Evaluation of methods for determination of a reconstructed history of gene sequence evolution

Molecular Biology and Evolution
D A Liberles

Abstract

With whole-genome sequences being completed at an increasing rate, it is important to develop and assess tools to analyze them. Following annotation of the protein content of a genome, one can compare sequences with previously characterized homologous genes to detect novel functions within specific proteins in the evolution of the newly sequenced genome. One common statistical method to detect such changes is to compare the ratios of nonsynonymous (K(a)) to synonymous (K(s)) nucleotide substitution rates. Here, the effects of several parameters that can influence this calculation (sequence reconstruction method, phylogenetic tree branch length weighting, GC content, and codon bias) are examined. Also, two new alternative measures of adaptive evolution, the point accepted mutations (PAM)/neutral evolutionary distance (NED) ratio and the sequence space assessment (SSA) statistic are presented. All of these methods are compared using two sequence families: the recent divergence of leptin orthologs in primates, and the more ancient divergence of the deoxyribonucleoside kinase family. The examination of these and other measures to detect changes of gene function along branches of a phylogenetic tree will become increasingly importan...Continue Reading

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Citations

Sep 16, 2008·Die Naturwissenschaften·Asa Tellgren-RothDavid A Liberles
Aug 19, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zabardast T BurievIbrokhim Y Abdurakhmonov
May 11, 2005·Journal of Molecular Evolution·Ann-Charlotte BerglundDavid A Liberles
Oct 18, 2003·Gene·Françoise MazetSebastian M Shimeld
Sep 13, 2007·Heredity·M Anisimova, D A Liberles
Oct 12, 2010·Molecular & Cellular Proteomics : MCP·Varodom CharoensawanSarah A Teichmann
Oct 24, 2009·Bioinformatics·Abdoulaye Banire DialloMathieu Blanchette
Mar 17, 2010·Molecular Biology and Evolution·Tong ZhouClaus O Wilke
Dec 21, 2004·Nucleic Acids Research·Christian RothDavid A Liberles
May 31, 2007·Journal of the Royal Society, Interface·Philip R KenscheMartijn A Huynen
Feb 23, 2012·Infection and Immunity·Renee A MarcsisinAlan G Barbour
Dec 13, 2012·BMC Genomics·Carsten PedersenPietro D Spanu
Oct 17, 2012·BMC Plant Biology·Marijn KnipPaul J J Hooykaas
Jun 21, 2006·BMC Plant Biology·Christian Roth, David A Liberles
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Nov 4, 2004·Molecular Phylogenetics and Evolution·Asa TellgrenDavid A Liberles
Jul 21, 2006·Molecular Phylogenetics and Evolution·Lucía F Franchini, A Belén Elgoyhen
Aug 14, 2015·BMC Genomics·Ana-Belen Martin-CuadradoFrancisco Rodriguez-Valera
Apr 24, 2007·Journal of Molecular Biology·Michael Paolo Bastner SandriniJure Piskur
Dec 3, 2016·Nucleosides, Nucleotides & Nucleic Acids·Zeeshan MutahirJure Piškur
Jul 14, 2006·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Christian RothDavid A Liberles
May 5, 2005·Journal of Molecular Evolution·Dennis L MaederEverly Conway de Macario

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