DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA

[1]  A. Eyre-Walker,et al.  The rate of adaptive evolution in animal mitochondria , 2015, Molecular ecology.

[2]  N. Galtier.  Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis , 2015, bioRxiv.

[3]  A. Barbadilla,et al.  Adaptive Evolution Is Substantially Impeded by Hill–Robertson Interference in Drosophila , 2015, Molecular biology and evolution.

[4]  G. Sella,et al.  Interpreting the Dependence of Mutation Rates on Age and Time , 2015, PLoS biology.

[5]  Timothy B Sackton,et al.  Natural Selection Constrains Neutral Diversity across A Wide Range of Species , 2014, bioRxiv.

[6]  B. Charlesworth.  Stabilizing Selection, Purifying Selection, and Mutational Bias in Finite Populations , 2013, Genetics.

[7]  P. Keightley,et al.  A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations , 2013, Genetics.

[8]  A. Cutter,et al.  Molecular hyperdiversity and evolution in very large populations , 2013, Molecular ecology.

[9]  N. Luscombe,et al.  Non‐random mutation: The evolution of targeted hypermutation and hypomutation , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[11]  Richard A. Goldstein,et al.  Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models , 2012, Genetics.

[12]  M. Lynch.  The Lower Bound to the Evolution of Mutation Rates , 2011, Genome biology and evolution.

[13]  M. Lynch.  Evolution of the mutation rate. , 2010, Trends in genetics : TIG.

[14]  Ya-ping Zhang,et al.  Adaptive evolution of energy metabolism genes and the origin of flight in bats , 2010, Proceedings of the National Academy of Sciences.

[15]  Kate E. Jones,et al.  PanTHERIA: a species‐level database of life history, ecology, and geography of extant and recently extinct mammals , 2009 .

[16]  Ya-ping Zhang,et al.  Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. , 2009, Genome research.

[17]  B. Charlesworth.  Effective population size and patterns of molecular evolution and variation , 2009, Nature Reviews Genetics.

[18]  A. Eyre-Walker,et al.  Evidence for Variation in the Effective Population Size of Animal Mitochondrial DNA , 2009, PloS one.

[19]  Ryan D. Hernandez,et al.  A flexible forward simulator for populations subject to selection and demography , 2008, Bioinform..

[20]  Ruth Hershberg,et al.  Selection on codon bias. , 2008, Annual review of genetics.

[21]  J. Welch,et al.  Divergence and Polymorphism Under the Nearly Neutral Theory of Molecular Evolution , 2008, Journal of Molecular Evolution.

[22]  Ryan D. Hernandez,et al.  Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome , 2008, PLoS genetics.

[23]  P. Higgs,et al.  Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. , 2008, Molecular biology and evolution.

[24]  N. Galtier,et al.  Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis. , 2007, Molecular biology and evolution.

[25]  Leila A. Mamirova,et al.  Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals , 2007, Proceedings of the National Academy of Sciences.

[26]  P. Keightley,et al.  A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations , 2013, Genetics.

[27]  Laurence Loewe,et al.  Inferring the distribution of mutational effects on fitness in Drosophila , 2006, Biology Letters.

[28]  A. Eyre-Walker,et al.  The Distribution of Fitness Effects of New Deleterious Amino Acid Mutations in Humans , 2006, Genetics.

[29]  L. Hurst,et al.  Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.

[30]  L. Hurst,et al.  Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals , 2005, Genome Biology.

[31]  A. Eyre-Walker,et al.  Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Ziheng Yang,et al.  Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. , 2003, Molecular biology and evolution.

[33]  Laurent Duret,et al.  Evolution of synonymous codon usage in metazoans. , 2002, Current opinion in genetics & development.

[34]  Adam Eyre-Walker,et al.  Adaptive protein evolution in Drosophila , 2002, Nature.

[35]  Shigehiko Kanaya,et al.  Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis , 2001, Journal of Molecular Evolution.

[36]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[37]  L. Duret,et al.  Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[38]  R. Suarez,et al.  Hummingbird flight: Sustaining the highest mass-specific metabolic rates among vertebrates , 1992, Experientia.

[39]  J. B. Walsh,et al.  Effects of linkage on rates of molecular evolution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[40]  S. Nee.  ON THE RATE OF ADAPTIVE EVOLUTION , 1985, Evolution; international journal of organic evolution.

[41]  M. A. Senar,et al.  MamPol: a database of nucleotide polymorphism in the Mammalia class , 2007 .

[42]  D. Carlini,et al.  Synonymous SNPs Provide Evidence for Selective Constraint on Human Exonic Splicing Enhancers , 2005, Journal of Molecular Evolution.

[43]  M. Pagel,et al.  The comparative method in evolutionary biology , 1991 .

[44]  K. Schmidt-Nielsen,et al.  Scaling, why is animal size so important? , 1984 .