Data from: Genome sequencing highlights the dynamic early history of dogs

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.

为了识别驱动犬类驯化的遗传改变并重构其早期演化历史，我们对三只灰狼（分别采自三个推测的犬类驯化中心）、两个基础犬类谱系（巴仙吉犬（Basenji）与澳洲野犬（Dingo）），以及作为外类群（outgroup）的金豺，开展了高质量基因组测序。对上述序列的分析支持了一个种群历史模型：犬与狼的分化是一个动态过程，涉及两个谱系的种群瓶颈（population bottleneck）以及分化后的基因流（gene flow）。在犬类中，驯化瓶颈导致种群规模至少缩减16倍，其剧烈程度远高于此前的估算结果。灰狼在与犬类分化后不久便经历了一次急剧的种群瓶颈，这意味着犬类起源所依托的遗传多样性库，其规模远大于现代灰狼种群所呈现的水平。我们将犬类初始驯化的可信时间范围缩小至1.1万至1.6万年前，该时间早于农业兴起的节点。基于这一发现，我们拓展了此前关于犬类淀粉酶基因（AMY2B）拷贝数增加的相关研究——该基因被认为可助力犬类消化农业废弃物中的淀粉。我们在灰狼中检测到了淀粉酶拷贝数变异（copy number variation）的现存遗传变异，且在澳洲野犬与哈士奇（Husky）谱系中几乎未观察到拷贝数的增加。结合犬类起源的估算时间，上述结果为考古发现提供了额外支撑，表明最早的犬类是与狩猎采集者一同出现的，而非伴随农业人群诞生。关于犬类的地理起源，我们意外发现：所有采自推测驯化中心的现存灰狼谱系，与犬类的亲缘关系均未更近；相反，本次采样的灰狼构成了一个单系姊妹支系（monophyletic clade）。这一结果，结合驯化过程中犬与狼之间发生的基因交流，表明有必要重新评估此前关于犬类起源的各类假说。