Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.
Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes.
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DOI：
10.1093/gbe/evs075
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发表时间：
2012
影响因子：
3.3
通讯作者：
Satta Y
中科院分区：
文献类型：
--
作者：
Hara Y;Imanishi T;Satta Y
人类的人口学历史将为识别塑造人类的进化事件提供有用的信息，但即使在基因组时代也仍然存在争议。为了解决这些争议，我们在全基因组比对的基础上推断了导致人类和类人猿的谱系中的物种形成时间(T)和祖先种群大小(N)。合并模拟确定了获得高频无重组块所需的对准块的大小和它们之间的间隔。模拟结果表明，块的大小对参数推理的影响很大，重组是实现最优参数推理的重要因素。从人类(H)、黑猩猩(C)、大猩猩(G)和猩猩的全基因组序列(1.9千兆碱基)中，抽取以≥5-kb为间隔的100bp比对区块，用马尔科夫链蒙特卡罗方法估计τ=μT和θ=4μgn，其中μ为突变率，g为世代时间。虽然估计的τHC在不同的染色体上是不同的，但τHC和τHcg在染色体上是强烈相关的，这表明τ的变异受到μ的变异，而不是T的变异，因此，所有染色体都共享一个物种形成时间。随后，假设不同谱系和染色体的μ不同，我们估计黑猩猩、大猩猩和猩猩的T_s分别为6·0-7·6、7·6-9·7和15-19 Ma。这些物种形成时间与化石记录一致。我们的结论是，在我们的无重组分析中，物种形成时间将是决定性的，人类和黑猩猩之间的物种形成是单一事件。
The demographic history of human would provide helpful information for identifying the evolutionary events that shaped the humanity but remains controversial even in the genomic era. To settle the controversies, we inferred the speciation times (T) and ancestral population sizes (N) in the lineage leading to human and great apes based on whole-genome alignment. A coalescence simulation determined the sizes of alignment blocks and intervals between them required to obtain recombination-free blocks with a high frequency. This simulation revealed that the size of the block strongly affects the parameter inference, indicating that recombination is an important factor for achieving optimum parameter inference. From the whole genome alignments (1.9 giga-bases) of human (H), chimpanzee (C), gorilla (G), and orangutan, 100-bp alignment blocks separated by ≥5-kb intervals were sampled and subjected to estimate τ = μT and θ = 4μgN using the Markov chain Monte Carlo method, where μ is the mutation rate and g is the generation time. Although the estimated τHC differed across chromosomes, τHC and τHCG were strongly correlated across chromosomes, indicating that variation in τ is subject to variation in μ, rather than T, and thus, all chromosomes share a single speciation time. Subsequently, we estimated Ts of the human lineage from chimpanzee, gorilla, and orangutan to be 6.0–7.6, 7.6–9.7, and 15–19 Ma, respectively, assuming variable μ across lineages and chromosomes. These speciation times were consistent with the fossil records. We conclude that the speciation times in our recombination-free analysis would be conclusive and the speciation between human and chimpanzee was a single event.
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影响因子：
9.8
作者：
Imanishi T;Itoh T;Suzuki Y;O'Donovan C;Fukuchi S;Koyanagi KO;Barrero RA;Tamura T;Yamaguchi-Kabata Y;Tanino M;Yura K;Miyazaki S;Ikeo K;Homma K;Kasprzyk A;Nishikawa T;Hirakawa M;Thierry-Mieg J;Thierry-Mieg D;Ashurst J;Jia L;Nakao M;Thomas MA;Mulder N;Karavidopoulou Y;Jin L;Kim S;Yasuda T;Lenhard B;Eveno E;Suzuki Y;Yamasaki C;Takeda J;Gough C;Hilton P;Fujii Y;Sakai H;Tanaka S;Amid C;Bellgard M;Bonaldo Mde F;Bono H;Bromberg SK;Brookes AJ;Bruford E;Carninci P;Chelala C;Couillault C;de Souza SJ;Debily MA;Devignes MD;Dubchak I;Endo T;Estreicher A;Eyras E;Fukami-Kobayashi K;Gopinath GR;Graudens E;Hahn Y;Han M;Han ZG;Hanada K;Hanaoka H;Harada E;Hashimoto K;Hinz U;Hirai M;Hishiki T;Hopkinson I;Imbeaud S;Inoko H;Kanapin A;Kaneko Y;Kasukawa T;Kelso J;Kersey P;Kikuno R;Kimura K;Korn B;Kuryshev V;Makalowska I;Makino T;Mano S;Mariage-Samson R;Mashima J;Matsuda H;Mewes HW;Minoshima S;Nagai K;Nagasaki H;Nagata N;Nigam R;Ogasawara O;Ohara O;Ohtsubo M;Okada N;Okido T;Oota S;Ota M;Ota T;Otsuki T;Piatier-Tonneau D;Poustka A;Ren SX;Saitou N;Sakai K;Sakamoto S;Sakate R;Schupp I;Servant F;Sherry S;Shiba R;Shimizu N;Shimoyama M;Simpson AJ;Soares B;Steward C;Suwa M;Suzuki M;Takahashi A;Tamiya G;Tanaka H;Taylor T;Terwilliger JD;Unneberg P;Veeramachaneni V;Watanabe S;Wilming L;Yasuda N;Yoo HS;Stodolsky M;Makalowski W;Go M;Nakai K;Takagi T;Kanehisa M;Sakaki Y;Quackenbush J;Okazaki Y;Hayashizaki Y;Hide W;Chakraborty R;Nishikawa K;Sugawara H;Tateno Y;Chen Z;Oishi M;Tonellato P;Apweiler R;Okubo K;Wagner L;Wiemann S;Strausberg RL;Isogai T;Auffray C;Nomura N;Gojobori T;Sugano S
通讯作者：
Sugano S
影响因子：
4.5
作者：
Hobolth A;Christensen OF;Mailund T;Schierup MH
通讯作者：
Schierup MH
影响因子：
7
作者：
Bouffard, GG;Idol, JR;Green, ED
通讯作者：
Green, ED
影响因子：
10.7
作者：
Hey, Jody
通讯作者：
Hey, Jody
影响因子：
10.7
作者：
Burgess, Ralph;Yang, Ziheng
通讯作者：
Yang, Ziheng