Data from: The evolutionary history of dogs in the Americas

Version 1.0

Leathlobhair, Máire Ní; Perri, Angela R.; Irving-Pease, Evan K.; Witt, Kelsey E.; Linderholm, Anna; Haile, James; Lebrasseur, Ophelie; Ameen, Carly; Blick, Jeffrey; Boyko, Adam R.; Brace, Selina; Nunes Cortes, Yahaira; Crockford, Susan J.; Devault, Alison; Dimopoulos, Evangelos A.; Eldridge, Morley; Enk, Jacob; Gopalakrishnan, Shyam; Gori, Kevin; Grimes, Vaughan; Guiry, Eric; Hansen, Anders J.; Hulme-Beaman, Ardern; Johnson, John; Kitchen, Andrew; Kasparov, Aleksei K.; Kwon, Young-Mi; Nikolskiy, Pavel A.; Peraza Lope, Carlos; Manin, Aurélie; Martin, Terrance; Meyer, Michael; Noack Myers, Kelsey; Omura, Mark; Rouillard, Jean-Marie; Pavlova, Elena Y.; Sciulli, Paul; Mikkel-Holger, Sinding S.; Strakova, Andrea; Ivanova, Varvara V.; Widga, Christopher; Willerslev, Eske; Pitulko, Vladimir V.; Barnes, Ian; Gilbert, M. Thomas P.; Dobney, Keith M.; Malhi, Ripan S.; Murchison, Elizabeth P.; Larson, Greger; Frantz, Laurent A. F., 2019, "Data from: The evolutionary history of dogs in the Americas", https://doi.org/10.5683/SP2/FFOWXI, Borealis, V1, UNF:6:0Zygxgf4f0+qMK4JwI4n1g== [fileUNF]

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Description	Abstract Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. Remarkably, the closest detectable extant lineage to pre-contact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8,000 years ago. (2020-06-24) Usage notes Mitochondrial DNA FASTA fileFASTA file containing 1166 dog mtDNA genomes used in this studyfull_mtDNA_alignment.fasta NEXUS treeMaximum likelihood tree (RAxML) of 1166 dogs mtDNA genomes used in this studyfull_mtDNA_alignment.tre Excel sheetPublication source of the 1166 mtDNA genomes used in this studyfull_mtDNA_alignment.xlsx Plink (bed) fileContains genotype for dogs 54 dogsfull_data.bed Plink file (bim)Contains genotype for 54 dogsfull_data.bim Plink file (fam)Contains genotype for 54 dogsfull_data.fam NJ tree in Figure 2bNJ tree in Figure 2b (see Table S2 for more info)Figure_b.tre Nexus fileNexus file used for producing Figure S12 (MKV model in MrBayes)Binary_char_MKV.nex NEXUS treeBayesian tree in Figure S12 (see Table S2 for more info)Figure_S12.tre (2020-06-24)
Subject	Other
Keyword	Canis lupus familiaris, Canis lupus
Related Publication	Article
Notes	Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/zrwzgCscLZcxNYNjilPA1tHuWTfUMkUZXmMpSDzv83k Storage size: 121385898 Visibility: public
License/Data Use Agreement	Custom Dataset Terms

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	1 to 10 of 10 Files	Original Format Archival Format (.tab)
	Binary_char_MKV.nex Plain Text - 1.5 MB Published May 20, 2021 12 Downloads MD5: 27bb7a232ee4e0e6ba505d9154b43fce Nexus file used for producing Figure S12 (MKV model in MrBayes)	Preview "Binary_char_MKV.nex" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	dryad_s1k47j4.json Plain Text - 11.3 KB Published May 20, 2021 3 Downloads MD5: 88008a7782ca3dc6a9b9721849c9cb39 Original JSON from Dryad CodeDocumentation	Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	Figure_b.tre Plain Text - 26.2 KB Published May 20, 2021 4 Downloads MD5: 29dc120a505bc3c0bd1280f20a811562 NJ tree in Figure 2b (see Table S2 for more info)	Preview "Figure_b.tre" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	Figure_S12.tre Plain Text - 20.3 KB Published May 20, 2021 3 Downloads MD5: 5b6f7ab537ec1ec7d1fe26fd4b730ed5 Bayesian tree in Figure S12 (see Table S2 for more info)	Preview "Figure_S12.tre" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text
	full_data.bed PLINK Binary - 27.5 MB Published May 20, 2021 3 Downloads MD5: 937b945c6ce91d4e51fb6a84c9230e56 Contains genotype for dogs 54 dogs	Access File File Access Public Download Options PLINK Binary Download Metadata Data File Citation EndNote XML RIS BibTeX
	full_data.bim Unknown - 67.3 MB Published May 20, 2021 3 Downloads MD5: 2e87c4aec9db336a49c808c11d2242e9 Contains genotype for 54 dogs	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	full_data.fam Unknown - 1.1 KB Published May 20, 2021 3 Downloads MD5: 873b78f6d156032f687fa659981159c8 Contains genotype for 54 dogs	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	full_mtDNA_alignment.fasta application/x-fasta - 18.6 MB Published May 20, 2021 5 Downloads MD5: da2b29e402c3f632e6cb0e2094bd3bfa FASTA file containing 1166 dog mtDNA genomes used in this study	Access File File Access Public Download Options application/x-fasta Download Metadata Data File Citation EndNote XML RIS BibTeX
	full_mtDNA_alignment.tab Tabular Data - 167.7 KB Published May 20, 2021 5 Downloads 4 Variables, 1166 Observations UNF:6:0Zygxgf4f0+qMK4JwI4n1g== Publication source of the 1166 mtDNA genomes used in this study	Access File File Access Public Download Options MS Excel Spreadsheet (Original File Format) Tab-Delimited RData Download Metadata Variable Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Data Explorer
	full_mtDNA_alignment.tre Plain Text - 632.2 KB Published May 20, 2021 4 Downloads MD5: 3f3177fa9dad01e0f05df310a7c24eac Maximum likelihood tree (RAxML) of 1166 dogs mtDNA genomes used in this study	Preview "full_mtDNA_alignment.tre" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX Explore Options Read Text

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Persistent Identifier	doi:10.5683/SP2/FFOWXI
Publication Date	2021-05-20
Citation Date
Title	Data from: The evolutionary history of dogs in the Americas
Other Identifier	Dryad: doi:10.5061/dryad.s1k47j4
Author	Leathlobhair, Máire Ní (University of Cambridge) Perri, Angela R. (Durham University) Irving-Pease, Evan K. (University of Oxford) Witt, Kelsey E. (University of Illinois at Urbana Champaign) Linderholm, Anna (University of Oxford) Haile, James (University of Oxford) Lebrasseur, Ophelie (University of Oxford) Ameen, Carly (University of Liverpool) Blick, Jeffrey (Georgia College & State University) Boyko, Adam R. (Cornell University) Brace, Selina (Natural History Museum) Nunes Cortes, Yahaira (University at Albany, State University of New York) Crockford, Susan J. (Pacific Identifications, Victoria, Canada.) Devault, Alison (Arbor Biosciences, Ann Arbor, MI, USA.) Dimopoulos, Evangelos A. (University of Oxford) Eldridge, Morley (Millennia Research, Victoria, Canada.) Enk, Jacob (Arbor Biosciences, Ann Arbor, MI, USA.) Gopalakrishnan, Shyam (University of Copenhagen) Gori, Kevin (University of Cambridge) Grimes, Vaughan (Memorial University of Newfoundland) Guiry, Eric (University of British Columbia) Hansen, Anders J. (University of Copenhagen) Hulme-Beaman, Ardern (University of Oxford) Johnson, John (Santa Barbara Museum of Natural History) Kitchen, Andrew (University of Iowa) Kasparov, Aleksei K. (Russian Academy of Sciences) Kwon, Young-Mi (University of Cambridge) Nikolskiy, Pavel A. (Russian Academy of Sciences) Peraza Lope, Carlos (National Institute of Anthropology and History) Manin, Aurélie (University of York) Martin, Terrance (Illinois State Museum) Meyer, Michael (Touray & Meyer Veterinary Clinic, Serrekunda, Gambia.) Noack Myers, Kelsey (Indiana University Bloomington) Omura, Mark (Harvard University) Rouillard, Jean-Marie (Arbor Biosciences, Ann Arbor, MI, USA.) Pavlova, Elena Y. (Russian Academy of Sciences) Sciulli, Paul (The Ohio State University) Mikkel-Holger, Sinding S. (University of Copenhagen) Strakova, Andrea (University of Cambridge) Ivanova, Varvara V. (VNIIOkeangeologia Research Institute, St. Petersburg, Russia.) Widga, Christopher (Tennessee State University) Willerslev, Eske (University of Copenhagen) Pitulko, Vladimir V. (Russian Academy of Sciences) Barnes, Ian (Natural History Museum) Gilbert, M. Thomas P. (University of Copenhagen) Dobney, Keith M. (University of Liverpool) Malhi, Ripan S. (University of Illinois at Urbana Champaign) Murchison, Elizabeth P. (University of Cambridge) Larson, Greger (University of Oxford) Frantz, Laurent A. F. (University of Oxford)
Point of Contact	Use email button above to contact. UBC Library Research Data Team
Description	Abstract Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. Remarkably, the closest detectable extant lineage to pre-contact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8,000 years ago. (2020-06-24) Usage notes Mitochondrial DNA FASTA fileFASTA file containing 1166 dog mtDNA genomes used in this studyfull_mtDNA_alignment.fasta NEXUS treeMaximum likelihood tree (RAxML) of 1166 dogs mtDNA genomes used in this studyfull_mtDNA_alignment.tre Excel sheetPublication source of the 1166 mtDNA genomes used in this studyfull_mtDNA_alignment.xlsx Plink (bed) fileContains genotype for dogs 54 dogsfull_data.bed Plink file (bim)Contains genotype for 54 dogsfull_data.bim Plink file (fam)Contains genotype for 54 dogsfull_data.fam NJ tree in Figure 2bNJ tree in Figure 2b (see Table S2 for more info)Figure_b.tre Nexus fileNexus file used for producing Figure S12 (MKV model in MrBayes)Binary_char_MKV.nex NEXUS treeBayesian tree in Figure S12 (see Table S2 for more info)Figure_S12.tre (2020-06-24)
Subject	Other
Keyword	Canis lupus familiaris (Dryad) Canis lupus (Dryad)
Related Publication	Article doi: https://doi.org/10.1126/science.aao4776
Notes	Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/zrwzgCscLZcxNYNjilPA1tHuWTfUMkUZXmMpSDzv83k Storage size: 121385898 Visibility: public
Distribution Date	2019-05-07
Deposit Date	2020-06-24

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