Genome Sequencing Highlights the Dynamic Early History of Dogs
Adam H. Freedman,Ilan Gronau,Rena M. Schweizer,Diego Ortega-Del Vecchyo,Eunjung Han,Pedro Silva,Marco Galaverni,Zhenxin Fan,Peter Marx,Belen Lorente-Galdos,Holly C. Beale,Oscar Ramirez,Fereydoun Hormozdiari,Can Alkan,Carles Vilà,Kevin Squire,Eli Geffen,Josip Kusak,Adam R. Boyko,Heidi G. Parker,Clarence Lee,Vasisht Tadigotla,Adam Siepel,Carlos Bustamante,Timothy T. Harkins,Stanley F. Nelson,Elaine A. Ostrander,Tomas Marques-Bonet,Tomas Marques-Bonet,Robert K. Wayne,John Novembre +30 more
TLDR
It is found that none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade, suggesting that a re-evaluation of past hypotheses regarding dog origins is necessary.Abstract:
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.read more
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Ancient gene flow from early modern humans into Eastern Neanderthals
Martin Kuhlwilm,Ilan Gronau,Melissa J. Hubisz,Cesare de Filippo,Javier Prado-Martinez,Martin Kircher,Qiaomei Fu,Hernán A. Burbano,Carles Lalueza-Fox,Marco de la Rasilla,Antonio Rosas,Pavao Rudan,Dejana Brajković,Željko Kućan,Ivan Gušić,Tomas Marques-Bonet,Tomas Marques-Bonet,Aida M. Andrés,Bence Viola,Svante Pääbo,Matthias Meyer,Adam Siepel,Adam Siepel,Sergi Castellano +23 more
TL;DR: It is concluded that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Journal ArticleDOI
Genomic and archaeological evidence suggest a dual origin of domestic dogs.
Laurent A. F. Frantz,Victoria E. Mullin,Maud Pionnier-Capitan,Maud Pionnier-Capitan,Ophélie Lebrasseur,Morgane Ollivier,Angela R. Perri,Anna Linderholm,Anna Linderholm,Valeria Mattiangeli,Matthew D. Teasdale,Evangelos A. Dimopoulos,Evangelos A. Dimopoulos,Anne Tresset,Marilyne Duffraisse,Finbar McCormick,László Bartosiewicz,Erika Gál,Éva Ágnes Nyerges,Mikhail V. Sablin,Stéphanie Bréhard,Marjan Mashkour,Adrian Bălăşescu,Benjamin Gillet,Sandrine Hughes,Olivier Chassaing,Christophe Hitte,Jean-Denis Vigne,Keith Dobney,Keith Dobney,Catherine Hänni,Daniel G. Bradley,Greger Larson +32 more
TL;DR: Results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations, and East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
The Big Data Center: from deposition to integration and to translation
TL;DR: The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry.
Journal ArticleDOI
Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
Yali Xue,Javier Prado-Martinez,Peter H. Sudmant,Vagheesh M. Narasimhan,Vagheesh M. Narasimhan,Qasim Ayub,Michal Szpak,Peter Frandsen,Yuan Chen,Bryndis Yngvadottir,David Neil Cooper,Marc de Manuel,Jessica Hernandez-Rodriguez,Irene Lobon,Hans R. Siegismund,Luca Pagani,Luca Pagani,Michael A. Quail,Christina Hvilsom,Antoine Mudakikwa,Evan E. Eichler,Evan E. Eichler,Michael R. Cranfield,Tomas Marques-Bonet,Chris Tyler-Smith,Aylwyn Scally +25 more
TL;DR: It is found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation.
Journal ArticleDOI
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
Leif Andersson,Leif Andersson,Alan Archibald,Cynthia D.K. Bottema,Rudiger Brauning,Shane C. Burgess,Dave Burt,Eduardo Casas,Hans H. Cheng,Laura Clarke,Christine Couldrey,Brian P. Dalrymple,Christine G. Elsik,Sylvain Foissac,Elisabetta Giuffra,Martien A. M. Groenen,Ben J. Hayes,Ben J. Hayes,Ben J. Hayes,Lu Sheng S. Huang,Hassan Khatib,James W. Kijas,Heebal Kim,Joan K. Lunney,Fiona M. McCarthy,John C. McEwan,Stephen S. Moore,Bindu Nanduri,Cedric Notredame,Yniv Palti,Graham Plastow,James M. Reecy,Gary A. Rohrer,Elena Sarropoulou,Carl J. Schmidt,Jeffrey T. Silverstein,Ross L. Tellam,Michèle Tixier-Boichard,Gwenola Tosser-Klopp,Christopher K. Tuggle,Johanna Vilkki,Stephen N. White,Stephen N. White,Shuhong Zhao,Huaijun Zhou +44 more
TL;DR: The organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species is described.
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Journal ArticleDOI
Genome sequence, comparative analysis and haplotype structure of the domestic dog
Kerstin Lindblad-Toh,Claire M. Wade,Claire M. Wade,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Elinor K. Karlsson,Elinor K. Karlsson,David B. Jaffe,Michael Kamal,Michele Clamp,Jean L. Chang,Edward J. Kulbokas,Michael C. Zody,Evan Mauceli,Xiaohui Xie,Matthew Breen,Robert K. Wayne,Elaine A. Ostrander,Chris P. Ponting,Francis Galibert,Douglas Smith,Pieter J. deJong,Ewen F. Kirkness,Pablo Alvarez,Tara Biagi,William Brockman,Jonathan Butler,Chee-Wye Chin,April Cook,James Cuff,Mark J. Daly,Mark J. Daly,David DeCaprio,Sante Gnerre,Manfred Grabherr,Manolis Kellis,Michael Kleber,Carolyne Bardeleben,Leo Goodstadt,Andreas Heger,Christophe Hitte,Lisa Kim,Klaus-Peter Koepfli,Heidi G. Parker,John P. Pollinger,Stephen M. J. Searle,Nathan B. Sutter,Rachael Thomas,Caleb Webber,Jennifer Baldwin,Jennifer Baldwin,Adal Abebe,Amr Abouelleil,Lynne Aftuck,Mostafa Ait-zahra,Tyler Aldredge,Nicole R. Allen,Peter An,Scott Anderson,Claudel Antoine,Harindra Arachchi,Ali Aslam,Laura Ayotte,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Mostafa Benamara,Aaron M. Berlin,Daniel Bessette,Berta Blitshteyn,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Adam Brown,Patrick Cahill,Nadia Calixte,Jody Camarata,Yama Cheshatsang,Jeffrey Chu,Mieke Citroen,Alville Collymore,Patrick Cooke,Tenzin Dawoe,Riza M. Daza,Karin Decktor,Stuart DeGray,Norbu Dhargay,Kimberly Dooley,Kathleen Dooley,Passang Dorje,Kunsang Dorjee,Lester Dorris,Noah Duffey,Alan Dupes,Osebhajajeme Egbiremolen,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Patricia Ferreira,Sheila A. Fisher,Michael Fitzgerald,Karen Foley,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Diane Gage,Manuel Garber,Gary Gearin,Georgia Giannoukos,Tina Goode,Audra Goyette,Joseph Graham,Edward Grandbois,Kunsang Gyaltsen,Nabil Hafez,Daniel S. Hagopian,Birhane Hagos,Jennifer Ruth Sadler Hall,Claire M. Healy,Ryan Hegarty,Tracey Honan,Andrea Horn,Nathan Houde,Leanne Hughes,Leigh Anne Hunnicutt,M. Husby,Benjamin Jester,Charlien Jones,Asha Kamat,Ben Kanga,Cristyn Kells,Dmitry Khazanovich,Alix Chinh Kieu,Peter Kisner,Mayank Kumar,Krista Lance,Thomas E. Landers,Marcia Lara,William H. Lee,Jean-Pierre Leger,Niall J. Lennon,Lisa Leuper,Sarah LeVine,Jinlei Liu,Xiaohong Liu,Yeshi Lokyitsang,Tashi Lokyitsang,Annie Lui,Jan Macdonald,John E. Major,Richard Marabella,Kebede Maru,Charles Matthews,Susan McDonough,Teena Mehta,James Meldrim,Alexandre Melnikov,Louis Meneus,Atanas Mihalev,Tanya Mihova,Karen Hughes Miller,Rachel Mittelman,Valentine Mlenga,Leonidas Mulrain,Glen Munson,Adam Navidi,Jerome Naylor,Tuyen T. Nguyen,Nga Nguyen,Cindy Nguyen,Thu Nguyen,Robert Nicol,Nyima Norbu,Choe Norbu,Nathaniel Novod,Tenchoe Nyima,Peter Olandt,Barry O'Neill,Keith O'Neill,Sahal Osman,Lucien Oyono,Christopher Patti,Danielle Perrin,Pema Phunkhang,Fritz Pierre,Margaret Priest,Anthony Rachupka,Sujaa Raghuraman,Rayale Rameau,Verneda Ray,Christina Raymond,Filip Rege,Cecil Rise,Julie Rogers,Peter Rogov,Julie Sahalie,Sampath Settipalli,Ted Sharpe,Terrance Shea,Mechele Sheehan,Ngawang Sherpa,Jianying Shi,Diana M. Shih,Jessie Sloan,Cherylyn Smith,Todd Sparrow,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Sabrina M. Stone,Sean M. Sykes,Pierre Tchuinga,Pema Tenzing,Senait Tesfaye,Dawa Thoulutsang,Yama Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Vijay Venkataraman,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane E. Wilkinson,Adam Wilson,Shailendra Yadav,Shuli Yang,Xiaoping Yang,Geneva Young,Qing Yu,Joanne Zainoun,Lisa Zembek,Andrew Zimmer,Eric S. Lander,Eric S. Lander +241 more
TL;DR: A high-quality draft genome sequence of the domestic dog is reported, together with a dense map of single nucleotide polymorphisms (SNPs) across breeds, to shed light on the structure and evolution of genomes and genes.
Journal ArticleDOI
Inference of human population history from individual whole-genome sequences
Heng Li,Richard Durbin +1 more
TL;DR: A more detailed history of human population sizes between approximately ten thousand and a million years ago is presented, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male, a Korean male, three European individuals, and two Yoruba males.
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