科學(xué)家們剛剛完成了紅毛猩猩的基因組測序，紅毛猩猩成為繼人類和黑猩猩之后第三個基因組成功測序的猿類,。
科學(xué)家們驚奇的發(fā)現(xiàn),，紅毛猩猩的DNA改變程度如此之小，遠(yuǎn)遠(yuǎn)小于人類和黑猩猩的DNA變化,。紅毛猩猩起源于約1200萬至1600萬年前,，而人類和黑猩猩則起源于約500萬至600萬年前，所以紅毛猩猩進(jìn)化的時間更久,。但是對這三種猿的基因組對比中發(fā)現(xiàn),，人類和黑猩猩得到或缺失的基因卻為紅毛猩猩的二倍多。
洛克和他的同事對六個蘇門答臘猩猩和五個婆羅洲猩猩進(jìn)行了測序,，先前的研究估計他們在100萬年前進(jìn)化成為不同的物種,。但是根據(jù)這篇1月26日的Nature文章報道，他們僅在40萬年前才進(jìn)化為不同的物種,。華盛頓大學(xué)結(jié)構(gòu)遺傳學(xué)家Devin Locke說,，先前的研究是建立在小部分基因組的數(shù)據(jù)之上的，當(dāng)擁有全部的紅毛猩猩基因組數(shù)據(jù)的時候,，這一切的分析變得更加的容易,。
26日發(fā)表在Genome Research的另外一篇相關(guān)研究顯示，通過對人類,、黑猩猩和紅毛猩猩三種基因組的對比發(fā)現(xiàn),，人類基因組更類似于紅毛猩猩的基因組，而不是黑猩猩的基因組,。這反映了人類和黑猩猩從同一個祖先進(jìn)化而來,，兩個物種擁有相同的紅毛猩猩DNA，但是,，經(jīng)過成千上萬年,，人類和黑猩猩分別進(jìn)化，在這個過程中,，黑猩猩因為某些原因失去了猩猩的DNA,，人類則保留了這個DNA.
在這些對比中,，更多的驚喜將會被發(fā)現(xiàn)。此外,，對大猩猩和巴諾布猿的基因組測序計劃正在順利進(jìn)行中,。（生物谷Bioon.com）
生物谷推薦原文出處：
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.
