Published in J Mol Evol on July 01, 2004
Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48
ALF--a simulation framework for genome evolution. Mol Biol Evol (2011) 1.86
Genome-wide signatures of convergent evolution in echolocating mammals. Nature (2013) 1.59
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol (2016) 1.41
Accelerated FoxP2 evolution in echolocating bats. PLoS One (2007) 1.34
Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics (2006) 1.27
Evolution of proteins and proteomes: a phylogenetics approach. Evol Bioinform Online (2007) 1.16
Adaptive functional divergence among triplicated alpha-globin genes in rodents. Genetics (2008) 1.14
Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity (Edinb) (2011) 1.13
A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol (2015) 1.11
Distinct evolutionary patterns between two duplicated color vision genes within cyprinid fishes. J Mol Evol (2009) 0.96
Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses. BMC Evol Biol (2009) 0.95
Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis. BMC Evol Biol (2009) 0.95
Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria? PLoS One (2008) 0.94
Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family. BMC Evol Biol (2006) 0.92
Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biol Rev Camb Philos Soc (2012) 0.91
Squeezers and leaf-cutters: differential diversification and degeneration of the venom system in toxicoferan reptiles. Mol Cell Proteomics (2013) 0.89
Three-fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of snake venom toxins. Toxins (Basel) (2013) 0.88
Divergent evolution among teleost V1r receptor genes. PLoS One (2007) 0.87
Differential stepwise evolution of SARS coronavirus functional proteins in different host species. BMC Evol Biol (2009) 0.87
Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3. PeerJ (2013) 0.87
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. Mol Biol Evol (2010) 0.87
Adaptive evolution of Toll-like receptor 5 in domesticated mammals. BMC Evol Biol (2012) 0.86
Exploiting models of molecular evolution to efficiently direct protein engineering. J Mol Evol (2010) 0.85
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLoS One (2011) 0.85
Selection-driven divergence after gene duplication in Arabidopsis thaliana. J Mol Evol (2011) 0.85
Rapid birth-and-death evolution of the xenobiotic metabolizing NAT gene family in vertebrates with evidence of adaptive selection. BMC Evol Biol (2013) 0.84
Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. J Mol Evol (2006) 0.84
Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins. BMC Genomics (2014) 0.83
Molecular evolution of the deuterolysin (M35) family genes in Coccidioides. PLoS One (2012) 0.82
Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis. Mol Biol Evol (2015) 0.82
Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment. Genome Biol Evol (2014) 0.82
Molecular evolution of cytochrome b in high- and low-altitude deer mice (genus Peromyscus). Heredity (Edinb) (2008) 0.82
Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf. PLoS One (2013) 0.82
Relaxation of adaptive evolution during the HIV-1 infection owing to reduction of CD4+ T cell counts. PLoS One (2012) 0.81
Evolutionary transformation of rod photoreceptors in the all-cone retina of a diurnal garter snake. Proc Natl Acad Sci U S A (2015) 0.81
Duplication and concerted evolution in a master sex determiner under balancing selection. Proc Biol Sci (2013) 0.81
Independent expansion of zincin metalloproteinases in Onygenales fungi may be associated with their pathogenicity. PLoS One (2014) 0.81
Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biol Evol (2015) 0.80
Molecular evolutionary analysis of vertebrate transducins: a role for amino acid variation in photoreceptor deactivation. J Mol Evol (2013) 0.80
Inference of functional divergence among proteins when the evolutionary process is non-stationary. J Mol Evol (2013) 0.80
Evolutionary history of LTR retrotransposon chromodomains in plants. Int J Plant Genomics (2012) 0.80
Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses. BMC Evol Biol (2012) 0.79
Genome-wide analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) genes in plants reveals the eudicot-wide PDAT gene expansion and altered selective pressures acting on the core eudicot PDAT paralogs. Plant Physiol (2015) 0.79
Genetic profiling of the isoprenoid and sterol biosynthesis pathway genes of Trypanosoma cruzi. PLoS One (2014) 0.79
Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. PLoS One (2011) 0.79
Divergence and adaptive evolution of the gibberellin oxidase genes in plants. BMC Evol Biol (2015) 0.78
Relaxed selective constraints drove functional modifications in peripheral photoreception of the cavefish P. andruzzii and provide insight into the time of cave colonization. Heredity (Edinb) (2016) 0.78
Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family. PLoS One (2013) 0.78
Encoding asymmetry of the N-glycosylation motif facilitates glycoprotein evolution. PLoS One (2014) 0.78
Increased constraints on MC4R during primate and human evolution. Hum Genet (2008) 0.78
Lineage pattern, trans-species polymorphism, and selection pressure among the major lineages of feline MHC-DRB peptide-binding region. Immunogenetics (2010) 0.78
Molecular evolution and functional divergence of tubulin superfamily in the fungal tree of life. Sci Rep (2014) 0.78
Microcephaly genes evolved adaptively throughout the evolution of eutherian mammals. BMC Evol Biol (2014) 0.78
Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini). BMC Evol Biol (2015) 0.77
Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion. Biol Lett (2015) 0.77
Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution. Genetics (2016) 0.77
Convergent evolution of marine mammals is associated with distinct substitutions in common genes. Sci Rep (2015) 0.77
The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex. BMC Evol Biol (2012) 0.77
Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga). Mol Ecol (2015) 0.77
New methods for inferring population dynamics from microbial sequences. Infect Genet Evol (2006) 0.77
Molecular adaptation of telomere associated genes in mammals. BMC Evol Biol (2013) 0.76
Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.). BMC Evol Biol (2012) 0.76
Hypothetical proteins present during recovery phase of radiation resistant bacterium Deinococcus radiodurans are under purifying selection. J Mol Evol (2013) 0.76
Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. Evol Bioinform Online (2012) 0.76
The 2014 Ebola virus outbreak in West Africa highlights no evidence of rapid evolution or adaptation to humans. Sci Rep (2016) 0.75
Differential strengths of selection on S-RNases from Physalis and Solanum (Solanaceae). BMC Evol Biol (2011) 0.75
Phylogenic analysis of adhesion related genes Mad1 revealed a positive selection for the evolution of trapping devices of nematode-trapping fungi. Sci Rep (2016) 0.75
Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors. PLoS Negl Trop Dis (2016) 0.75
Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes. Sci Rep (2017) 0.75
Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi. PeerJ (2017) 0.75
LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics (2016) 0.75
Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification. BMC Evol Biol (2017) 0.75
Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish. Genome Biol Evol (2015) 0.75
The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees. Genome Biol Evol (2017) 0.75
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol (1985) 47.78
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
The evolutionary fate and consequences of duplicate genes. Science (2000) 24.22
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol (1994) 24.04
A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol (1994) 19.91
Preservation of duplicate genes by complementary, degenerative mutations. Genetics (1999) 18.29
Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics (2000) 14.84
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics (1998) 11.25
The probability of duplicate gene preservation by subfunctionalization. Genetics (2000) 10.27
Statistical methods for detecting molecular adaptation. Trends Ecol Evol (2000) 10.10
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol (1998) 8.74
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol (1994) 7.55
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21
The evolution of functionally novel proteins after gene duplication. Proc Biol Sci (1994) 5.99
Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence. Mol Phylogenet Evol (1998) 5.55
Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A (1998) 5.54
Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol (1988) 4.75
Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science (1993) 4.43
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol (2001) 4.03
The genomic record of Humankind's evolutionary roots. Am J Hum Genet (1999) 3.40
Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol (2002) 3.26
Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol (2002) 2.71
The recruitment of crystallins: new functions precede gene duplication. Science (1991) 2.46
Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc Natl Acad Sci U S A (1997) 1.97
Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol (2001) 1.87
Gene number. What if there are only 30,000 human genes? Science (2001) 1.83
Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci (2002) 1.77
Evolution of novel genes. Curr Opin Genet Dev (2001) 1.73
Genome duplication, divergent resolution and speciation. Trends Genet (2001) 1.62
Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics (2003) 1.61
A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci U S A (2001) 1.56
Shh-Bmp2 signaling module and the evolutionary origin and diversification of feathers. J Exp Zool (2002) 1.53
Duplication of the gamma-globin gene mediated by L1 long interspersed repetitive elements in an early ancestor of simian primates. Proc Natl Acad Sci U S A (1991) 1.48
Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc Natl Acad Sci U S A (2002) 1.36
Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol Biol Evol (2002) 1.32
Evolutionary and developmental aspects of two hemoglobin beta-chain genes (epsilon M and beta M) of opossum. Proc Natl Acad Sci U S A (1988) 1.31
Molecular phylogeny of Old World monkeys (Cercopithecidae) as inferred from gamma-globin DNA sequences. Mol Phylogenet Evol (1999) 1.22
Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication. Genetics (1993) 1.17
Regulation of oxygen affinity of mammalian haemoglobins. J Mol Biol (1980) 1.14
A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol Biol Evol (2003) 1.06
Analysing gene function after duplication. Bioessays (2001) 1.04
Adaptive evolution after gene duplication. Trends Genet (2002) 1.02
Molecular adaptation of hemoglobin function in mammals. Respir Physiol (1992) 0.99
Eosinophils, ribonucleases and host defense: solving the puzzle. Immunol Res (1999) 0.95
Fetal globin expression in New World monkeys. J Biol Chem (1996) 0.94
Expansion of genome coding regions by acquisition of new genes. Genetica (2002) 0.92
The evolution of engrailed genes after duplication and speciation events. Dev Genes Evol (2002) 0.89
Evolution of antiviral activity in the ribonuclease A gene superfamily: evidence for a specific interaction between eosinophil-derived neurotoxin (EDN/RNase 2) and respiratory syncytial virus. Nucleic Acids Res (1998) 0.85
Fate of a redundant gamma-globin gene in the atelid clade of New World monkeys: implications concerning fetal globin gene expression. Proc Natl Acad Sci U S A (1995) 0.80
Molecular phylogeny of ateline new world monkeys (Platyrrhini, atelinae) based on gamma-globin gene sequences: evidence that brachyteles is the sister group of lagothrix. Mol Phylogenet Evol (1999) 0.79
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Mol Biol Evol (2003) 4.10
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Inferring speciation times under an episodic molecular clock. Syst Biol (2007) 3.85
INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol (2009) 3.29
Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol (2002) 3.26
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol (2009) 3.04
Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet (2008) 2.98
A new time-scale for ray-finned fish evolution. Proc Biol Sci (2007) 2.92
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol (2008) 2.90
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Best practices for justifying fossil calibrations. Syst Biol (2011) 2.51
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol (2003) 2.29
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol (2002) 2.15
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol (2004) 2.01
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol (2010) 2.01
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol (2007) 1.77
Exploring uncertainty in the calibration of the molecular clock. Biol Lett (2011) 1.74
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol (2005) 1.69
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics (2003) 1.61
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol Biol Evol (2011) 1.58
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol (2003) 1.49
Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol (2002) 1.46
Evaluation of a bayesian coalescent method of species delimitation. Syst Biol (2011) 1.34
PAMLX: a graphical user interface for PAML. Mol Biol Evol (2013) 1.30
Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol (2005) 1.19
Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol (2007) 1.14
The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol (2008) 1.11
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol Phylogenet Evol (2009) 1.10
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett (2014) 1.08
Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol (2011) 1.06
Improved reversible jump algorithms for Bayesian species delimitation. Genetics (2013) 1.05
The influence of gene flow on species tree estimation: a simulation study. Syst Biol (2013) 1.04
Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol Biol Evol (2004) 1.04
Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst Biol (2012) 1.04
Somatosensory projections to cochlear nucleus are upregulated after unilateral deafness. J Neurosci (2012) 1.02
Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol Biol Evol (2007) 0.99
Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol Biol (2011) 0.97
In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A (2009) 0.96
The trouble with sliding windows and the selective pressure in BRCA1. PLoS One (2008) 0.96
Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS One (2008) 0.95
A likelihood look at the supermatrix-supertree controversy. Gene (2008) 0.94
Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol Biol Evol (2012) 0.93
Looking for Darwin in genomic sequences--validity and success of statistical methods. Mol Biol Evol (2012) 0.92
Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene (2006) 0.92
Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol (2004) 0.90
Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes Genet Syst (2006) 0.90
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. Philos Trans R Soc Lond B Biol Sci (2008) 0.90
Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC Evol Biol (2010) 0.89
Dating phylogenies with sequentially sampled tips. Syst Biol (2013) 0.88
Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics (2011) 0.88
Bayesian dating of shallow phylogenies with a relaxed clock. Syst Biol (2009) 0.88
Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. New Phytol (2013) 0.87
Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol Biol Evol (2002) 0.87
A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. Gene (2006) 0.87
Bayesian relaxed clock estimation of divergence times in foraminifera. Mol Phylogenet Evol (2011) 0.86
Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection? J Mol Evol (2004) 0.86
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLoS One (2011) 0.85
Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). J Mol Evol (2004) 0.84
Diversifying and purifying selection in the peptide binding region of DRB in mammals. J Mol Evol (2008) 0.84
Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics (2013) 0.81
Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol (2014) 0.80
Comparative genomics coming of age. Heredity (Edinb) (2003) 0.76