Journal ArticleDOI
Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios
Andrew G. Clark,Stephen Glanowski,Rasmus Nielsen,Paul Thomas,Anish Kejariwal,Melissa A. Todd,David M. Tanenbaum,Daniel Civello,Fu Lu,Brian Murphy,Steve Ferriera,Gary Wang,Xianqgun Zheng,Thomas J. White,John J. Sninsky,Mark Raymond Adams,Michele Cargill +16 more
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TLDR
Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport and human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.Abstract:
Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.read more
Citations
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疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
A Draft Sequence of the Neandertal Genome
Richard E. Green,Johannes Krause,Adrian W. Briggs,Tomislav Maricic,Udo Stenzel,Martin Kircher,Nick Patterson,Heng Li,Weiwei Zhai,Markus Hsi-Yang Fritz,Nancy F. Hansen,Eric Durand,Anna-Sapfo Malaspinas,Jeffrey D. Jensen,Tomas Marques-Bonet,Tomas Marques-Bonet,Can Alkan,Kay Prüfer,Matthias Meyer,Hernán A. Burbano,Jeffrey M. Good,Jeffrey M. Good,Rigo Schultz,Ayinuer Aximu-Petri,Anne Butthof,Barbara Höber,Barbara Höffner,Madien Siegemund,Antje Weihmann,Chad Nusbaum,Eric S. Lander,Carsten Russ,Nathaniel Novod,Jason P. Affourtit,Michael Egholm,Christine Verna,Pavao Rudan,Dejana Brajković,Željko Kućan,Ivan Gušić,Vladimir B. Doronichev,Liubov V. Golovanova,Carles Lalueza-Fox,Marco de la Rasilla,Javier Fortea,Antonio Rosas,Ralf Schmitz,Philip L. F. Johnson,Evan E. Eichler,Daniel Falush,Ewan Birney,James C. Mullikin,Montgomery Slatkin,Rasmus Nielsen,Janet Kelso,Michael Lachmann,David Reich,David Reich,Svante Pääbo +58 more
TL;DR: The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Journal ArticleDOI
A Map of Recent Positive Selection in the Human Genome
TL;DR: A set of SNPs is developed that can be used to tag the strongest ∼250 signals of recent selection in each population, and it is found that by some measures the authors' strongest signals of selection are from the Yoruba population.
Journal ArticleDOI
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
Matthieu Foll,Oscar E. Gaggiotti +1 more
TL;DR: It is shown that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives, and it is demonstrated that it is possible to avoid them by carefully choosing the populations that should be included in the analysis.
Journal ArticleDOI
Initial sequence of the chimpanzee genome and comparison with the human genome
Tarjei S. Mikkelsen,LaDeana W. Hillier,Evan E. Eichler,Michael C. Zody,David B. Jaffe,Shiaw-Pyng Yang,Wolfgang Enard,Ines Hellmann,Kerstin Lindblad-Toh,Tasha K. Altheide,Nicoletta Archidiacono,Peer Bork,Jonathan Butler,Jean L. Chang,Ze Cheng,Asif T. Chinwalla,Pieter J. de Jong,Kimberley D. Delehaunty,Catrina Fronick,Lucinda L. Fulton,Yoav Gilad,Gustavo Glusman,Sante Gnerre,Tina Graves,Toshiyuki Hayakawa,Karen E. Hayden,Xiaoqiu Huang,Hongkai Ji,W. James Kent,Mary Claire King,Edward J. Kulbokasl,Ming K. Lee,Ge Liu,Carlos López-Otín,Kateryna D. Makova,Orna Man,Elaine R. Mardis,Evan Mauceli,Tracie L. Miner,William E. Nash,Joanne O. Nelson,Svante Pääbo,Nick Patterson,Craig Pohl,Katherine S. Pollard,Kay Prüfer,Xose S. Puente,David Reich,Mariano Rocchi,Kate R. Rosenbloom,Maryellen Ruvolo,Daniel J. Richter,Stephen F. Schaffner,Arian F.A. Smit,Scott M. Smith,Mikita Suyama,James E. Taylor,David Torrents,Eray Tüzün,Ajit Varki,Gloria Velasco,Mario Ventura,John W. Wallis,Michael C. Wendl,Richard K. Wilson,Eric S. Lander,Robert H. Waterston +66 more
TL;DR: It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
References
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疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
Evolutionary trees from DNA sequences: A maximum likelihood approach
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Journal ArticleDOI
The sequence of the human genome.
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TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI
Evolution at two levels in humans and chimpanzees
Mary Claire King,Allan C. Wilson +1 more
Journal ArticleDOI
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Nick Goldman,Ziheng Yang +1 more
TL;DR: Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.
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