Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci.

Gene
Sang Chul ChoiJeffrey L Thorne

Abstract

We consider the inference of which of two alleles is ancestral when the alleles have a single nonsynonymous difference and when natural selection acts via protein tertiary structure. Whereas the probability that an allele is ancestral under neutrality is equal to its frequency, under selection this probability depends on allele frequency and on the magnitude and direction of selection pressure. Although allele frequencies can be well estimated from intraspecific data, small fitness differences have a large evolutionary impact but can be difficult to estimate with only intraspecific data. Methods for predicting aspects of phenotype from genotype can supplement intraspecific sequence data. Recently developed statistical techniques can assess effects of phenotypes, such as protein tertiary structure on molecular evolution. While these techniques were initially designed for comparing protein-coding genes from different species, the resulting interspecific inferences can be assigned population genetic interpretations to assess the effect of selection pressure, and we use them here along with intraspecific allele frequency data to estimate the probability that an allele is ancestral. We focus on 140 nonsynonymous single nucleotide po...Continue Reading

References

Apr 1, 1977·Theoretical Population Biology·G A Watterson, H A Guess
Jul 2, 1992·Nature·D T JonesJ M Thornton
Nov 1, 1993·Protein Science : a Publication of the Protein Society·T P FloresJ M Thornton
Jun 13, 1997·Journal of Molecular Biology·R B RussellM J Sternberg
Jun 1, 1997·Theoretical Population Biology·S M Krone, C Neuhauser
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jul 10, 1998·Molecular Biology and Evolution·A L Halpern, W J Bruno
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Mar 7, 2001·Human Molecular Genetics·S SunyaevP Bork
Apr 11, 2001·Human Mutation·Z Wang, J Moult
Aug 31, 2002·Nucleic Acids Research·Vasily RamenskyShamil Sunyaev
Apr 12, 2003·Theoretical Population Biology·Rasmus Nielsen, James Signorovitch
Jul 30, 2003·Molecular Biology and Evolution·Douglas M RobinsonJeffrey L Thorne
Dec 9, 2003·Proceedings of the National Academy of Sciences of the United States of America·Austin L HughesMeredith Yeager
Sep 15, 2004·Genome Research·Robert J LivingstonDeborah A Nickerson
Oct 30, 2004·BMC Evolutionary Biology·Johannes BergMichael Lässig
Jun 28, 2005·Proceedings of the National Academy of Sciences of the United States of America·Guy Sella, Aaron E Hirsh
Sep 2, 2005·Nature·UNKNOWN Chimpanzee Sequencing and Analysis Consortium
Sep 20, 2005·Journal of Molecular Biology·Peng YueJohn Moult
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Oct 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ville Mustonen, Michael Lässig
Oct 28, 2005·Genome Research·Andrew G ClarkRasmus Nielsen
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium
Jan 18, 2006·Journal of Molecular Biology·Peng Yue, John Moult
May 25, 2006·Molecular Biology and Evolution·Jiaye Yu, Jeffrey L Thorne
Jun 22, 2006·Molecular Biology and Evolution·Nicolas RodrigueNicolas Lartillot
Jun 30, 2006·Molecular and Cellular Probes·Maria StepanovaAncha Baranova
Jul 1, 2006·BMC Bioinformatics·Claudia L KleinmanNicolas Lartillot
Oct 31, 2006·Nature Genetics·Kevin Chen, Nikolaus Rajewsky
Dec 8, 2006·Nucleic Acids Research·Daryl J ThomasW James Kent
May 2, 2007·Molecular Biology and Evolution·Jeffrey L ThorneHirohisa Kishino
May 25, 2007·Molecular Biology and Evolution·Sang Chul ChoiJeffrey L Thorne
Jun 5, 2007·Molecular Biology and Evolution·Ryan D HernandezCarlos D Bustamante

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Citations

Jul 5, 2012·PLoS Computational Biology·Claus O Wilke
Jul 14, 2010·Genome Biology and Evolution·Kate E RidoutDmitry A Filatov

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