Genome sequencing highlights the dynamic early history of dogs.
Genome sequencing highlights the dynamic early history of dogs.
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DOI：
10.1371/journal.pgen.1004016
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发表时间：
2014-01
期刊：
影响因子：
4.5
通讯作者：
Novembre J
中科院分区：
文献类型：
--
作者：
Freedman AH;Gronau I;Schweizer RM;Ortega-Del Vecchyo D;Han E;Silva PM;Galaverni M;Fan Z;Marx P;Lorente-Galdos B;Beale H;Ramirez O;Hormozdiari F;Alkan C;Vilà C;Squire K;Geffen E;Kusak J;Boyko AR;Parker HG;Lee C;Tadigotla V;Wilton A;Siepel A;Bustamante CD;Harkins TT;Nelson SF;Ostrander EA;Marques-Bonet T;Wayne RK;Novembre J
为了识别狗驯化的遗传变化并重建其早期进化史，我们从三只灰狼中产生了高质量的基因组序列，其中一只来自三个公认的狗驯化中心，两个基础狗谱系（Basenji和Dingo）和一只金豺作为外群。这些序列的分析支持一个人口模型，其中狗和狼分歧通过一个动态的过程，涉及人口瓶颈的血统和后分歧基因流。在狗中，驯化瓶颈涉及人口规模至少减少16倍，这比以前估计的要严重得多。在狼与狗分化后不久，狼的数量就出现了一个急剧的瓶颈，这意味着狗的多样性远远大于现代狼的数量。我们将狗最初驯化的合理时间范围缩小到1.1 - 1.6万年前，早于农业的兴起。鉴于这一发现，我们扩展了以前的工作，增加了狗的淀粉酶基因（AMY 2B）的拷贝数，这被认为有助于消化农业垃圾中的淀粉。我们发现常设变化的淀粉酶拷贝数变化的狼和小或没有拷贝数增加的野狗和哈士奇血统。结合狗起源的估计时间，这些结果为考古发现提供了额外的支持，表明最早的狗是与狩猎采集者而不是农业家一起出现的。关于狗的地理起源，我们发现，令人惊讶的是，没有一个现存的狼谱系从假定的驯化中心是更密切相关的狗，相反，采样狼形成一个姐妹单系分支。这一结果，结合狗狼混合物在驯化过程中，表明重新评估过去的假设狗的起源是必要的。狗的驯化过程仍然知之甚少，主要是因为迄今为止还没有研究利用狼和狗的全基因组进行深度测序，以同时评估对拟议来源地区的支持：东亚，中东和欧洲。为了调查狗的起源，我们从假定的起源中心，两个基础的狗品种（Basenji和Dingo），和一个金豺作为外群的三个狼的基因组序列。我们发现，没有一个来自假设的驯化中心的狼谱系被支持为狗的来源谱系，狗和狼在11000 - 16000年前在一个涉及广泛混合的过程中分化，随后是狼的瓶颈。此外，我们调查了淀粉酶（AMY 2B）基因家族在狗，最近被认为是至关重要的驯化，以增加膳食淀粉的扩展。我们在狼中发现了AMY 2B拷贝数的常设变异，并表明一些品种，如Dingo和Husky，缺乏AMY 2B扩增。这表明，在驯化过程开始时，狗的特点可能是比现代狗更食肉，这与早期狩猎采集者的饮食相同。
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. The process of dog domestication is still poorly understood, largely because no studies thus far have leveraged deeply sequenced whole genomes from wolves and dogs to simultaneously evaluate support for the proposed source regions: East Asia, the Middle East, and Europe. To investigate dog origins, we sequence three wolf genomes from the putative centers of origin, two basal dog breeds (Basenji and Dingo), and a golden jackal as an outgroup. We find that none of the wolf lineages from the hypothesized domestication centers is supported as the source lineage for dogs, and that dogs and wolves diverged 11,000–16,000 years ago in a process involving extensive admixture and that was followed by a bottleneck in wolves. In addition, we investigate the amylase (AMY2B) gene family expansion in dogs, which has recently been suggested as being critical to domestication in response to increased dietary starch. We find standing variation in AMY2B copy number in wolves and show that some breeds, such as Dingo and Husky, lack the AMY2B expansion. This suggests that, at the beginning of the domestication process, dogs may have been characterized by a more carnivorous diet than their modern day counterparts, a diet held in common with early hunter-gatherers.
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影响因子：
9.8
作者：
Boyko AR;Quignon P;Li L;Schoenebeck JJ;Degenhardt JD;Lohmueller KE;Zhao K;Brisbin A;Parker HG;vonHoldt BM;Cargill M;Auton A;Reynolds A;Elkahloun AG;Castelhano M;Mosher DS;Sutter NB;Johnson GS;Novembre J;Hubisz MJ;Siepel A;Wayne RK;Bustamante CD;Ostrander EA
通讯作者：
Ostrander EA
影响因子：
30.8
作者：
Alkan, Can;Kidd, Jeffrey M.;Marques-Bonet, Tomas;Aksay, Gozde;Antonacci, Francesca;Hormozdiari, Fereydoun;Kitzman, Jacob O.;Baker, Carl;Malig, Maika;Mutlu, Onur;Sahinalp, S. Cenk;Gibbs, Richard A.;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
3.7
作者：
Ovodov ND;Crockford SJ;Kuzmin YV;Higham TF;Hodgins GW;van der Plicht J
通讯作者：
van der Plicht J
影响因子：
10.7
作者：
Pang JF;Kluetsch C;Zou XJ;Zhang AB;Luo LY;Angleby H;Ardalan A;Ekström C;Sköllermo A;Lundeberg J;Matsumura S;Leitner T;Zhang YP;Savolainen P
通讯作者：
Savolainen P
影响因子：
64.8
作者：
Li, Heng;Durbin, Richard
通讯作者：
Durbin, Richard