Statistical methods for detecting molecular adaptation.
Ziheng Yang,Joseph P. Bielawski +1 more
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TLDR
Recent statistical methods for detecting molecular adaptation are summarized, and their limitations and possible improvements are discussed.Abstract:
The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.read more
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TL;DR: Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
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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.
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Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
TL;DR: A modified branch-site model is described and used to construct two LRTs, one of which is a direct test of positive selection on the lineages of interest and is recommended for use in real data analysis and the other appears robust against violations of model assumptions.
References
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Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Journal ArticleDOI
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Masatoshi Nei,Takashi Gojobori +1 more
TL;DR: It is shown that all available methods tend to give an underestimate of the number of nonsynonymous substitutions when the number is large and computer simulation indicates that estimates of synonymous substitutions obtained by the two methods are quite accurate unless the numberof nucleotide substitutions per site is very large.
The neutral theory of molecular evolution.
TL;DR: The neutral theory as mentioned in this paper states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Journal ArticleDOI
Adaptive protein evolution at the Adh locus in Drosophila
John H. McDonald,Martin Kreitman +1 more
TL;DR: A simple statistical test of the neutral protein evolution hypothesis is proposed based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus, finding that there are more fixed replacement differences between species than expected.
Journal Article
Codon-substitution models for heterogeneous selection pressure at amino acid sites.
Shira N Goldman,Rasmus Nielsen,Qiaofeng Yang,Gloria A. Pedersen,David R. Nielsen,Ziheng Yang,Nick Goldman,sebnem ozemri sag,Daniel Wai Hung Ho +8 more
TL;DR: In this paper, the authors developed models that account for heterogeneous omega ratios among amino acid sites and applied them to phylogenetic analyses of protein-coding DNA sequences, which are useful for testing for adaptive molecular evolution and identifying amino acid points under diversifying selection.
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Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
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