), we
interpret this result as a bias associated with the severe Miocene aridification of
Australia and wholesale reduction of its mesic biota45, as the New Guinea region largely
remained submerged until the Late Miocene or Early Pliocene35,37.
Cool subtropical environments persisted across much of the Australian continent during
the Eocene to Early Oligocene, harboring diverse rainforest communities with strong
Gondwanan affinity. As Australia drifted to warmer latitudes, its climate gradually shifted
and periods of drought became more pronounced, resulting in the first signs of
contraction among rainforest habitats by the Late Oligocene46,47. Widespread
aridification intensified around the mid-Miocene climatic optimum, driving Australia’s
once extensive mesic biome into small refugia along the eastern coast, further
compounding the sharp decline and extinction of rainforest-adapted taxa that was
already underway45,48. Importantly, the concomitant development of New Guinea’s
emerging highland landscape in the Late Miocene provided a vast new refuge for these
relictual lineages to colonize along Australia’s northern continental margin, which likely
prevented extinction of numerous temperate and subtropical groups. Thus, in many
respects, the rich montane biota that now inhabits the New Guinea highlands provides a
unique window to Australia’s past, and some of the early ancestral Gondwanan lineages
that once characterized its subtropical rainforest environments. We suggest that this
regional paleoclimatic history likely explains the presence of early oscine lineages in
New Guinea that predate the island’s recent geological development. Prime examples
of lineages exhibiting long and bare branches indicative of this relictual hypothesis
include the New Guinea endemic Satinbirds (Cnemophilidae) and Berrypeckers
(Melanocharitidae), as well as several endemic monotypic genera within the Corvidan
radiation (Eulacestoma, Oreocharis, and Rhagologus), all montane taxa that arose prior
to the emergence of New Guinea’s central cordillera.
Although this hypothesis differs markedly from recent studies of oscine
diversification5,9,11,12, our results strongly corroborate an earlier hypothesis developed by
Schodde49 that has largely been overlooked because of incongruent temporal
frameworks or unconstrained biogeographic analyses. Schodde and colleagues49–51
examined the distribution and community composition of Australasian avifaunae in the
context of regional tectonic history, paleoecology, and phylogeny. They identified an

ancestral “Tumbunan” avifauna endemic to subtropical montane forests of New Guinea
and a narrow corridor of rainforest refugia along the northeastern Australian coast. This
community is diverse and elevationally structured within New Guinea, but comparatively
depauperate in Australia. Schodde49 hypothesized that aridification of Australia likely
depleted the once widespread wet-adapted communities, which subsequently found
refuge in New Guinea during its rapid orogenesis in the Late Miocene to Early Pliocene.
Schodde and Christidis51 questioned the hypothesis that New Guinea comprises the
area of initial diversification of Corvides9,11,12, citing geological, temporal, and
distributional inconsistencies, and concluded that New Guinea was more likely a refuge
for relictual lineages as opposed to a “launch pad” for the corvoid radiation.
This signal of impoverishment and extinction among some early oscine lineages is part
of a larger biogeographic pattern that is widely manifest in the Australasian mesic biota,
suggesting a number of non-avian groups were similarly impacted by the mid-Miocene
aridification of Australia. Byrne et al.45 documented the decline of Australia’s mesic biota
throughout the Neogene, with the most extensive extinctions and range restrictions
occurring in taxa associated with temperate and subtropical rainforest environments.
The palynological record for Australia provides some of the clearest evidence of this
dramatic and large-scale biotic restructuring45,47. For example, the Nothofagus
subgenus Brassospora was once widespread among Australian subtropical rainforest
environments during the Eocene to Early Oligocene. Macrofossils from Brassospora
have been recovered in Australia that date to the Oligocene, and Brassospora pollen
has been recorded on the continent as recently as 2 Ma. Although this drought-
sensitive clade is now extinct in Australia, several Brassospora species remain a central
component of humid mid-montane forests throughout New Guinea. A similar pattern is
seen in some Australasian conifers (Podocarpaceae), with Dacrydium and Dacrycarpus
formerly common among subtropical environments in Australia, and members of the
later genus persisting until the late Pliocene along the southern coast52. Both genera are
now ubiquitous across the New Guinea highlands.
The fossil record for Australasian mammals is far more extensive than that for birds,
and highlights several robust examples of wet-adapted marsupial clades that went
extinct in Australia during the Miocene or Early Pliocene, but have persisted in New
Guinea’s extensive rainforest habitats48,53. The Dactylopsine possums (Petauridae)
were once thought to originate in New Guinea, which comprises their present-day
center of diversity, but fossils of an undescribed species of Dactylopsila from the Late
Oligocene to mid Miocene deposits at the Riversleigh site in Queensland now indicate
an Australian origin for the group54. The Phalangerids (cuscuses, brush-tailed possums,
and scaly-tailed possums: Phalangeridae) are the most diverse of the Australasian
possum families with 19 of the 23 species present in the New Guinea region. Although
the distribution of present-day diversity suggests that the clade arose in New Guinea,

the presence of multiple cuscus species and at least one scaly-tailed possum taxon
from the Early Miocene deposits at Riversleigh indicate that an Australian origin is
equally if not more likely48,53. A similar pattern is seen in the endemic forest wallabies
(Dorcopsulus and Dorcopsis: Macropodidae) of New Guinea, which include two and
three species respectively, yet an extinct Dorcopsis species has been described from a
Pliocene fossil bed in western Victoria and multiple fossil specimens of a closely related
forest wallaby (Dorcopsoides fossilis) has been described from the Late Miocene site of
Alcoota in the Northern Territory53. We predict that as additional Miocene to Early
Pliocene fossil sites are uncovered, further evidence of this general biogeographic trend
within the Australasian mesic biota will become apparent in other marsupial groups
such as the echymiperin and peroryctin bandicoots (Peramelidae), which are thought to
have originated in Australia and secondarily diversified in the rainforests of New
Guinea55.
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