科学家们刚刚完成了红毛猩猩的基因组测序，红毛猩猩成为继人类和黑猩猩之后第三个基因组成功测序的猿类。

科学家们惊奇的发现，红毛猩猩的DNA改变程度如此之小，远远小于人类和黑猩猩的DNA变化。红毛猩猩起源于约1200万至1600万年前，而人类和黑猩猩则起源于约500万至600万年前，所以红毛猩猩进化的时间更久。但是对这三种猿的基因组对比中发现，人类和黑猩猩得到或缺失的基因却为红毛猩猩的二倍多。

洛克和他的同事对六个苏门答腊猩猩和五个婆罗洲猩猩进行了测序，先前的研究估计他们在100万年前进化成为不同的物种。但是根据这篇1月26日的Nature文章报道，他们仅在40万年前才进化为不同的物种。华盛顿大学结构遗传学家Devin Locke说，先前的研究是建立在小部分基因组的数据之上的，当拥有全部的红毛猩猩基因组数据的时候，这一切的分析变得更加的容易。

26日发表在Genome Research的另外一篇相关研究显示，通过对人类、黑猩猩和红毛猩猩三种基因组的对比发现，人类基因组更类似于红毛猩猩的基因组，而不是黑猩猩的基因组。这反映了人类和黑猩猩从同一个祖先进化而来，两个物种拥有相同的红毛猩猩DNA，但是，经过成千上万年，人类和黑猩猩分别进化，在这个过程中，黑猩猩因为某些原因失去了猩猩的DNA，人类则保留了这个DNA.

在这些对比中，更多的惊喜将会被发现。此外，对大猩猩和巴诺布猿的基因组测序计划正在顺利进行中。

原文出处：

Nature   doi:10.1038/nature09687

Comparative and demographic analysis of orang-utan genomes

Devin P. Locke,LaDeana W. Hillier,Wesley C. Warren,Kim C. Worley,Lynne V. Nazareth,Donna M. Muzny,Shiaw-Pyng Yang,Zhengyuan Wang,Asif T. Chinwalla,Pat Minx,Makedonka Mitreva,Lisa Cook,Kim D. Delehaunty,Catrina Fronick,Heather Schmidt,Lucinda A. Fulton,Robert S. Fulton,Joanne O. Nelson,Vincent Magrini,Craig Pohl,Tina A. Graves,Chris Markovic,Andy Cree,Huyen H. Dinh,Jennifer Hume,Christie L. Kovar,Gerald R. Fowler,Gerton Lunter,Stephen Meader,Andreas Heger,Chris P. Ponting,Tomas Marques-Bonet,Can Alkan,Lin Chen,Ze Cheng,Jeffrey M. Kidd,Evan E. Eichler,Simon White,Stephen Searle,Albert J. Vilella,Yuan Chen,Paul Flicek,Jian Ma,Brian Raney,Bernard Suh,Richard Burhans,Javier Herrero,David Haussler,Rui Faria,Olga Fernando,Fleur Darré,Domènec Farré,Elodie Gazave,Meritxell Oliva,Arcadi Navarro,Roberta Roberto,Oronzo Capozzi,Nicoletta Archidiacono,Giuliano Della Valle,Stefania Purgato,Mariano Rocchi,Miriam K. Konkel,Jerilyn A. Walker,Brygg Ullmer,Mark A. Batzer,Arian F. A. Smit,Robert Hubley,Claudio Casola,Daniel R. Schrider,Matthew W. Hahn,Victor Quesada,Xose S. Puente,Gonzalo R. Ordo?ez,Carlos López-Otín,Tomas Vinar,Brona Brejova,Aakrosh Ratan,Robert S. Harris,Webb Miller,Carolin Kosiol,Heather A. Lawson,Vikas Taliwal,André L. Martins,Adam Siepel,Arindam RoyChoudhury,Xin Ma,Jeremiah Degenhardt,Carlos D. Bustamante,Ryan N. Gutenkunst,Thomas Mailund,Julien Y. Dutheil,Asger Hobolth,Mikkel H. Schierup,Oliver A. Ryder,Yuko Yoshinaga,Pieter J. de Jong,George M. Weinstock,Jeffrey Rogers,Elaine R. Mardis,Richard A. Gibbs& Richard K. Wilson

‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000?years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Genome Res. doi: 10.1101/gr.114751.110

Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection

Asger Hobolth1, Julien Y. Dutheil1, John Hawks2, Mikkel H. Schierup1,3 and Thomas Mailund1

Abstract

We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent HMM framework. We find ILS present in ~1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9-13 mya (contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at ~4 mya and a diverse ancestor of human and chimpanzee with an effective population size of ~50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS found to be reduced in exons and gene dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad scale recombination rate to be conserved through the complete ape phylogeny.