Biological Samples

27 Nipponia nippon tissue samples American Museum of Natural History Data S1

19 Nipponia nippon tissue samples Natural History Museum (London) Data S1

2 Nipponia nippon tissue samples World Museum, Liverpool Data S1

1 Nipponia nippon tissue sample Naturalis Biodiversity Center Leiden, the Netherlands Data S1

1 Nipponia nippon tissue sample Senckenberg Natural History Museum Data S1

2 Nipponia nippon tissue samples Stuttgart State Museum of Natural History Data S1

2 Nipponia nippon tissue samples Smithsonian Institute National Museum of Natural History Data S1

2 Nipponia nippon tissue samples Natural History Museum Vienna Data S1

1 Nipponia nippon tissue sample Natural History Museum of Denmark Data S1

Deposited Data

Whole-genome sequencing data of 57 historical Nipponia nippon samples This paper NCBI Project ID: PRJNA481495; CNSA: CNP0000084

Whole-genome sequencing data of 8 contemporary Nipponia nippon samples [ 10 Li S.

Li B.

Cheng C.

Xiong Z.

Liu Q.

Lai J.

Carey H.V.

Zhang Q.

Zheng H.

Wei S.

et al. Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. NCBI Project ID: PRJNA232572

Nipponia nippon reference genome [ 10 Li S.

Li B.

Cheng C.

Xiong Z.

Liu Q.

Lai J.

Carey H.V.

Zhang Q.

Zheng H.

Wei S.

et al. Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. NCBI Project ID: PRJNA232572

Whole-genome sequencing data of 13 Pan paniscus [ 43 Prado-Martinez J.

Sudmant P.H.

Kidd J.M.

Li H.

Kelley J.L.

Lorente-Galdos B.

Veeramah K.R.

Woerner A.E.

O’Connor T.D.

Santpere G.

et al. Great ape genetic diversity and population history. SRA: SRP018689

Whole-genome sequencing data of 5 Pongo abelii [ 43 Prado-Martinez J.

Sudmant P.H.

Kidd J.M.

Li H.

Kelley J.L.

Lorente-Galdos B.

Veeramah K.R.

Woerner A.E.

O’Connor T.D.

Santpere G.

et al. Great ape genetic diversity and population history. SRA: SRP018689

Whole-genome sequencing data of 5 Pongo pygmaeus [ 43 Prado-Martinez J.

Sudmant P.H.

Kidd J.M.

Li H.

Kelley J.L.

Lorente-Galdos B.

Veeramah K.R.

Woerner A.E.

O’Connor T.D.

Santpere G.

et al. Great ape genetic diversity and population history. SRA: SRP018689

Whole-genome sequencing data of 25 Pan troglodytes [ 43 Prado-Martinez J.

Sudmant P.H.

Kidd J.M.

Li H.

Kelley J.L.

Lorente-Galdos B.

Veeramah K.R.

Woerner A.E.

O’Connor T.D.

Santpere G.

et al. Great ape genetic diversity and population history. SRA: SRP018689

Whole-genome sequencing data of 31 Gorilla gorilla [ 43 Prado-Martinez J.

Sudmant P.H.

Kidd J.M.

Li H.

Kelley J.L.

Lorente-Galdos B.

Veeramah K.R.

Woerner A.E.

O’Connor T.D.

Santpere G.

et al. Great ape genetic diversity and population history. SRA: SRP018689

Whole-genome sequencing data of 10 Vulpes vulpes [ 44 Kukekova A.V.

Johnson J.L.

Xiang X.

Feng S.

Liu S.

Rando H.M.

Kharlamova A.V.

Herbeck Y.

Serdyukova N.A.

Xiong Z.

et al. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. SRA: SRP100625

Whole-genome sequencing data of 18 Ursus maritimus [ 45 Liu S.

Lorenzen E.D.

Fumagalli M.

Li B.

Harris K.

Xiong Z.

Zhou L.

Korneliussen T.S.

Somel M.

Babbitt C.

et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. SRA: SRA092289

Whole-genome sequencing data of 10 Ursus arctos [ 45 Liu S.

Lorenzen E.D.

Fumagalli M.

Li B.

Harris K.

Xiong Z.

Zhou L.

Korneliussen T.S.

Somel M.

Babbitt C.

et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. SRA: SRA092289

Whole-genome sequencing data of 14 Anas platyrhynchos [ 46 Zhang Z.

Jia Y.

Almeida P.

Mank J.E.

van Tuinen M.

Wang Q.

Jiang Z.

Chen Y.

Zhan K.

Hou S.

et al. Whole-genome resequencing reveals signatures of selection and timing of duck domestication. SRA: SRP125660

Whole-genome sequencing data of 6 Tibetan fowl from Qinghai [ 47 Li D.

Che T.

Chen B.

Tian S.

Zhou X.

Zhang G.

Li M.

Gaur U.

Li Y.

Luo M.

et al. Genomic data for 78 chickens from 14 populations. SRA: SRP040477

Whole-genome sequencing data of 5 Platyspiza crassirostris [ 48 Lamichhaney S.

Berglund J.

Almén M.S.

Maqbool K.

Grabherr M.

Martinez-Barrio A.

Promerová M.

Rubin C.J.

Wang C.

Zamani N.

et al. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. SRA: SRP048643

Whole-genome sequencing data of 20 Ficedula albicollis [ 49 Nadachowska-Brzyska K.

Burri R.

Smeds L.

Ellegren H. PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. SRA: ERA362744,

ERA362838,

ERA391986,

ERA391991

Whole-genome sequencing data of 34 Ailuropoda melanoleuca [ 50 Zhao S.

Zheng P.

Dong S.

Zhan X.

Wu Q.

Guo X.

Hu Y.

He W.

Zhang S.

Fan W.

et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. SRA: SRP013618

Whole-genome sequencing data of 6 Ectopistes migratorius [ 51 Murray G.G.R.

Soares A.E.R.

Novak B.J.

Schaefer N.K.

Cahill J.A.

Baker A.J.

Demboski J.R.

Doll A.

Da Fonseca R.R.

Fulton T.L.

et al. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. SRA: SRP042357,

SRP103042

MHC class 1 region sequences of Nipponia nippon NCBI KP182409.1

MHC class 2 region sequences of Nipponia nippon NCBI KP182408.1

MHC extended region sequences of Nipponia nippon NCBI KP182407.1

Locality data of crested ibis fromm American Museum of Natural History. AMNH Bird Collection (published on 2013-10-30) VertNet database http://ipt.vertnet.org:8080/ipt/resource.do?r=amnh_birds

Locality data of crested ibis from California Academy of Sciences. CAS Ornithology (ORN) (published on 2016-10-31) VertNet database http://ipt.calacademy.org:8080/ipt/resource.do?r=orn

Locality data of crested ibis from Museum of Comparative Zoology, Harvard University (published on 2017-07-11) VertNet database http://digir.mcz.harvard.edu/ipt/resource.do?r=mcz_subset_for_vertnet

Locality data of crested ibis from Museum of Vertebrate Zoology, UC Berkeley. MVZ Bird Collection (Arctos) (published on 2015-10-27) VertNet database http://ipt.vertnet.org:8080/ipt/resource.do?r=mvz_bird

Locality data of crested ibis from National Museum of Natural History, Smithsonian Institution. NMNH Birds (published on 2016-07-21) VertNet database https://collections.nmnh.si.edu/ipt/resource?r=nmnh_extant_dwc-a

Locality data of crested ibis (1842.1.19.90) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/7e36ff64-1cf0-44f6-b30d-ae0715a85a53

Locality data of crested ibis (1852.2.5.12) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/5a4a8a93-ead3-42ce-9229-a8d34a8d0a0e

Locality data of crested ibis (1891.10.19.20) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/b1a0a925-5132-40c7-a9c3-2a999d336660

Locality data of crested ibis (1892.4.2.492) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/1a589acb-26c9-48c0-9365-6a7620d12e5d

Locality data of crested ibis (1892.4.2.493) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/7be93e6c-f56d-4922-95ce-31635a6e3c30

Locality data of crested ibis (1897.10.30.2) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/f7ca4de8-0772-4743-9c82-59656231504d

Locality data of crested ibis (1897.10.30.3) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/f9b28058-f974-40c1-9300-0248271cf128

Locality data of crested ibis (1897.10.30.4) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/927fb79d-4100-49a0-894a-3a8cfa644e1f

Locality data of crested ibis (1897.10.30.5) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/218dc4cd-6aa4-4349-956b-9bd253b1e036

Locality data of crested ibis (1897.10.30.6) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/69828014-8f2c-4e67-8fc2-f1ac1e623b63

Locality data of crested ibis (1900.9.9.12) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/e04fe7fe-46c3-43e2-89d4-cb106558181f

Locality data of crested ibis (1900.9.9.13) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/1e5fed44-06b0-4cfe-959c-e1d3902947f3

Locality data of crested ibis (1908.1.5.20) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/3ff29518-a451-416a-9e56-42992ea304fb

Locality data of crested ibis (1908.1.5.21) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/1a3f8ba6-4d7f-45fe-b165-07fd1ef26207

Locality data of crested ibis (1908.1.5.22) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/786144ad-774e-49d8-9ed9-b6378db8cdfe

Locality data of crested ibis (1908.1.5.23) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/7a9df17a-c7d3-4d73-8ddf-e72c3ece16e6

Locality data of crested ibis (1908.1.5.24) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/365367ee-fd32-4981-a62d-853df63b0a35

Locality data of crested ibis (1908.1.5.25) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/35a1776c-7568-4876-b800-753f527569ec

Locality data of crested ibis (1908.1.5.26) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/d580fe99-1e9d-4540-9ca0-2e10ab18dcc3

Locality data of crested ibis (1912.9.23.14) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/ec073508-ceae-4688-880c-3fd00f855aaf

Locality data of crested ibis (1988.17.1) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/141067d4-2105-438d-b128-2388ffd3670d

Locality data of crested ibis (1988.17.2) from Natural History Museum. Natural History Museum (London) Collection Specimens (published on 2015-10-10) VertNet database http://data.nhm.ac.uk/object/21cd5738-ae0f-496c-b798-8fa4b60715f7

Locality data of crested ibis from University Museum of Zoology Cambridge (Zoology). UMZC Zoological Specimens (published on 2015-02-16) VertNet database http://ipt.vertnet.org:8080/ipt/resource.do?r=umzc_vertebrates

Locality data of crested ibis from University of Michigan Museum of Zoology. UMMZ Birds Collection (published on 2015-10-28) VertNet database http://ipt.vertnet.org:8080/ipt/resource.do?r=ummz_birds

WorldClim v1.4 [ 52 Hijmans R.J.

Cameron S.E.

Parra J.L.

Jones P.G.

Jarvis A. Very high resolution interpolated climate surfaces for global land areas. http://www.worldclim.org/current

Software and Algorithms

PALEOMIX [ 53 Schubert M.

Ermini L.

Der Sarkissian C.

Jónsson H.

Ginolhac A.

Schaefer R.

Martin M.D.

Fernández R.

Kircher M.

McCue M.

et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. https://geogenetics.ku.dk/publications/paleomix;

RRID: SCR_015057

ANGSD v0.615 [ 11 Korneliussen T.S.

Albrechtsen A.

Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data. https://github.com/ANGSD/angsd

RapidNJ v2.3.2 [ 54 Simonsen M.

Mailund T.

Pedersen C.N. Rapid neighbour-joining. http://birc.au.dk/software/rapidnj/

R package ‘pcadapt’ [ 13 Luu K.

Bazin E.

Blum M.G. pcadapt: an R package to perform genome scans for selection based on principal component analysis. https://cran.r-project.org/web/packages/pcadapt/index.html

STRUCTURE v2.3.4 [ 14 Falush D.

Stephens M.

Pritchard J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. https://web.stanford.edu/group/pritchardlab/structure.html;

RRID: SCR_002151

PSMC [ 16 Li H.

Durbin R. Inference of human population history from individual whole-genome sequences. https://github.com/lh3/psmc

PopSizeABC v2.1 [ 17 Boitard S.

Rodríguez W.

Jay F.

Mona S.

Austerlitz F. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. https://forge-dga.jouy.inra.fr/projects/popsizeabc/

Maxent v3.4.0 [ 55 Phillips S.J.

Anderson R.P.

Schapire R.E. Maximum entropy modeling of species geographic distributions. https://github.com/mrmaxent/Maxent

GRASS GIS v7.2.1 N/A https://grass.osgeo.org/grass7/

R v3.2.2 [ 56 R Core Development Team

R: a language and environment for statistical computing. https://www.r-project.org

NeEstimator v2.1 [ 57 Do C.

Waples R.S.

Peel D.

Macbeth G.M.

Tillett B.J.

Ovenden J.R. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data. http://www.molecularfisherieslaboratory.com.au/neestimator-software/

Genome-wide Complex Trait Analysis (GCTA) v1.91.4 [ 58 Yang J.

Lee S.H.

Goddard M.E.

Visscher P.M. GCTA: a tool for genome-wide complex trait analysis. http://cnsgenomics.com/software/gcta/

PLINK v1.07 [ 59 Purcell S.

Neale B.

Todd-Brown K.

Thomas L.

Ferreira M.A.

Bender D.

Maller J.

Sklar P.

de Bakker P.I.

Daly M.J.

Sham P.C. PLINK: a tool set for whole-genome association and population-based linkage analyses. http://zzz.bwh.harvard.edu/plink/;

RRID: SCR_001757

GERMLINE v1.5.1 [ 60 Gusev A.

Lowe J.K.

Stoffel M.

Daly M.J.

Altshuler D.

Breslow J.L.

Friedman J.M.

Pe’er I. Whole population, genome-wide mapping of hidden relatedness. http://gusevlab.org/software/germline/;

RRID: SCR_001720

R package ‘pegas’ v0.10 [ 61 Paradis E. pegas: an R package for population genetics with an integrated-modular approach. https://cran.r-project.org/web/packages/pegas/index.html

SnpEff v4.3 [ 62 Cingolani P.

Platts A.

Wang L.

Coon M.

Nguyen T.

Wang L.

Land S.J.

Lu X.

Ruden D.M. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. http://snpeff.sourceforge.net/SnpEff.html;

RRID: SCR_005191

GERBIL v1.1 [ 63 Kimmel G.

Shamir R. GERBIL: Genotype resolution and block identification using likelihood. https://github.com/dice-group/gerbil