title: Worldwide patterns of genomic variation and admixture in gray wolves.
abstract: The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter-gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.
authors.affiliation: Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA;
authors.forename: Zhenxin
authors.initials: Z
authors.lastname: Fan
authors.affiliation: CIBIO-UP, University of Porto, Vairão, 4485-661, Portugal;
authors.forename: Pedro
authors.initials: P
authors.lastname: Silva
authors.affiliation: Efi Arazi School of Computer Science, the Herzliya Interdisciplinary Center (IDC), Herzliya 46150, Israel;
authors.forename: Ilan
authors.initials: I
authors.lastname: Gronau
authors.affiliation: Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA;
authors.forename: Shuoguo
authors.initials: S
authors.lastname: Wang
authors.affiliation: Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain;
authors.forename: Aitor Serres
authors.initials: AS
authors.lastname: Armero
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA;
authors.forename: Rena M
authors.initials: RM
authors.lastname: Schweizer
authors.affiliation: ICREA at Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain;
authors.forename: Oscar
authors.initials: O
authors.lastname: Ramirez
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA;
authors.forename: John
authors.initials: J
authors.lastname: Pollinger
authors.affiliation: ISPRA, Ozzano dell'Emilia, 40064, Italy;
authors.forename: Marco
authors.initials: M
authors.lastname: Galaverni
authors.affiliation: Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California 90095-1606, USA;
authors.forename: Diego
authors.initials: D
authors.lastname: Ortega Del-Vecchyo
authors.affiliation: Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China;
authors.forename: Lianming
authors.initials: L
authors.lastname: Du
authors.affiliation: Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, People's Republic of China, 610081;
authors.forename: Wenping
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, People's Republic of China, 610081;
authors.forename: Zhihe
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA; Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA;
authors.forename: Jinchuan
authors.initials: J
authors.lastname: Xing
authors.affiliation: Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Vilà
authors.affiliation: ICREA at Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain; Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: CIBIO-UP, University of Porto, Vairão, 4485-661, Portugal;
authors.forename: Raquel
authors.initials: R
authors.lastname: Godinho
authors.affiliation: Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China;
authors.forename: Bisong
authors.initials: B
authors.lastname: Yue
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA;
authors.forename: Robert K
authors.initials: RK
authors.lastname: Wayne
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D004285:Dogs / Q000235:genetics*; D005260:Female; D016678:Genome; D006824:Hybridization, Genetic; D008297:Male; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D019596:Wolves / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial