supplementary information - media.nature.com · acciptridae, strigiformes, caprimulgidae and...

Diversification analyses:

Table S1. Sampling for diversification analyses

Table S2. Summary statistics for diversification analyses

Figure S1. Effects of sampling fraction and phylogenetic uncertainty on diversification analyses.

Posterior distributions accounting for sampling fraction, both sampling fraction and

phylogenetic uncertainty, or neither for the three groups most sensitive to these effects

(Striginae+Suriinae, Falconidae, Caprimulgidae)

Supplementary Note: Effects of differences in sampling levels for CP and non-CP taxa on

speciation and transition rates and tip branch length estimates.

Phylogenies:

Supplementary Methods: Detailed phylogenetic methods and key references for molecular

phylogenetic data

Table S3. Number of sites and accessions for each gene used in each family-level phylogeny

Table S4. Number of sites, accessions and proportion of taxa with each gene for passerine

phylogeny

Table S5. List of genes for all phylogenies

Table S6. Datamatrix summary statistics and node support

Table S7. Proportion of tips and internal nodes with mitochondrial and nuclear genes for each

phylogeny

Figure S2. Genes contributing information across the depth of the passerine phylogeny

Figures S3-S7. Phylogenies for the Accipitridae, Strigiformes, Caprimulgiformes, Falconidae and

Galliformes.

SUPPLEMENTARY INFORMATIONdoi:10.1038/nature11050

WWW.NATURE.COM/NATURE | 1

Table S1. Sampling for diversification analyses

Group Sub-group Taxonomy Data Sampling fraction

all CP Proportion CP all CP non-CP CP

Accipitridae 250 53 0.21 178 43 0.69 0.81

Buteonines & Sea Eagles 71 17 0.24 68 17 0.94 1.00

Strigiformes 220 61 0.28 108 45 0.40 0.74

Striginae & Surniinae 174 59 0.34 92 44 0.42 0.75

Surniinae 39 12 0.31 23 8 0.56 0.67

Striginae 138 47 0.34 69 36 0.36 0.77

Caprimulgidae 92 21 0.23 57 15 0.59 0.71

Falconidae 65 9 0.14 50 9 0.73 1.00

Phasianidae 181 15 0.08 130 12 0.71 0.80

Taxonomy and sampling based on IOC 2.4 species. Data and sampling fraction show the absolute numbers

and proportions of species in the molecular phylogenies used for diversification analyses.

SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature11050


Tab

le S

2. S

um

ma

ry s

tati

stic

s fo

r d

ive

rsif

icat

ion

an

alys

es.

Ti

p

bran

ch

leng

ths

Phyl

ogen

etic

clus

terin

g

BiS

SE

div

ersi

ficat

ion

anal

yses

M

axim

um L

ikel

ihoo

d Ba

yesi

an M

CM

C

Gro

up

Sub-

grou

p

all/C

P

ratio

MP

step

s

Pro

porti

on

resh

uffle

s

with

MP

step

s ≤

CP

λ 1/λ

0∆

lnL

p

q 10/

q 01

∆ln

L p

q 10/ λ 1

µ/λ

λ 1/λ

0

Pro

porti

on

of s

teps

with

λ1≤λ 0

q 10/q

01

Pro

porti

on

of s

teps

with

q 10≤

q 01

q 10/

λ1

µ/λ

Acci

pitri

dae

0.

88

30/4

3 0.

001

2.71

9.

49

1.3E

-05

6.92

12

.75

4.4E

-07

0.95

1.

4E-0

52.

83

<0.0

001

6.18

<0

.000

1 1.

00

0.17

Bu

teon

ines

+

Sea

Eagl

es

0.63

12

/17

0.02

3 3.

96

9.99

7.

8E-0

621

.83

6.71

2.

5E-0

4 0.

69

2.9E

-07

4.42

<0

.000

1 12

.39

<0.0

001

0.73

0.

25

Stri

gifo

rmes

0.84

26

/45

0.00

2 1.

36

0.56

0.

2910

15.4

610

.05

7.3E

-06

0.59

3.

7E-0

71.

57

0.06

48

10.1

0 0.

0018

0.

62

0.10

Strig

inae

+Sur

niin

ae

0.82

25

/44

0.02

0 1.

97

2.15

0.

0379

>>10

7.78

8.

0E-0

5 0.

64

7.7E

-07

1.99

0.

0453

4.

42

0.00

40

0.64

0.

16

Su

rniin

ae

0.67

5/

8 0.

088

5.40

3.

61

0.00

72>>

103.

15

0.01

20

0.64

6.

6E-0

65.

11

0.00

46

6.91

0.

0025

0.

78

0.36

St

rigin

ae

0.94

20

/36

0.09

9 0.

48

0.36

0.

3992

1.61

0.

64

0.25

73

2.73

1.

9E-0

80.

38

0.90

81

1.39

0.

2795

0.

76

1.12

Cap

rimul

gida

e

0.86

12

/15

0.18

5 4.

58

5.04

0.

0015

>>10

5.32

0.

0011

0.

75

2.5E

073.

84

0.13

18

9.51

0.

0113

0.

69

0.14

Falc

onid

ae

0.

62

9/9

1.00

0 3.

19

0.55

0.

5763

7.79

2.

14

0.03

86

1.93

5.

3E07

2.03

0.

2960

5.

27

0.01

40

2.4

0.17

Phas

iani

dae

1.

19

11/1

2 0.

294

0.13

0.

97

0.16

328.

04

0.35

0.

4057

4.

71

9.3E

050.

38

0.84

58

6.36

0.

0417

13

.3

2.00

CP

= C

olou

r Pol

ymor

phic

spe

cies

= s

tate

1, n

on-C

P =

sta

te 0

. Ana

lyse

s us

e B

EA

ST

trees

, cal

ibra

ted

to a

n ar

bitra

ry m

ean

rate

of 0

.01,

ther

efor

e ab

solu

te v

alue

s of

rate

par

amet

ers

are

arbi

trary

an

d un

ique

to e

ach

maj

or g

roup

and

sho

uld

not b

e co

mpa

red.

Bay

esia

n an

alys

es (M

CM

C) u

se 5

0 BE

AST

sam

ple

trees

with

100

0 st

ep M

CM

C e

ach

(= p

ool o

f 50,

000

step

s). A

ll ot

her a

naly

ses

use

the

BE

AS

T m

edia

n no

de h

eigh

t max

imum

cla

de c

redi

bilit

y (M

CC

) tre

e. T

he M

P s

teps

col

umn

show

s th

e ob

serv

ed n

umbe

r of m

axim

um p

arsi

mon

y in

ferre

d ch

ange

s fo

r the

CP

sta

te, w

ith th

e m

axim

um p

ossi

ble

num

ber o

f cha

nges

afte

r the

forw

ard

slas

h. T

he p

ropo

rtion

of r

eshu

ffles

with

MP

ste

ps ≤

CP

refe

rs to

the

frequ

ency

that

rand

omis

atio

ns s

how

gre

ater

than

or e

qual

clu

ster

ing

than

obs

erve

d. P

hylo

gene

tic c

lust

erin

g an

alys

es w

ere

done

in M

esqu

ite u

sing

100

0 ra

ndom

isat

ions

. BiS

SE

div

ersi

ficat

ion

rate

ana

lyse

s us

ing

Div

ersi

tree

0.6-

1 an

d 0.

7-6,

with

sam

plin

g fra

ctio

n.

λ 1 =

spe

ciat

ion

rate

for s

tate

1 (C

P), λ 0

= s

peci

atio

n ra

te fo

r sta

te 0

(non

-CP

). S

peci

atio

n ra

te ra

tio =

λ1/λ

0. Tr

ansi

tion

away

ratio

= q

10/q

01 =

ratio

of t

rans

ition

rate

from

CP

to n

on-C

P, o

ver t

he

trans

ition

rate

from

non

-CP

to C

P. ∆

lnL

= lo

g lik

elih

ood

diffe

renc

e be

twee

n op

timal

and

equ

al s

peci

atio

n ra

te m

odel

s. P

= p

roba

bilit

y th

at e

qual

rate

mod

el is

wor

se fi

t, by

AN

OV

A P

r(>|C

hi|)

6 vs

5

d.f.

q 10/λ

1 is

the

ratio

of t

he tr

ansi

tion

rate

aw

ay fr

om p

olym

orph

ism

to th

e sp

ecia

tion

rate

for t

he p

olym

orph

ic s

tate

: the

se tw

o ra

tes

are

gene

rally

of s

imila

r mag

nitu

de (r

atio

clo

se to

one

). C

P

µ/λ

is th

e ra

tio o

f ext

inct

ion

rate

µ to

spe

ciat

ion

rate

λ fo

r the

col

our p

olym

orph

ic s

tate

. Rat

ios

are

subs

tant

ially

less

than

one

(in

all b

ut tw

o in

stan

ces)

indi

catin

g m

uch

high

er s

peci

atio

n ra

te th

an

extin

ctio

n ra

te.

Cap

rim

ulg

idae

Stri

gin

ae+

Surn

iinae

Falc

on

idae

Figu

re S

1. E

xam

ples

of t

he e

ffect

of a

ccou

ntin

g fo

r sam

plin

g fra

ctio

n an

d ph

ylog

enet

ic u

ncer

tain

ty in

pos

terio

r dis

tribu

tions

of B

ISS

E s

peci

atio

n ra

te; l

ambd

a0 =

mon

omor

phic

sp

ecie

s, la

mbd

a1 =

col

our p

olym

orph

ic s

peci

es. T

op: 2

0,00

0 st

ep M

CM

C u

sing

BE

AS

T m

edia

n M

CC

tree

with

no

sam

plin

g fra

ctio

n; m

iddl

e: a

pply

ing

sam

plin

g.f =

kno

wn

taxo

n sa

mpl

ing

for e

ach

clas

s (0

,1);

botto

m: p

ool o

f 100

0 st

eps

for e

ach

of 5

0 B

EA

ST

sam

ple

trees

(with

sam

plin

g fra

ctio

n). D

iver

sitre

e 0.

6-1;

exp

onet

ial p

rior 1

/(2r)

; opt

imiz

ed s

tep

size

(w);

MC

MC

sta

rting

with

ML

para

met

er v

alue

s. N

umbe

r of s

peci

es a

nd s

ampl

ing

fract

ion

in e

ach

cate

gory

(0,1

): Fa

lcon

idae

41/

9, 0

.73/

1.00

; Stri

gina

e+S

urni

inae

48/

44, 0

.42/

0.75

; C

aprim

ulgi

dae

42/1

5, 0

.59/

0.71

. S

ampl

ing

fract

ion

mos

tly h

ad a

qua

ntita

tive

effe

ct, w

eake

ning

app

aren

t sig

nific

ance

leve

l, in

crea

sing

any

bim

odal

tren

d in

pos

terio

r dis

tribu

tion.

Effe

ct in

Acc

ipitr

idae

and

Pha

sian

idae

w

as n

eglig

ible

(not

sho

wn)

. Phy

loge

netic

unc

erta

inty

had

a n

eglig

ible

effe

ct. S

ome

anal

yses

gav

e un

stab

le re

sults

pro

babl

y du

e to

lim

ited

taxa

and

mul

ti-m

odal

like

lihoo

d su

rface

, as

seen

in b

oth

Bay

esia

n an

d M

L m

etho

ds (e

.g. F

alco

nida

e). A

lthou

gh th

ere

may

be

limita

tions

to th

e B

iSS

E m

etho

d, re

sults

qua

litat

ivel

y m

atch

thos

e tip

bra

nch

leng

th re

sults

(Tab

le S

2).

No

sam

plin

g

Sam

plin

g fr

acti

on

an

d p

hyl

og

enet

ic

un

cert

ain

ty

Sam

plin

g

Supplementary Note

In order to gauge the effect of the difference in sampling of CP and non CP species on

relative speciation and transition rates we randomly sub-sampled the CP species to give equal

CP and non CP species sampling fractions (Table S1). We repeated this ten times each for the

Acciptridae, Strigiformes, Caprimulgidae and Falconidae phylogenies, and calculated median

parameter estimates from the MCMC samples and average tip branch lengths. In all cases, the

trend is the same as for the more complete sampling but with greater variance due to the

weakened sampling. For the Acciptridae, Strigiformes, Caprimulgidae and Falconidae

respectively, the speciation ratios λi/λ0 are 3.2, 1.6, 4.5 and 1.1, the transition ratios q10/q01

are 8.0, 5.7, 11.9 and 5.8 and the tip branch length ratios CP/non CP are 0.88, 0.80; 0.82 and

0.59.



Supplementary Methods

We used Hackett et al.31 as the overall high level phylogenetic framework demarking major

groups and suitable outgroups, and further within family nomenclature follows that used in

the key references for molecular phylogenetic data and inference (listed below). We

constructed species-level phylogenies for groups containing the highest proportions and/or

absolute numbers of polymorphic species. These are the Accipitridae, Strigiformes,

Caprimulgiformes, Falconidae and Galliformes. We then identified monophyletic, well-

sampled, biologically and phylogenetically coherent groups within these phylogenies for

diversification analyses. This resulted in the exclusion of certain clades within some of these

groups due to their phylogenetic distinctiveness, poor sampling and/or because they

contained few or no CP species. Thus, we restricted our diversification analyses to the clade

containing the Striginae and Suriinae within the Strigiformes; to the Caprimulgidae within the

Caprimulgiformes and to the Phasianidae within the Galliformes. We also constructed several

very large phylogenies for the Passeriformes.

Genes were chosen on the basis of the density of coverage and therefore datasets are by-and-

large combinations of previously published studies, listed in the key references below.

Additional details are provided on the passerine data as these are more complex. Tables S3-5

provide information on genes and GenBank accessions used in the sequence alignments,

while Tables S6-7 and Figure S2 provide summaries of node support, gene density and

coverage across phylogenetic levels. Trees in newick format (with node support values) are

proved as a supplementary text file, and the Accipitridae, Strigiformes, Caprimulgiformes,

Falconidae and Galliformes trees shown in Figures S3-7.

Sequences were aligned with Clustal programs36, either desktop ClustalX or via the EMBL

Clustal Portal (http://www.ebi.ac.uk/Tools/msa/clustalw2). For all but some passerine dataset

introns alignment was straightforward. For the more complex cases a three-stage strategy was

used: a first alignment to identify sequences with large insertions and/or inversions, followed

by a second alignment with iteration, and then subsequent deletion of some chaotic sections.

Preliminary phylogenies for each gene-by-group alignment were done with RAxML37 via the

CIPRES Gateway for RAxML (http://www.phylo.org) to check for possibly mislabelled

GenBank accessions. Alignments were then assembled into supermatrices e.g22,33 to give

nexus format datasets with the maximum possible number of IOC species for that particular



group. Again, RAxML trees (with fast bootstrapping) were produced to check for

phylogenetic stability. In a few cases some taxa were then excluded due to inadequate data.

Model and partition strategies were assessed by the second order AIC38,39 via RAxML

likelihood scores, and by BEAST 1.5.440 MCMC parameter stability using Tracer 1.540,41. A

two-partition GTR-gamma model (one for mitochondrial genes and one for nuclear genes)

was chosen as this structure provides for the major features of sequence evolution while

linking what might otherwise be a disparate patchwork of data 42,43.

Final relaxed-clock trees for the diversification analyses were produced by BEAST 1.5.440

using the uncorrelated lognormal model. No attempt was made to infer actual ages and all

phylogenies were calibrated to an arbitrary mean rate of 0.01 to remove the confounding

effect of uncertainty in absolute dates. Although this results in arbitrary absolute values of

rate parameters unique to each major group, here we are only interested in relative speciation

rates.

The RAxML phylogenies were used as starting trees, with a Yule node height (speciation)

prior, and the two-partition GTR-gamma model. Two 20 million step chains were run

sampling every 1000 steps and the data combined allowing for a 25% burnin, giving all

parameter effective sample sizes greater than 200, and a final median node height maximum

clade credibility (MCC) tree. In addition, a set of 100 trees were taken from the post burnin

samples for assessing the effect of phylogenetic uncertainty. Trees were subsequently

manipulated using PAUP 4.0b1044 TreeEdit v1.0a4-6145 and FigTree 1.3.140.

Phylogenetic clustering was assessed by maximum parsimony (MP) steps for character state

changes on the BEAST MCC tree, done in Mesquite using 1000 randomizations

(http://www.mesquiteproject.org). Across all groups the CP state is present in multiple

lineages, appearing to be relatively scattered, although there is some signal of clustering in

most groups (Table S2).

Phylogenetic analysis of the passerines involved first accumulating all GenBank accessions

for genes that appeared to have a large coverage of species or genera or families. Libraries of

25 genes were assembled amounting to some fifty thousand accessions totalling 41

Megabases of sequence, and alignments built for twenty thousand accessions of 16 Mb. This



followed the above general procedure of aligning and generating gene trees for data-

checking, and also included building family- and genus- level trees as part of the process. The

different gene and taxon level trees were checked against each other for consistency and

unstable taxa identified to check the component genes.

Owing to the massive scale of the species level phylogeny, the passerines were broken down

into three sub-trees: sub-oscines (878 = 68% of IOC 2.4 species), lower oscines up to the

Corvoidea (709, 66%), the Passeroidea and attendant lineages (2541, 69%). These shared a

common datamatrix of 11 nuclear and 7 mitochondrial genes, a common framework of four

family-level outgroups and complementary sets of family-level passerine lineages to enable

linking of the sub-trees. Due to the size of these trees CIPRES RAxML was used to generate

trees, employing the two-partition model and fast bootstrap method37. Altogether the data

were able to generate reasonable trees for 120/123 families, 1134/1255 genera, and

4128/6213 species (66.5%). Within the genus and species level trees >60% of nodes have

bootstraps >70% (Table S6). Ultrametric versions (suitable for analysis of relative branch

length) of this tree were then created using PATHd846 arbitrarily calibrated to a tree height of

one.

All trees are based on at least one nuclear gene as well as several mitochondrial genes with an

average of more than 2.5 kilobases per taxon but a considerable proportion of missing data

(Tables S3-6). In an incomplete supermatrix sister lineages must have some data in common:

two lineages with sets of genes A and B respectively are directly linked by A B genes in

common, and together they contribute A B genes to the next lineage down22,33,43. Thus the

phylogenetic data in a supermatrix accumulates through the depth of the tree. Table S7 and

Figure S2 give a brief summary of this accumulation in the passerines. Individual species

have a median of three genes in common linking them to the tree (with 78% having at least

two genes), this rises to median 5 genes for genera (93%) and 10 genes for families (100%).

Across all the different datasets most species have both mitochondrial and nuclear data and

virtually all deeper nodes have mitochondrial and nuclear genes in common (Table S7). In

the passerines 71% of species have cytochrome b and 67% have ND2 (Table S4). While only

61% percent of species have a nuclear gene, in the context of the phylogeny this adds up to

74% of genera having at least one mitochondrial and one nuclear gene in common, rising to

95% at the family level (Table S7).



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Arshad, M., Gonzalez, J., El-Sayed, A. A., Osborne, T. & Wink, M. Phylogeny and

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Gamauf, A. & Haring, E. Molecular phylogeny and biogeography of Honey-buzzards (genera

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Griffiths, C. S., Barrowclough, G. F., Groth, J. G. & Mertz, L. A. Phylogeny, diversity, and

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Falconidae

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Galliformes

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Table S3. Number of sites and accessions for each gene used in each family-level phylogeny

Group Gene Total

Accipitridae RAG-1 BFib7 cytb ND6 12S ATPase COI

Sites 2872 972 1077 519 805 842 827 7914

accessions 88 92 161 61 68 53 57 580

Strigiformes RAG-1 MYO TGFB2 cytb ND2 COI

Sites 948 728 605 1143 1056 693 5173

accessions 72 37 39 104 45 39 336

Caprimulgiformes RAG-1 v-myc GH1 cytb COI

Sites 2872 1288 2190 1143 693 8186

accessions 35 76 65 87 22 285

Falconidae RAG-1 cytb COI ND2

Sites 2836 1143 693 1041 5713

accessions 50 48 15 34 147

Galliformes BFib7 OvoG mtDNA cytb ND2

Sites 951 469 17132 1146 1044 20742

accessions 57 72 37 181 109 456



Table S4. Number of sites, accessions and proportion of taxa with each gene for passerine

phylogeny

Gene sequence Genes Accessions Proportion of taxa in trees with gene

Family Genus Species Sites Family Genus Species

Nuclear RAG-1 122 642 915 2910 0.98 0.56 0.22

c-myc 78 192 229 513 0.62 0.17 0.06

c-mos 79 153 193 624 0.63 0.13 0.05

Zenk 60 100 120 1224 0.48 0.09 0.03

RAG-2 105 463 574 1155 0.84 0.41 0.14

bFib7 46 228 466 1110 0.37 0.2 0.11

bFib5 79 415 836 675 0.63 0.36 0.2

MYO 111 689 1438 787 0.89 0.61 0.35

ODC 101 521 1110 895 0.81 0.46 0.27

TGFB2 47 156 442 633 0.38 0.14 0.11

GAPDH 71 464 823 466 0.57 0.41 0.2

Mitochondrial cytb 107 902 2950 1143 0.86 0.79 0.71

ND2 110 871 2785 1041 0.88 0.77 0.67

COI 74 478 1302 1311 0.59 0.42 0.31

ATPase 52 206 542 985 0.42 0.18 0.13

12S 77 285 590 941 0.62 0.25 0.14

ND3 68 309 919 351 0.54 0.27 0.22

16S 58 219 425 611 0.46 0.19 0.1

Total 1445 7293 16659 17375



Table S5. Genes used for phylogeny reconstruction

Gene sequences code gene Nuclear RAG-1 Recombination activating protein 1 c-myc Proto-oncogene protein, exon 3 c-mos Oocyte maturation factor Mos zenk Zinc finger protein (ZENK = EGR-1), exon 2 RAG-2 Recombination activating protein 2 OvoG Ovomucoid gene, intron G v-myc Myelocytomatosis viral oncogene-like protein, exon 3 GH1 Growth hormone 1, intron 2 Bfib7 Beta-Fibrinogen intron 7 BFib5 Beta-Fibrinogen intron 5 MYO Myoglobin, intron 2 to intron 3 ODC Ornithine decarboxylase, intron 6 to intron 7 TGFB2 Transforming growth factor beta 2, intron 5 ALDOB Aldolase B fructose-bisphosphate GAPDH Glyceraldehyde-3-phosphate dehydrogenase, intron 11 Mitochondrial cytb Cytochrome b ND2 NADH dehydrogenase subunit 2 COI Cytochrome oxidase subunit 1 ATPase ATPase subunits 6, 8 ND6 NADH dehydrogenase subunit 6 ND3 NADH dehydrogenase subunit 6 12S 12S ribosomal RNA Genbank accession numbers available from authors on request.



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Table S7. Proportion of tips and internal nodes with mitochondrial and nuclear genes for each phylogeny

Phylogeny Nuclear Mitochondrial Both Accipitridae 0.69 0.96 0.65 Strigiformes 0.77 0.98 0.75 Caprimulgiformes 0.87 1 0.87 Falconidae 0.94 1 0.94 Galliformes 0.42 0.99 0.41 Passeriformes Nuclear Mitochondrial Both Multiple both family taxon 1 0.95 0.95 0.85 contribute to node 1 1 1 0.97 common to node 1 0.95 0.95 0.84 genus taxon 0.8 0.95 0.76 0.52 contribute to node 0.93 0.99 0.92 0.83 common to node 0.79 0.95 0.74 0.51 species taxon 0.61 0.95 0.56 0.27 contribute to node 0.83 0.99 0.83 0.66 common to node 0.6 0.95 0.55 0.29

both = at least one nuclear and one mitochondrial gene multiple both = multiple nuclear and multiple mitochondrial genes contribute to node = proportion of internal nodes with genes contributing information common to node = proportion of internal nodes with genes in common



Figure S2. Minimum number of genes contributing information to nodes across phylogenetic depth of the passerine phylogeny



Buteo_buteo_1n5m_p

Haliaeetus_pelagicus_0n3m_p

Gyps_coprotheres_2n1m

Buteo_solitarius_0n4m_p

Nisaetus_nanus_0n1m

Hamirostra_melanosternon_2n1m

Pithecophaga_je�eryi_1n1m

Buteo_albigula_1n4m

Buteo_platypterus_1n5m_p

Lophotriorchis_kienerii_0n1m

Ichthyophaga_ichthyaetus_0n1m

Leucopternis_albicollis_1n4m

Haliaeetus_sanfordi_0n1m

Accipiter_erythronemius_0n1m

Nisaetus_pinskeri_0n1m

Elanus_caeruleus_1n0m

Eutriorchis_astur_0n1m

Haliaeetus_leucocephalus_2n5m

Accipiter_ru�ventris_1n1m

Pernis_ptilorhynchus_0n1m_p

Lophaetus_occipitalis_2n1m

Aquila_clanga_1n2m_p

Torgos_tracheliotus_2n1m

Buteo_augur_0n4m_p

Dryotriorchis_spectabilis_0n1m

Buteo_lineatus_1n5m

Kaupifalco_monogrammicus_1n2mAccipiter_trivirgatus_0n1m

Aquila_gurneyi_0n1m

Ichthyophaga_humilis_0n1m

Nisaetus_bartelsi_0n1m

Necrosyrtes_monachus_2n1m

Nisaetus_nipalensis_2n4m

Buteo_auguralis_0n1m

Leucopternis_semiplumbeus_1n4m

Haliastur_indus_2n1m

Buteo_polyosoma_1n5m_p

Aviceda_cuculoides_0n1m

Cathartes_aura_1n0m

Pernis_apivorus_1n3m_p

Milvus_milvus_1n1m

Gyps_rueppellii_2n1m

Circaetus_cinereus_1n1m

Buteo_albonotatus_0n5m

Butastur_ru�pennis_1n1m

Aquila_africana_0n1m

Gampsonyx_swainsonii_1n2m

Urotriorchis_macrourus_0n1m_p

Aquila_pomarina_1n1m_p

Accipiter_cirrocephalus_1n1m

Morphnus_guianensis_2n1m_p

Accipiter_novaehollandiae_1n0m_p

Spilornis_cheela_1n3m

Buteo_brachypterus_0n1m

Buteo_jamaicensis_2n5m_p

Leucopternis_princeps_1n4m

Circus_cinereus_0n1m

Aquila_spilogaster_1n1m

Aquila_chrysaetos_2n4m

Leucopternis_polionotus_1n4m

Harpia_harpyja_2n1m

Gyps_indicus_1n1m

Circaetus_gallicus_1n3m_p

Micronisus_gabar_1n1m_p

Hieraaetus_morphnoides_2n1m_p

Buteogallus_anthracinus_2n5m

Butastur_teesa_1n1m

Circus_ranivorus_1n1m

Leucopternis_occidentalis_1n4m

Haliaeetus_leucogaster_1n2m

Aquila_heliaca_2n2m

Leucopternis_plumbeus_1n4m

Haliaeetus_leucoryphus_0n1m

Buteo_albicaudatus_1n5m_p

Melierax_poliopterus_0n1m

Buteo_swainsoni_1n5m_p

Geranospiza_caerulescens_2n5m

Aquila_fasciata_2n3m

Rostrhamus_sociabilis_2n5m

Nisaetus_kelaarti_0n1m

Accipiter_imitator_1n0m_p

Circus_aeruginosus_2n3m_p

Accipiter_superciliosus_0n2m_p

Polemaetus_bellicosus_2n1m

Haliaeetus_vocifer_1n1m

Circaetus_cinerascens_0n1m

Buteo_nitidus_2n5m

Nisaetus_philippensis_1n1m

Leptodon_cayanensis_2n1m_p

Sagittarius_serpentarius_2n2m

Parabuteo_unicinctus_1n5m

Pernis_celebensis_0n1m

Leucopternis_melanops_1n4m

Aegypius_monachus_2n2m

Nisaetus_alboniger_0n4m

Lophoictinia_isura_1n1m

Hieraaetus_wahlbergi_2n1m_p

Polyboroides_typus_2n1m

Butastur_indicus_0n2m

Leucopternis_kuhli_1n4m

Spizaetus_tyrannus_2n1mSpizaetus_melanoleucus_2n1m

Gyps_bengalensis_2n1m

Leucopternis_schistaceus_1n4m

Circus_cyaneus_0n2mAccipiter_tachiro_1n0m_p

Circaetus_pectoralis_2n1m

Gyps_himalayensis_1n1m

Buteogallus_meridionalis_2n5m

Aviceda_subcristata_1n0m

Gyps_tenuirostris_0n1m

Spizaetus_isidori_2n1m

Accipiter_gentilis_2n5m_p

Accipiter_nisus_2n3m

Spizaetus_ornatus_2n1m

Accipiter_bicolor_1n2m_p

Milvus_migrans_0n3m

Aquila_audax_1n1m

Harpagus_bidentatus_1n0m

Buteo_oreophilus_1n1m

Gypohierax_angolensis_2n1m

Buteo_galapagoensis_0n5m

Harpyhaliaetus_solitarius_2n4m

Buteo_regalis_1n5m_p

Nisaetus_cirrhatus_1n1m_p

Spilornis_ru�pectus_0n1m

Harpyopsis_novaeguineae_2n1m

Spilornis_holospilus_0n1m

Melierax_canorus_2n1m

Ictinaetus_malayensis_1n1m

Gyps_africanus_2n1m

Hieraaetus_pennatus_2n1m_p

Gypaetus_barbatus_1n1m

Buteo_refectus_0n3m

Aquila_verreauxii_2n1m

Chondrohierax_uncinatus_1n1m_pElanus_leucurus_1n2m

Busarellus_nigricollis_1n5m

Accipiter_virgatus_0n1m

Macheiramphus_alcinus_1n0m_p

Buteo_rufofuscus_1n4m_p

Hieraaetus_ayresii_1n1m_p

Buteo_magnirostris_2n5m

Elanoides_for�catus_2n4m

Pandion_haliaetus_2n5m

Buteo_brachyurus_0n5m_p

Trigonoceps_occipitalis_1n1m

Circaetus_fasciolatus_1n1m

Accipiter_soloensis_0n1m

Accipiter_striatus_0n2m

Gyps_fulvus_1n3m

Accipiter_gularis_0n2m

Circus_bu�oni_0n1m_p

Neophron_percnopterus_2n2m

Ictinia_plumbea_2n5m

Aquila_adalberti_1n1m

Buteo_ru�nus_1n4m_p

Buteo_ventralis_0n1m_p

Aquila_rapax_2n1m_p

Buteogallus_aequinoctialis_0n4m

Leucopternis_lacernulatus_0n4m

Stephanoaetus_coronatus_2n1m

Henicopernis_longicauda_0n1m

Buteo_ridgwayi_0n4m

Terathopius_ecaudatus_2n1m_p

Haliaeetus_albicilla_1n4m

Buteogallus_urubitinga_1n5m

Geranoaetus_melanoleucus_2n5m

Buteo_japonicus_1n4m

Buteo_leucorrhous_0n5m_p

Haliastur_sphenurus_1n1m

Spilornis_elgini_0n1m

Haliaeetus_vociferoides_1n1m

Sarcogyps_calvus_2n1m

Buteo_lagopus_1n5m_p

Nisaetus_lanceolatus_0n1m

Buteo_hemilasius_0n4m_p

Aquila_nipalensis_2n2m

Ictinia_mississippiensis_0n5m

Accipiter_cooperii_1n2m

Harpyhaliaetus_coronatus_0n4m

0.58

1

1

0.32

1

0.28

1

1

1

0.04

0.94

1

1

0.84

0.98

0.7

1

1

1

0.92

0.75

1

1

0.33

1

1

1

1

1

1

1

0.91

0.96

0.56

0.99

0.34

1

0.99

0.96

0.99

1

0.73

0.86

0.73

1

0.97

0.99

1

11

0.42

0.79

0.03

0.93

1

0.55

1

1

0.95

0.95

1

0.45

0.45

0.97

1

0.15

1

0.51

0.73

1

0.94

1

0.92

1

0.5

0.98

1

1

1

1

1

1

1

1

0.72

0.64

0.17

0.98

0.84

0.98

1

0.44

0.96

1

1

1

1

0.94

0.76

1

0.37

0.98

1

0.76

0.53

0.98

0.99

1

1

1

1

1

0.88

1

1

1

1

0.38

0.17

1

0.97

10.68

1

0.99

0.96

1

1

0.28

0.94

0.55

0.43

1

1

0.98

1

0.91

0.07

0.99

1

0.97

0.99

0.94

0.76

1

1

0.52

1

1

1

0.47

0.92

1

1

1

0.7

0.99

0.44

1

0.74

1

1

1

0.34

1

1

1

0.99

1

0.98

0.74

1

1

0.63

1

1

0.36

1

1

Figure S3. Accipitridae datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_CP status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty).

Sea Eagles100%

Buteonine Hawks 95%

Booted Eagles 92%

Vultures & Serpent Eagles 86%

Pernine Kites67%

Accipiters & Harriers 32%

Asio_otus_3n3m

Athene_brama_0n1m

Tyto_alba_3n3m

Megascops_asio_3n3m_p

Pulsatrix_perspicillata_1n1m

Otus_mirus_2n2m

Otus_capnodes_2n2m_p

Glaucidium_minutissimum_0n1m

Bubo_magellanicus_0n2m

Megascops_watsonii_0n1m_p

Megascops_trichopsis_0n1m_p

Bubo_nipalensis_1n1m

Otus_rutilus_2n2m_p

Megascops_albogularis_0n1m

Asio_�ammeus_2n2m

Otus_insularis_2n2m

Ninox_rudol�_1n1m

Ninox_connivens_1n2m

Phodilus_badius_3n1m

Ninox_scutulata_1n2m

Ninox_novaeseelandiae_0n3m

Glaucidium_tephronotum_0n1m

Tyto_tenebricosa_1n2m

Otus_ireneae_2n2m_p

Otus_lempiji_3n3m_p

Megascops_sanctaecatarinae_0n1m_p

Bubo_lacteus_1n1m

Otus_elegans_0n1m

Glaucidium_bolivianum_1n1m_p

Glaucidium_capense_0n1m

Aegolius_acadicus_3n3m

Strix_occidentalis_3n2m

Glaucidium_brasilianum_1n3m_p

Ketupa_ketupu_1n1m

Otus_brucei_1n1m_p

Otus_megalotis_3n3m_p

Aegolius_funereus_1n2m

Ninox_philippensis_0n2m

Glaucidium_perlatum_1n1m

Otus_lettia_3n3m_p

Strix_leptogrammica_0n1m

Bubo_virginianus_3n3m_p

Glaucidium_cuculoides_2n1m

Strix_butleri_1n1m_p

Ketupa_zeylonensis_1n1m

Mimizuku_gurneyi_0n1m

Aegolius_harrisii_1n1m

Megascops_napensis_1n0m

Megascops_kennicottii_3n3m_p

Megascops_koepckeae_1n2m

Strix_virgata_0n1m_p

Megascops_choliba_1n2m_p

Otus_scops_3n3m_p

Strix_varia_0n2m

Otus_sunia_3n3m_p

Glaucidium_peruanum_1n1m

Tyto_glaucops_0n1m

Ninox_squamipila_0n1m

Bubo_bengalensis_1n1m_p

Otus_mayottensis_2n2m

Otus_spilocephalus_3n2m_p

Glaucidium_hardyi_1n1m_p

Otus_moheliensis_2n2m_p

Athene_noctua_3n2m_p

Megascops_�ammeolus_1n2m_p

Otus_pauliani_2n2m_p

Strix_aluco_3n2m_p

Tyto_novaehollandiae_1n1m_p

Bubo_africanus_1n1m_p

Otus_semitorques_0n1m

Colius_striatus_2n3m

Strix_woodfordii_3n2m_p

Megascops_hoyi_2n3m_p

Megascops_guatemalae_0n1m_p

Bubo_capensis_1n1m

Otus_bakkamoena_3n2m_p

Glaucidium_nana_1n2m_p

Glaucidium_jardinii_1n1m_p

Ptilopsis_leucotis_2n2m

Otus_longicornis_2n2m

Ptilopsis_granti_1n1m

Pandion_haliaetus_3n3m

Athene_cunicularia_3n2m

Megascops_petersoni_0n1m

Glaucidium_californicum_1n1m_p

Bubo_bubo_3n3m_p

Bubo_scandiacus_1n2m

Bubo_ascalaphus_1n1m

Ninox_rufa_1n2m

Pseudoscops_clamator_1n2mAsio_capensis_1n1m

Otus_pembaensis_2n2m_pOtus_senegalensis_2n2m_p

Strix_uralensis_1n2mStrix_davidi_0n1m

Micrathene_whitneyi_0n2m

Megascops_atricapilla_1n1m_p

Tyto_capensis_0n2m

Leptosomus_discolor_3n2m

Ninox_strenua_1n2m

Megascops_roboratus_1n2m_p

Tyto_longimembris_1n1m

Glaucidium_gnoma_3n2m_p

Pulsatrix_koeniswaldiana_1n1m

Strix_nebulosa_1n3m

Glaucidium_griseiceps_1n1m

Glaucidium_passerinum_1n1m

Strix_ru�pes_1n2m_p

Ninox_boobook_1n0m

Lophostrix_cristata_0n1m_p

Surnia_ulula_1n2m

1

0.93

0.99

1

1

0.53

0.25

0.63

1

1

0.99

1

1

1

0.38

0.87

0.83

1

1

0.6

1

0.27

1

1

0.73

1

1

1

0.96

0.96

1

1

0.97

0.45

1

1

0.69

0.34

0.56

0.77

0.29

1

0.99

1

0.43

0.99

0.44

1

1

1

0.91

0.68

0.92

1

1

0.26

0.7

1

1

0.99

0.99

1

0.89

0.98

1

1

1

1

1

1

0.84

0.98

1

0.57

0.87

0.9

0.81

1

0.99

1

1

1

0.8

1

1

1

1

0.85

1

0.58

0.85

1

1

1

0.82

0.94

1

1

0.98

0.61

0.96

0.86

1

0.2

1

0.95

0.97

0.73

1

1

Figure S4. Strigiformes datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_ CP status. Major sub-groups denoted. Outgroups in grey.Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty).

Strigidae 50%

Tytonidae 39%

Surniinae 59%

Striginae 50%

33%

46%

54%

Caprimulgus_ru�gena_2n1mCaprimulgus_europaeus_3n2m

Chordeiles_minor_2n2m_p

Caprimulgus_carolinensis_3n2m_p

Eurostopodus_argus_2n1m

Aegotheles_archboldi_0n1m_p

Caprimulgus_aegyptius_2n1m

Caprimulgus_salvini_2n1m

Caprimulgus_pectoralis_2n1m_p

Nyctiphrynus_mcleodii_3n2m_p

Caprimulgus_indicus_2n2m

Nyctibius_bracteatus_2n1m

Caprimulgus_batesi_2n1m

Caprimulgus_anthonyi_2n1m

Caprimulgus_enarratus_2n1m

Caprimulgus_poliocephalus_2n1m

Caprimulgus_maculicaudus_3n1m

Caprimulgus_candicans_0n1m

Caprimulgus_madagascariensis_2n1m_p

Hydropsalis_climacocerca_3n1m

Caprimulgus_inornatus_0n1m_p

Aegotheles_wallacii_0n1m

Aegotheles_novaezealandiae_0n1m

Caprimulgus_vociferus_3n2m

Caprimulgus_rufus_2n1m

Caprimulgus_a�nis_3n1m_p

Caprimulgus_nigrescens_2n1m

Hemiprocne_3n1m

Caprimulgus_ridgwayi_2n1m

Nyctiphrynus_rosenbergi_2n1m

Caprimulgus_saturatus_2n1m

Uropsalis_segmentata_3n1m

Batrachostomus_cornutus_0n1m_p

Nyctibius_maculosus_1n1m

Aegotheles_savesi_0n1m

Podargus_strigoides_3n2m_p

Aegotheles_cristatus_1n2m_p

Caprimulgus_cayennensis_2n1m

Strix_2n2m

Grus_3n2m

Podager_nacunda_3n2m

Chordeiles_rupestris_2n1m

Eleothreptus_anomalus_2n2m

Psittaciformes_2n2m

Chordeiles_pusillus_2n1m

Caprimulgus_manillensis_2n1m

Nyctibius_aethereus_2n1m

Pandion_2n2m

Phalaenoptilus_nuttallii_3n2m

Tauraco_3n1m

Macrodipteryx_vexillarius_3n1m

Nyctibius_leucopterus_1n1m

Caprimulgus_parvulus_3n2m

Nyctibius_grandis_3n1m

Podargus_papuensis_1n1m_p

Caprimulgus_nigriscapularis_2n1m_p

Nyctiphrynus_ocellatus_3n1m_p

Aegotheles_tatei_0n1m

Nyctidromus_albicollis_3n2m_p

Caprimulgus_climacurus_3n1m_p

Nyctibius_jamaicensis_1n1m_p

Batrachostomus_septimus_3n1m_p

Podargus_ocellatus_1n1m_p

Caprimulgus_fraenatus_0n1m

Lurocalis_semitorquatus_3n1m

Steatornis_caripensis_3n1m

Hydropsalis_torquata_2n2m

Eurostopodus_papuensis_2n1m

Macrodipteryx_longipennis_2n1m_p

Eurostopodus_macrotis_3n1m

Aegotheles_albertisi_2n1m_p

Caprimulgus_macrurus_3n1m

Caprimulgus_longirostris_3n1m_p

Caprimulgus_whitelyi_2n1m

Eurostopodus_mystacalis_2n1m

Nyctiprogne_leucopyga_3n1m

Chordeiles_acutipennis_3n2m

Aegotheles_bennettii_1n1m

Nyctiphrynus_yucatanicus_2n1m_p

Uropsalis_lyra_2n1m

Aerodramus_3n2m

Aegotheles_crinifrons_0n1m_p

Nyctibius_griseus_1n2m_p

Rigidipenna_inexpectata_0n1m

Aegotheles_insignis_3n1m_p

Caprimulgus_fossii_2n1m_p

Siphonorhis_brewsteri_2n1m

Lurocalis_ru�ventris_2n1m

0.78

1

1

1

1

1

11

0.99 0.98

0.8

1

1

0.57

1

1

1

1

1

1

0.94

1

1

1

1

1

0.85

1

0.59

1

1

0.54

1

0.39

1

1

0.5

1

1

1

10.88

1

1

0.41

1

0.98

11

1

1

0.59

0.98

1

0.34

10.95

1

1

1

1

0.76

0.95

0.36

0.89

1

0.98

1

0.88

0.83

1

1

1

1

1

1

1

0.51

1

0.98

0.63

0.51

0.96

0.68

1

1 Nyctibiidae 100%

Aegothelidae 91%

Apodiformes

Caprimulgidae 62%

Podargidae 43%

Steatornithidae 100%

Figure S5. Caprimulgiformes datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_CP status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty).

Milvago_chimachima_1n2m

Falco_concolor_1n1m

Falco_vespertinus_1n1m

Micrastur_semitorquatus_1n2m_p

Falco_deiroleucus_1n1m

Phalcoboenus_australis_1n1m

Falco_longipennis_1n2m

Pandionidae_1n3m

Micrastur_mintoni_1n1m

Falco_cuvierii_1n1m

Falco_amurensis_1n2m

Falco_araeus_0n1m

Caracara_plancus_1n3m

Falco_subniger_1n1m

Falco_berigora_1n1m_p

Herpetotheres_cachinnans_1n2m

Falco_pelegrinoides_1n1m

Falco_rupicoloides_1n1m

Falco_zoniventris_1n1m

Polihierax_semitorquatus_1n2m

Falco_femoralis_1n2m

Microhierax_caerulescens_1n2m

Falco_cenchroides_1n1m

Falco_dickinsoni_1n1m

Micrastur_plumbeus_1n1m

Falco_naumanni_1n2m

Phalcoboenus_megalopterus_1n2m

Falco_rusticolus_1n2m_p

Falco_eleonorae_1n1m_p

Falco_peregrinus_1n3m_p

Falco_columbarius_1n3m

Micrastur_buckleyi_1n1m

Daptrius_ater_1n1m

Falco_newtoni_0n1m_p

Micrastur_ru�collis_1n1m_p

Microhierax_erythrogenys_0n1m

Falco_mexicanus_1n2m

Falco_cherrug_1n1m_p

Psittacidae_1n3m

Ibycter_americanus_1n2m

Falco_chicquera_1n1m

Falco_jugger_1n1m

Falco_sparverius_1n3m_p

Spiziapteryx_circumcincta_1n2m

Corvidae_1n3m

Falco_punctatus_1n1m

Falco_subbuteo_1n3m

Falco_biarmicus_1n1m

Falco_tinnunculus_1n3m

Micrastur_mirandollei_1n1m

Micrastur_gilvicollis_1n2m

Falco_novaeseelandiae_1n1m

Milvago_chimango_1n2m

11

1

1

1

11

0.61

0.64

0.98

0.65

1

0.89

1

1

1

1

1

0.31

1

0.25

1

1

1

1

0.25

1

0.4

1

1

1

0.28

0.99

1

1

0.76

1

1

1

0.95

1

1

1

1

0.65

1

0.32

0.54

1

0.44

0.81

1

Falconinae 74%

Figure S6. Falconidae datamatrix BEAST median node height MCC tree with posterior probability values. CP species high-lighted in orange; taxon label shows genus_species_mt and nuclear genes_ CP status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty).

Herpetotherinae 100%

79%

Lophura_erythrophthalma_0n1m

Bonasa_umbellus_0n2m_p

Pternistis_bicalcaratus_0n1m_p

Nothocrax_urumutum_1n1m

Alectoris_chukar_2n3m

Penelope_montagnii_0n1m

Mitu_salvini_0n1m

Peliperdix_lathami_1n2m

Lophura_nycthemera_2n3m

Colinus_virginianus_2n2m

Chamaepetes_goudotii_1n1m

Agelastes_meleagrides_0n1m

Perdicula_asiatica_0n1m

Oreophasis_derbianus_1n1m

Lagopus_lagopus_0n2m_p

Tetrao_parvirostris_0n2m

Penelope_obscura_1n0m

Megapodius_cumingii_0n1m

Rollulus_rouloul_0n1m

Gallus_lafayetii_2n2m

Alectoris_rufa_2n1m

Francolinus_pintadeanus_0n1m

Chrysolophus_pictus_2n3m

Lagopus_muta_0n2m

Gallus_gallus_2n3m

Polyplectron_katsumatae_0n1m

Pternistis_swainsonii_1n2m

Margaroperdix_madagarensis_0n1m

Megapodius_layardi_2n2m

Chrysolophus_amherstiae_1n3m

Coturnix_japonica_2n2m

Callipepla_gambelii_1n2m

Dendroperdix_sephaena_1n2m

Tetraogallus_altaicus_0n1m

Falcipennis_canadensis_2n2m_p

Excalfactoria_chinensis_0n2m

Penelope_argyrotis_0n1m

Tragopan_blythii_2n2m

Lophura_inornata_2n2m

Crossoptilon_auritum_0n2m

Ortalis_vetula_2n2m

Arborophila_javanica_1n1m

Polyplectron_inopinatum_2n2m

Crax_alberti_0n1m_p

Gallus_sonneratii_2n2m

Crax_rubra_2n2m_p

Crax_alector_0n1m

Ortalis_guttata_0n1m

Megapodius_pritchardii_0n1m

Tragopan_temminckii_2n3m

Francolinus_pondicerianus_1n2m

Centrocercus_urophasianus_0n2m

Gallus_varius_2n3m

Catreus_wallichii_2n2m

Mitu_tomentosum_0n1m

Ortalis_canicollis_1n1m

Lophura_ignita_0n2m

Lophura_bulweri_0n1m

Megapodius_tenimberensis_0n1m

Pternistis_hartlaubi_0n1m_p

Francolinus_gularis_0n1m

Lagopus_leucura_0n2m

Guttera_pucherani_2n2m

Tympanuchus_cupido_0n2m

Polyplectron_germaini_2n2m

Ortalis_poliocephala_0n1m

Ortalis_ru�cauda_0n1m

Mitu_tuberosum_1n1m

Callipepla_squamata_0n2m

Scleroptila_levaillantii_1n2m

Pipile_cumanensis_0n1m

Arborophila_gingica_0n1m

Meleagris_gallopavo_2n3m

Tetraogallus_caspius_0n1m

Crax_daubentoni_0n1m

Penelope_superciliaris_0n1m

Penelope_jacquacu_0n1m

Ortalis_motmot_0n1m

Eulipoa_wallacei_0n1m

Arborophila_torqueola_0n1m

Pipile_jacutinga_1n0m

Alectoris_graeca_0n1m

Megapodius_eremita_0n2m

Syrmaticus_mikado_1n2m

Numida_meleagris_2n3m

Aburria_aburri_1n1m

Leipoa_ocellata_2n2m

Tetraophasis_szechenyii_0n3m

Rheinardia_ocellata_0n1m

Pucrasia_macrolopha_2n3m_p

Pternistis_natalensis_1n2m_p

Pavo_muticus_2n3m

Syrmaticus_soemmerringii_0n2m

Caloperdix_oculeus_0n1m

Guttera_plumifera_0n1m

Ithaginis_cruentus_1n2m

Polyplectron_bicalcaratum_2n3m

Lophura_edwardsi_0n1m

Coturnix_coturnix_0n2m

Lophophorus_impejanus_2n2m_p

Ortalis_leucogastra_0n1m

Talegalla_fuscirostris_0n1m

Cyrtonyx_montezumae_2n2m

Crossoptilon_crossoptilon_2n2m

Pternistis_capensis_1n2m

Scleroptila_levaillantoides_0n2m

Pipile_cujubi_0n1m

Callipepla_douglasii_0n2m

Polyplectron_schleiermacheri_1n1m

Callipepla_californica_0n2m_p

Alectoris_philbyi_0n1m

Phasianus_versicolor_0n2m

Tragopan_satyra_0n1m

Polyplectron_napoleonis_2n2m

Syrmaticus_humiae_1n3m

Penelope_purpurascens_0n1m

Lophura_diardi_0n1m

Oreortyx_pictus_2n2m_p

Pternistis_squamatus_1n2m_p

Pavo_cristatus_2n2m

Afropavo_congensis_2n2m

Macrocephalon_maleo_0n2m

Crax_globulosa_0n1m

Perdix_perdix_2n2m

Dendragapus_obscurus_0n2m

Lophophorus_sclateri_0n2m

Perdix_hodgsoniae_0n2m

Ammoperdix_heyi_0n1m

Tympanuchus_phasianellus_2n2m

Pauxi_unicornis_0n1m

Argusianus_argus_1n1m

Coturnix_pectoralis_0n1m

Scleroptila_shelleyi_1n2m

Pauxi_pauxi_2n1m_p

Syrmaticus_ellioti_2n3m

Francolinus_francolinus_0n1m

Arborophila_ru�pectus_0n1m

Ptilopachus_petrosus_1n2m

Crossoptilon_harmani_0n1m

Megapodius_decollatus_0n1m

Tetrastes_bonasia_0n3m

Chamaepetes_unicolor_0n1m

Pternistis_hildebrandti_0n1m

Megapodius_forsteni_0n1m

Crossoptilon_mantchuricum_0n1m

Tragopan_caboti_0n2m

Scleroptila_africana_1n2m

Polyplectron_malacense_2n2m

Megapodius_freycinet_0n2m

Megapodius_reinwardt_1n1m

Ptilopachus_nahani_1n2m

Tympanuchus_pallidicinctus_0n2m

Tetrastes_sewerzowi_0n2m

Phasianus_colchicus_2n3m

Tetraophasis_obscurus_0n2m

Perdix_dauurica_0n3m

Scleroptila_�nschi_0n2m

Galloperdix_lunulata_0n1m

Pternistis_griseostriatus_1n2m

Pternistis_castaneicollis_0n1m_p

Anas_1n2m

Ortalis_garrula_0n1m

Haematortyx_sanguiniceps_0n1m

Crax_fasciolata_0n1m

Tetrao_urogallus_0n2m

Pternistis_leucoscepus_1n2m

Syrmaticus_reevesii_2n3m

Colinus_cristatus_0n1m

Acryllium_vulturinum_1n3m

Pternistis_adspersus_1n2m

Alectoris_barbara_0n1m

Tetraogallus_tibetanus_0n2m

Lyrurus_mlokosiewiczi_0n2m

Pternistis_erckelii_0n1m

Polyplectron_chalcurum_2n2m

Lyrurus_tetrix_0n2m_p

Coturnix_ypsilophora_0n2m

Alectura_lathami_2n3m

Alectoris_magna_0n2m

Lophura_swinhoii_2n2m

Lophura_hatinhensis_0n1m

Arborophila_rufogularis_0n1m

Mitu_mitu_0n1m

Bambusicola_fytchii_0n2m

Alectoris_melanocephala_0n1m

Penelopina_nigra_1n1m

Lophophorus_lhuysii_0n3m

Xenoperdix_udzungwensis_1n1m

Rhizothera_longirostris_0n1m

Falcipennis_falcipennis_0n2m

Crax_blumenbachii_1n1m

Pternistis_afer_1n2m

Lophura_leucomelanos_0n1m_p

Tetraogallus_himalayensis_0n2m

Peliperdix_coqui_1n2m

Bambusicola_thoracicus_2n3m

Ortalis_cinereiceps_0n1m

Aepypodius_arfakianus_0n1m

1

0.49

0.99

1

0.44

1

1

1

1

0.51

0.97

0.36

1

1

1

1

0.5

1

0.96

1

0.57

1

1

0.31

1

1

1

0.84

1

0.98

0.39

1

0.49

0.78

1

0.19

0.95

0.85

0.21

1

1

0.91

1

0.45

0.87

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0.98

1

1

1

1

0.64

0.91

1

1

1

0.88

1

1

1

0.86

0.55

0.92

1

0.95

0.99

1

1

0.91

0.38

1

1

1

1

1

0.94

1

0.33

1

0.79

1

0.62

1

0.97

1

1

1

1

1

1

1

1

1

11

0.96

0.96

1

1

1

1

1

1

1

1

1

0.66

1

0.26

1

1

1

0.95

1

0.33

0.97

0.46

1

0.55

0.57

0.94

0.45

0.98

1

1

1

0.12

1

0.74

0.84

1

1

0.76

1

0.55

1

1

1

1

0.89

0.55

0.79

1

1

0.97

0.81

1

0.99

1

1

1

1

0.95

1

0.73

1

1

1

1

0.89

1

1

1

0.96

1

1

1

1

0.46

10.97

0.91

0.39

1

0.31

0.34

0.94

0.7

0.14

1

1

1

0.36

1

1

0.21

1

1

0.45

0.99

1

0.9

0.9

1

1

0.66

Figure S7. Galliformes datamatrix BEAST median node height MCC tree with posterior probability values. CP species highlighted in orange; taxon label shows genus_species_mt and nuclear genes_CP status. Major sub-groups denoted. Outgroups in grey. Approximate percentage of species sampled shown for some major clades (notwithstanding phylogenetic uncertainty).

Megapodidae 78%

Cracidae 69%

Phasianidae 72%

Odontophoridae 29%

Numididae 83%

supplementary information - media.nature.com · acciptridae, strigiformes, caprimulgidae and...

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