Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection.

PubWeight™: 0.88‹?›

🔗 View Article (PMC 3242499)

Published in Genome Biol Evol on October 31, 2011

Authors

Axel Künstner1, Benoit Nabholz, Hans Ellegren

Author Affiliations

1: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

Articles cited by this

PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol (2000) 35.86

Evolutionary rate at the molecular level. Nature (1968) 33.15

A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics (1966) 30.66

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature (2004) 21.40

Ultraconserved elements in the human genome. Science (2004) 17.14

Estimate of the mutation rate per nucleotide in humans. Genetics (2000) 15.08

Slightly deleterious mutant substitutions in evolution. Nature (1973) 13.79

Cytosine methylation and the ecology of intragenomic parasites. Trends Genet (1997) 13.66

Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31

Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58

A phylogenomic study of birds reveals their evolutionary history. Science (2008) 9.00

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91

High genomic deleterious mutation rates in hominids. Nature (1999) 6.23

Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet (2006) 5.97

Whole-genome resequencing reveals loci under selection during chicken domestication. Nature (2010) 5.48

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics (2004) 4.88

The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet (2002) 4.46

PHOSPHOGLUCOMUTASE POLYMORPHISM IN MAN. Nature (1964) 4.26

Conserved non-genic sequences - an unexpected feature of mammalian genomes. Nat Rev Genet (2005) 3.97

Selection on codon bias. Annu Rev Genet (2008) 3.83

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nat Genet (2011) 3.59

Raising the estimate of functional human sequences. Genome Res (2007) 3.43

DNA methylation and mutation. Mutat Res (1993) 3.23

Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol (2006) 3.16

Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res (2004) 3.00

Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev (2002) 2.95

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94

Conservation of core gene expression in vertebrate tissues. J Biol (2009) 2.84

RED CELL ACID PHOSPHATASE VARIANTS: A NEW HUMAN POLYMORPHISM. Nature (1963) 2.78

A molecular approach to estimating the human deleterious mutation rate. Hum Mutat (1993) 2.76

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res (2006) 2.64

Calibration of avian molecular clocks. Mol Biol Evol (2001) 2.52

Human genome ultraconserved elements are ultraselected. Science (2007) 2.34

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci U S A (2003) 1.98

Massive turnover of functional sequence in human and other mammalian genomes. Genome Res (2010) 1.89

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol (2010) 1.75

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res (2004) 1.73

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol (2011) 1.55

Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics (2004) 1.45

Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol (2007) 1.43

Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A (2011) 1.40

Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol (2009) 1.20

Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol (2009) 1.15

Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res (2004) 1.14

Molecular evolution of genes in avian genomes. Genome Biol (2010) 1.12

Gene expression, synteny, and local similarity in human noncoding mutation rates. Mol Biol Evol (2004) 1.09

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol (2011) 1.01

A selection model of molecular evolution incorporating the effective population size. Evolution (2009) 0.99

Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion. Mol Biol Evol (2010) 0.79

Articles by these authors

The genome of a songbird. Nature (2010) 5.90

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24

Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc Biol Sci (2003) 2.76

Genes of domestic mammals augmented by backcrossing with wild ancestors. Trends Genet (2005) 2.04

Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey. Mol Biol Evol (2004) 2.01

Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe. Proc Biol Sci (2005) 2.01

Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap. PLoS Genet (2013) 1.91

Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution. Genetics (2004) 1.80

Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle. Proc Natl Acad Sci U S A (2005) 1.74

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res (2004) 1.73

The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res (2010) 1.72

Limited number of patrilines in horse domestication. Nat Genet (2004) 1.70

Deterministic mutation rate variation in the human genome. Genome Res (2002) 1.63

Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proc Natl Acad Sci U S A (2002) 1.59

From wild wolf to domestic dog: gene expression changes in the brain. Brain Res Mol Brain Res (2004) 1.59

Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds. Mitochondrion (2008) 1.53

Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression. Am Nat (2008) 1.51

Strong regional biases in nucleotide substitution in the chicken genome. Mol Biol Evol (2006) 1.50

The evolutionary causes and consequences of sex-biased gene expression. Nat Rev Genet (2013) 1.50

Fast-X on the Z: rapid evolution of sex-linked genes in birds. Genome Res (2007) 1.49

Ecological and genetic spatial structuring in the Canadian lynx. Nature (2003) 1.49

Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics (2004) 1.45

Male-driven biased gene conversion governs the evolution of base composition in human alu repeats. Mol Biol Evol (2005) 1.44

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol (2010) 1.44

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genet (2008) 1.43

Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics (2006) 1.41

Reduced variation on the chicken Z chromosome. Genetics (2004) 1.39

To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations? Mol Ecol (2008) 1.37

Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Mol Ecol (2007) 1.36

The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata. Genetics (2008) 1.33

Low levels of nucleotide diversity in mammalian Y chromosomes. Mol Biol Evol (2003) 1.33

Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation. Mol Ecol (2012) 1.33

Compositional evolution of noncoding DNA in the human and chimpanzee genomes. Mol Biol Evol (2003) 1.32

Next generation molecular ecology. Mol Ecol (2010) 1.30

A gene-based genetic linkage map of the collared flycatcher (Ficedula albicollis) reveals extensive synteny and gene-order conservation during 100 million years of avian evolution. Genetics (2008) 1.28

Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Res (2008) 1.27

Chicken W: a genetically uniform chromosome in a highly variable genome. Proc Natl Acad Sci U S A (2004) 1.26

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res (2010) 1.26

Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline. Biol Lett (2006) 1.24

Sex-linkage of sexually antagonistic genes is predicted by female, but not male, effects in birds. Evolution (2009) 1.22

The unique genomic properties of sex-biased genes: insights from avian microarray data. BMC Genomics (2008) 1.22

Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci. Nucleic Acids Res (2002) 1.22

Faster-Z evolution is predominantly due to genetic drift. Mol Biol Evol (2009) 1.20

Recombination drives vertebrate genome contraction. PLoS Genet (2012) 1.20

Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol Biol Evol (2011) 1.17

Ontogenetic complexity of sexual dimorphism and sex-specific selection. Mol Biol Evol (2010) 1.16

Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol (2009) 1.15

Levels of linkage disequilibrium in a wild bird population. Biol Lett (2006) 1.15

Life history and the male mutation bias. Evolution (2003) 1.14

Speciation in Ficedula flycatchers. Philos Trans R Soc Lond B Biol Sci (2010) 1.14

The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) Genome: a high frequency of deletions in tandem duplicates. Genetics (2007) 1.13

Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds. J Mol Evol (2005) 1.12

Molecular evolution of genes in avian genomes. Genome Biol (2010) 1.12

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Mol Ecol (2014) 1.11

Y chromosome conserved anchored tagged sequences (YCATS) for the analysis of mammalian male-specific DNA. Mol Ecol (2003) 1.11

Nonrandom distribution of genes with sex-biased expression in the chicken genome. Evolution (2006) 1.09

Gene expression, synteny, and local similarity in human noncoding mutation rates. Mol Biol Evol (2004) 1.09

Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome. Mol Biol Evol (2005) 1.08

Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds. Mol Biol Evol (2006) 1.07

Are sex-biased genes more dispensable? Biol Lett (2009) 1.07

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data. PLoS Genet (2013) 1.03

Natural selection in avian protein-coding genes expressed in brain. Mol Ecol (2008) 1.03

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol (2011) 1.01

MHC class II genes in European wolves: a comparison with dogs. Immunogenetics (2002) 1.01

Rapid evolution of female-biased, but not male-biased, genes expressed in the avian brain. Mol Biol Evol (2007) 1.00

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi. Mol Phylogenet Evol (2011) 0.97

Parallel divergence and degradation of the avian W sex chromosome. Trends Ecol Evol (2007) 0.97

Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype. Mol Biol Evol (2013) 0.97

Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biol Evol (2013) 0.96

An evolutionary genome scan for longevity-related natural selection in mammals. Mol Biol Evol (2009) 0.96

A guide to the genomics of ecological speciation in natural animal populations. Ecol Lett (2010) 0.95

QTL linkage mapping of zebra finch beak color shows an oligogenic control of a sexually selected trait. Evolution (2011) 0.94

Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection. Mol Biol Evol (2009) 0.93

A low rate of simultaneous double-nucleotide mutations in primates. Mol Biol Evol (2003) 0.93

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array. Mol Ecol Resour (2014) 0.93

Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Mol Ecol (2009) 0.91

Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. BMC Genomics (2014) 0.91

Adaptive molecular evolution of HINTW, a female-specific gene in birds. Mol Biol Evol (2003) 0.90

Individual variation in microsatellite mutation rate in barn swallows. Mutat Res (2004) 0.90

Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol (2014) 0.89

Inferring the demographic history of European Ficedula flycatcher populations. BMC Evol Biol (2013) 0.89

Microsatellite genotyping of DNA isolated from claws left on tanned carnivore hides. Int J Legal Med (2005) 0.89

Sampling strategies for species trees: the effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Mol Phylogenet Evol (2013) 0.89

Mismatch repair and mutational bias in microsatellite DNA. Trends Genet (2002) 0.88

Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res (2015) 0.88

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics (2014) 0.88

The genomic signature of sexual selection in the genetic diversity of the sex chromosomes and autosomes. Evolution (2012) 0.88

Effective size of fluctuating populations with two sexes and overlapping generations. Evolution (2007) 0.88

The relationship between microsatellite polymorphism and recombination hot spots in the human genome. Mol Biol Evol (2008) 0.88

Substitution rate heterogeneity and the male mutation bias. J Mol Evol (2006) 0.87

A high-density scan of the Z chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection. Evolution (2010) 0.87

Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches. Mol Biol Evol (2013) 0.87

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol (2014) 0.86

Positive diversifying selection in avian Mx genes. Immunogenetics (2008) 0.86

Is the rate of insertion and deletion mutation male biased?: Molecular evolutionary analysis of avian and primate sex chromosome sequences. Genetics (2003) 0.86

Trisomy and triploidy are sources of embryo mortality in the zebra finch. Proc Biol Sci (2010) 0.85

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. BMC Genomics (2013) 0.84