Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species
作者： Carina F Mugal , Verena E Kutschera , Fidel Botero-Castro , Jochen B W Wolf , Ingemar Kaj
关键词:
摘要: The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate the fixation rate ω, which measures extent to natural selection modulates protein evolution. Its computation based on phylogenetic approach and computes divergence protein-coding DNA between species, traditionally using single representative per species. This ignores presence polymorphisms relies indirect assumption that new mutations fix instantaneously, an generally violated reasonable only for distantly related violation underlying leads time-dependence biased estimates ω in particular closely where contribution ancestral lineage-specific substantial. We here use time-dependent Poisson random field model derive analytical expression dN/dS as function time sample size. then extend our framework estimation proportion adaptive evolution α. mathematical treatment enables us show joint usage polymorphism data can assist inference Moreover, results provide basis protocol α illustrate performance this by studying population set four corvid involves at different time-scales several choices sizes.
oup.com
sci-hub.se 参考文章(118)
Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood Molecular Biology and Evolution. ,vol. 24, pp. 1586- 1591 ,(2007) , 10.1093/MOLBEV/MSM088
J. Charlesworth, A. Eyre-Walker, The McDonald–Kreitman Test and Slightly Deleterious Mutations Molecular Biology and Evolution. ,vol. 25, pp. 1007- 1015 ,(2008) , 10.1093/MOLBEV/MSN005
Ziheng Yang, Rasmus Nielsen, Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models Molecular Biology and Evolution. ,vol. 17, pp. 32- 43 ,(2000) , 10.1093/OXFORDJOURNALS.MOLBEV.A026236
Nicolas Bierne, Adam Eyre-Walker, The Genomic Rate of Adaptive Amino Acid Substitution in Drosophila Molecular Biology and Evolution. ,vol. 21, pp. 1350- 1360 ,(2004) , 10.1093/MOLBEV/MSH134
W. G. HILL, ALAN ROBERTSON, The effect of linkage on limits to artificial selection. Genetics Research. ,vol. 8, pp. 269- 294 ,(1966) , 10.1017/S001667230800949X
A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, M. A. DePristo, The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Genome Research. ,vol. 20, pp. 1297- 1303 ,(2010) , 10.1101/GR.107524.110
P. W. Messer, D. A. Petrov, Frequent adaptation and the McDonald–Kreitman test Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 8615- 8620 ,(2013) , 10.1073/PNAS.1220835110
Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon YW Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R Da Fonseca, Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, Ganesh Ganapathy, Bastien Boussau, Md Shamsuzzoha Bayzid, Volodymyr Zavidovych, Sankar Subramanian, Toni Gabaldón, Salvador Capella-Gutiérrez, Jaime Huerta-Cepas, Bhanu Rekepalli, Kasper Munch, Mikkel Schierup, Bent Lindow, Wesley C Warren, David Ray, Richard E Green, Michael W Bruford, Xiangjiang Zhan, Andrew Dixon, Shengbin Li, Ning Li, Yinhua Huang, Elizabeth P Derryberry, Mads Frost Bertelsen, Frederick H Sheldon, Robb T Brumfield, Claudio V Mello, Peter V Lovell, Morgan Wirthlin, Maria Paula Cruz Schneider, Francisco Prosdocimi, José Alfredo Samaniego, Amhed Missael Vargas Velazquez, Alonzo Alfaro-Núñez, Paula F Campos, Bent Petersen, Thomas Sicheritz-Ponten, An Pas, Tom Bailey, Paul Scofield, Michael Bunce, David M Lambert, Qi Zhou, Polina Perelman, Amy C Driskell, Beth Shapiro, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Qiuemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnea Smeds, Frank E Rheindt, Michael Braun, Jon Fjeldsa, Ludovic Orlando, F Keith Barker, Knud Andreas Jønsson, Warren Johnson, Klaus-Peter Koepfli, Stephen O’Brien, David Haussler, Oliver A Ryder, Carsten Rahbek, Eske Willerslev, Gary R Graves, Travis C Glenn, John McCormack, Dave Burt, Hans Ellegren, Per Alström, Scott V Edwards, Alexandros Stamatakis, David P Mindell, Joel Cracraft, Edward L Braun, Tandy Warnow, Wang Jun, M Thomas P Gilbert, Guojie Zhang, None, Whole-genome analyses resolve early branches in the tree of life of modern birds Science. ,vol. 346, pp. 1320- 1331 ,(2014) , 10.1126/SCIENCE.1253451
Sergei L. Kosakovsky Pond, Ben Murrell, Mathieu Fourment, Simon D.W. Frost, Wayne Delport, Konrad Scheffler, A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection Molecular Biology and Evolution. ,vol. 28, pp. 3033- 3043 ,(2011) , 10.1093/MOLBEV/MSR125
H. A. Lessios, Speciation Genes in Free-Spawning Marine Invertebrates Integrative and Comparative Biology. ,vol. 51, pp. 456- 465 ,(2011) , 10.1093/ICB/ICR039