Published in Mol Biol Evol on March 01, 2003
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet (2006) 3.53
A neutral model of transcriptome evolution. PLoS Biol (2004) 3.44
Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. J Virol (2005) 3.26
On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biol (2005) 2.72
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc Natl Acad Sci U S A (2012) 2.54
Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol (2011) 2.37
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. Genome Res (2009) 2.35
Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One (2007) 2.35
Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol (2007) 2.34
Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc Natl Acad Sci U S A (2005) 2.18
Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates. Proc Natl Acad Sci U S A (2003) 2.14
The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol Biol Evol (2009) 2.01
More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci U S A (2007) 2.00
Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet (2012) 1.75
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res (2005) 1.68
Rapid diversification and dispersal during periods of global warming by plethodontid salamanders. Proc Natl Acad Sci U S A (2007) 1.66
Hominin life history: reconstruction and evolution. J Anat (2008) 1.64
Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence. Proc Natl Acad Sci U S A (2004) 1.62
Genetic basis for the evolution of vertebrate mineralized tissue. Proc Natl Acad Sci U S A (2004) 1.56
Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol (2014) 1.56
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (2014) 1.55
Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res (2006) 1.54
Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biol Evol (2010) 1.45
Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A (2003) 1.43
Brain maps, great and small: lessons from comparative studies of primate visual cortical organization. Philos Trans R Soc Lond B Biol Sci (2005) 1.41
The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet (2013) 1.41
Widespread balancing selection and pathogen-driven selection at blood group antigen genes. Genome Res (2008) 1.40
A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans. Proc Natl Acad Sci U S A (2007) 1.38
Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol (2010) 1.38
Toward a neutral evolutionary model of gene expression. Genetics (2005) 1.38
Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. BMC Genomics (2012) 1.38
Inferring phylogenies from RAD sequence data. PLoS One (2012) 1.34
Dynamic evolution of bitter taste receptor genes in vertebrates. BMC Evol Biol (2009) 1.32
An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PLoS Genet (2008) 1.29
Evolutionary history of chimpanzees inferred from complete mitochondrial genomes. Mol Biol Evol (2010) 1.29
Positive selection on protein-length in the evolution of a primate sperm ion channel. Proc Natl Acad Sci U S A (2003) 1.26
Rate of recombinational deletion among human endogenous retroviruses. J Virol (2007) 1.25
Primate chromosome evolution: ancestral karyotypes, marker order and neocentromeres. Chromosome Res (2008) 1.24
CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res (2008) 1.19
Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res (2013) 1.19
Colloquium paper: how grandmother effects plus individual variation in frailty shape fertility and mortality: guidance from human-chimpanzee comparisons. Proc Natl Acad Sci U S A (2010) 1.17
Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution. J Mol Evol (2006) 1.16
Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination. J Virol (2011) 1.16
Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences. J Mol Evol (2004) 1.12
Phylogenomics of primates and their ancestral populations. Genome Res (2009) 1.12
The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. J Mol Evol (2008) 1.10
Directional and balancing selection in human beta-defensins. BMC Evol Biol (2008) 1.09
Responses to the Assurance game in monkeys, apes, and humans using equivalent procedures. Proc Natl Acad Sci U S A (2011) 1.07
The molecular origin and consequences of escape from miRNA regulation by HLA-C alleles. Am J Hum Genet (2011) 1.06
Genome sequences reveal divergence times of malaria parasite lineages. Parasitology (2010) 1.06
More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philos Trans R Soc Lond B Biol Sci (2010) 1.05
Action at a distance: dependency sensitivity in a New World primate. Biol Lett (2013) 1.03
The evolution of MDM2 family genes. Gene (2011) 1.03
A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Res (2011) 1.02
Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal. BMC Evol Biol (2005) 1.02
Population Genomics of Human Adaptation. Annu Rev Ecol Evol Syst (2013) 1.01
Reconstructing phylogenies and phenotypes: a molecular view of human evolution. J Anat (2008) 1.01
Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region. Proc Natl Acad Sci U S A (2006) 1.01
The phylogenetic origins of natural killer receptors and recognition: relationships, possibilities, and realities. Immunogenetics (2010) 1.01
Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations. Am J Hum Genet (2011) 1.00
Patterns of genetic variation within and between Gibbon species. Mol Biol Evol (2011) 0.99
Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum Genet (2006) 0.99
Diverse evolutionary histories for beta-adrenoreceptor genes in humans. Am J Hum Genet (2009) 0.98
Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles. Immunogenetics (2007) 0.98
Chimpanzees do not take advantage of very low cost opportunities to deliver food to unrelated group members. Anim Behav (2008) 0.98
Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans. PLoS One (2011) 0.97
Long-term persistence of both functional and non-functional alleles at the leukocyte immunoglobulin-like receptor A3 (LILRA3) locus suggests balancing selection. Hum Genet (2006) 0.97
Four principles of bio-musicology. Philos Trans R Soc Lond B Biol Sci (2015) 0.96
The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res (2010) 0.95
Evolution of X-degenerate Y chromosome genes in greater apes: conservation of gene content in human and gorilla, but not chimpanzee. J Mol Evol (2009) 0.94
Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene. Hum Genet (2010) 0.93
Differential rates of local and global homogenization in centromere satellites from Arabidopsis relatives. Genetics (2005) 0.93
Genome-wide patterns of genetic polymorphism and signatures of selection in Plasmodium vivax. Genome Biol Evol (2014) 0.93
Primate TNF promoters reveal markers of phylogeny and evolution of innate immunity. PLoS One (2007) 0.92
Patterns of selective constraints in noncoding DNA of rice. BMC Evol Biol (2007) 0.91
The evolution of the immunoglobulin heavy chain variable region (IgVH) in Leporids: an unusual case of transspecies polymorphism. Immunogenetics (2005) 0.90
Impact of endogenous intronic retroviruses on major histocompatibility complex class II diversity and stability. J Virol (2008) 0.90
Tool-use learning by common marmosets (Callithrix jacchus). Exp Brain Res (2011) 0.89
Chimpanzee autarky. PLoS One (2008) 0.89
Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving. BMC Evol Biol (2011) 0.88
An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns. PLoS Genet (2014) 0.88
Paleogenomic record of the extinction of human endogenous retrovirus ERV9. J Virol (2005) 0.88
How to summarize estimates of ancestral divergence times. Evol Bioinform Online (2008) 0.88
Testing synchrony in historical biogeography: the case of new world primates and hystricognathi rodents. Evol Bioinform Online (2012) 0.88
Primate aging in the mammalian scheme: the puzzle of extreme variation in brain aging. Age (Dordr) (2012) 0.86
The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae. BMC Biol (2007) 0.86
Investigation of the origin and spread of a Mammalian transposable element based on current sequence diversity. J Mol Evol (2012) 0.85
Genome-wide analysis of chimpanzee genes with premature termination codons. BMC Genomics (2009) 0.85
Evolutionary optimization of material properties of a tropical seed. J R Soc Interface (2011) 0.85
Evolution of subterminal satellite (StSat) repeats in hominids. Genetica (2010) 0.85
Visual motion integration by neurons in the middle temporal area of a New World monkey, the marmoset. J Physiol (2011) 0.84
Sex-linked inheritance in macaque monkeys: implications for effective population size and dispersal to Sulawesi. Genetics (2010) 0.84
On theoretical models of gene expression evolution with random genetic drift and natural selection. PLoS One (2009) 0.84
Evaluating the relationship between spermatogenic silencing of the X chromosome and evolution of the Y chromosome in chimpanzee and human. PLoS One (2010) 0.83
Neogene biomarker record of vegetation change in eastern Africa. Proc Natl Acad Sci U S A (2016) 0.83
Chemical characterization of oligosaccharides in the milk of six species of New and Old World monkeys. Glycoconj J (2010) 0.83
Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting. BMC Evol Biol (2007) 0.82
Ancient and recent selective pressures shaped genetic diversity at AIM2-like nucleic acid sensors. Genome Biol Evol (2014) 0.82
NKp44 expression, phylogenesis and function in non-human primate NK cells. Int Immunol (2009) 0.82
An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. PLoS Genet (2014) 0.82
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform (2004) 72.40
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform (2008) 24.69
Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A (2004) 20.53
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol (2009) 2.68
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A (2002) 2.63
Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One (2007) 2.35
Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci U S A (2005) 2.32
Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci U S A (2003) 1.97
Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J Hum Genet (2006) 1.94
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A (2009) 1.94
Genomic drift and copy number variation of sensory receptor genes in humans. Proc Natl Acad Sci U S A (2007) 1.80
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc Natl Acad Sci U S A (2002) 1.79
Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proc Natl Acad Sci U S A (2006) 1.72
Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proc Natl Acad Sci U S A (2009) 1.70
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol Biol Evol (2004) 1.64
Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc Natl Acad Sci U S A (2004) 1.62
Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene (2005) 1.55
Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol Biol Evol (2002) 1.50
Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family. Mol Biol Evol (2002) 1.50
Evolutionary dynamics of olfactory receptor genes in Drosophila species. Proc Natl Acad Sci U S A (2007) 1.48
Evolutionary change of the numbers of homeobox genes in bilateral animals. Mol Biol Evol (2005) 1.37
Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages. Gene (2004) 1.32
Origins and evolution of microRNA genes in Drosophila species. Genome Biol Evol (2010) 1.31
Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J Mol Evol (2003) 1.30
Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol Biol Evol (2003) 1.24
Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals. Proc Natl Acad Sci U S A (2006) 1.21
Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA. Genetics (2008) 1.20
Origins and evolution of microRNA genes in plant species. Genome Biol Evol (2012) 1.20
Origin and evolution of influenza virus hemagglutinin genes. Mol Biol Evol (2002) 1.19
Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes. Mol Biol Evol (2003) 1.17
Birth-and-death evolution in primate MHC class I genes: divergence time estimates. Mol Biol Evol (2003) 1.11
The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution. Nucleic Acids Res (2007) 1.10
Purifying selection and birth-and-death evolution in the histone H4 gene family. Mol Biol Evol (2002) 1.09
Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates. Immunogenetics (2008) 1.09
Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes. Gene (2005) 1.09
Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers. Proc Natl Acad Sci U S A (2008) 1.05
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments. Mol Biol Evol (2008) 1.03
Ultraconserved coding regions outside the homeobox of mammalian Hox genes. BMC Evol Biol (2008) 0.98
Origin and evolution of the Ig-like domains present in mammalian leukocyte receptors: insights from chicken, frog, and fish homologues. Immunogenetics (2005) 0.98
Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids. Mol Biol Evol (2002) 0.97
Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication. Immunogenetics (2004) 0.96
Origin and evolution of the chicken leukocyte receptor complex. Proc Natl Acad Sci U S A (2005) 0.95
Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biol Evol (2010) 0.88
Analysis of the immunoglobulin light chain genes in zebra finch: evolutionary implications. Mol Biol Evol (2010) 0.86
Genomic drift and evolution of microsatellite DNAs in human populations. Mol Biol Evol (2009) 0.85
Genomic organization and evolution of immunoglobulin kappa gene enhancers and kappa deleting element in mammals. Mol Immunol (2009) 0.79
Eighty percent of proteins are different between humans and chimpanzees. Gene (2005) 0.79
A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes. Nucleic Acids Res (2005) 0.79
Evolution of the sex-lethal gene in insects and origin of the sex-determination system in Drosophila. J Mol Evol (2013) 0.78
Is positive selection responsible for the evolution of a duplicate UV-sensitive opsin gene in Heliconius butterflies? Proc Natl Acad Sci U S A (2010) 0.78
Random fluctuation of selection coefficients and the extent of nucleotide variation in human populations. Proc Natl Acad Sci U S A (2013) 0.75