Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model.
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model.
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DOI：
10.1371/journal.pgen.0030007
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发表时间：
2007-02-23
期刊：
影响因子：
4.5
通讯作者：
Schierup MH
中科院分区：
文献类型：
--
作者：
Hobolth A;Christensen OF;Mailund T;Schierup MH
人类、黑猩猩和大猩猩的谱系关系在基因组中存在差异。我们开发了一种隐马尔可夫模型（HMM），该模型纳入了这种差异，并将模型参数与种群遗传学数量相关联，例如物种形成时间和祖先种群规模。我们的HMM是对有重组的溯祖过程的一种易于分析的近似，在模拟中我们发现HMM的估计没有明显偏差。我们将HMM应用于四个常染色体连续的人 - 黑猩猩 - 大猩猩 - 红毛猩猩比对，总共包含190万个碱基对。我们发现人 - 黑猩猩的物种形成时间非常近（410 ± 40万年），并且祖先有效种群规模相当大（人 - 黑猩猩祖先为65000 ± 30000，人 - 黑猩猩 - 大猩猩祖先为45000 ± 10000）。此外，大约50%的人类基因组在与大猩猩物种形成之后才与黑猩猩溯祖。我们还考虑了25万个碱基对的X染色体比对，发现其有效种群规模远小于常染色体有效种群规模的75%。最后，我们发现不同谱系之间的转换率与区域范围内现今人类的重组率有很好的相关性，但与精细尺度的重组率和重组热点无关，这表明后者在进化上是暂时的。
灵长类动物进化是生物学的一个核心主题，从DNA序列数据中可以获得很多信息。一个关键参数是“我们何时成为人类”的时间，即过去人 - 黑猩猩祖先的后代分化为人类和黑猩猩的时间。其他重要参数包括过去人 - 黑猩猩 - 大猩猩祖先的后代分化为人 - 黑猩猩祖先和大猩猩祖先的时间，以及人 - 黑猩猩和人 - 黑猩猩 - 大猩猩祖先的种群规模。为了估计物种形成时间和祖先种群规模，我们开发了一种新的方法，该方法明确利用了连续基因组比对中的空间信息。此外，我们将这种方法应用于四个长的常染色体人 - 黑猩猩 - 大猩猩 - 红毛猩猩比对，并估计出人类和黑猩猩非常近的物种形成时间（约400万年）以及比现今人类有效种群规模大得多的祖先种群规模。我们还分析了X染色体序列数据，发现X染色体经历了与常染色体不同的历史，可能是由于选择的原因。
The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human–chimp ancestor and 45,000 ± 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient. Primate evolution is a central topic in biology and much information can be obtained from DNA sequence data. A key parameter is the time “when we became human,” i.e., the time in the past when descendents of the human–chimp ancestor split into human and chimpanzee. Other important parameters are the time in the past when descendents of the human–chimp–gorilla ancestor split into descendents of the human–chimp ancestor and the gorilla ancestor, and population sizes of the human–chimp and human–chimp–gorilla ancestors. To estimate speciation times and ancestral population sizes we have developed a new methodology that explicitly utilizes the spatial information in contiguous genome alignments. Furthermore, we have applied this methodology to four long autosomal human–chimp–gorilla–orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years) and ancestral population sizes much larger than the present-day human effective population size. We also analyzed X-chromosome sequence data and found that the X chromosome has experienced a different history from that of autosomes, possibly because of selection.
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影响因子：
1.7
作者：
Siepel, A;Haussler, D
通讯作者：
Haussler, D
影响因子：
64.8
作者：
Patterson, Nick;Richter, Daniel J.;Reich, David
通讯作者：
Reich, David
影响因子：
9.8
作者：
Chen, FC;Li, WH
通讯作者：
Li, WH
影响因子：
64.8
作者：
Haile-Selassie, Y
通讯作者：
Haile-Selassie, Y
DOI：
10.1016/s1251-8050(01)01529-4
发表时间：
2001-01-30
期刊：
COMPTES RENDUS DE L ACADEMIE DES SCIENCES SERIE II FASCICULE A-SCIENCES DE LA TERRE ET DES PLANETES
影响因子：
--
作者：
Senut, B;Pickford, M;Coppens, Y
通讯作者：
Coppens, Y