Adaptive gene expression divergence inferred from population genomics.

PubWeight™: 1.13‹?› | Rank: Top 10%

🔗 View Article (PMC 2042001)

Published in PLoS Genet on October 01, 2007

Authors

Alisha K Holloway1, Mara K N Lawniczak, Jason G Mezey, David J Begun, Corbin D Jones

Author Affiliations

1: Section of Evolution and Ecology, University of California Davis, Davis, California, USA. akholloway@ucdavis.edu

Articles citing this

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet (2010) 7.05

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. PLoS Biol (2012) 2.29

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature (2017) 2.14

Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics (2008) 1.29

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol Biol (2011) 1.25

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun (2014) 1.24

Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution. Mol Biol Evol (2012) 1.23

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet (2012) 1.22

Population-specific gene expression responses to hybridization between farm and wild Atlantic salmon. Evol Appl (2009) 1.17

Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol (2009) 1.10

Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA. Genetics (2008) 1.08

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana. Genome Res (2012) 1.04

Evolution of gene expression in the Drosophila olfactory system. Mol Biol Evol (2008) 1.01

Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. BMC Evol Biol (2008) 0.96

Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. Mol Biol Evol (2012) 0.91

Genome-wide polymorphisms show unexpected targets of natural selection. Proc Biol Sci (2011) 0.90

Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol (2008) 0.89

Trypsin isozymes in the lobster Panulirus argus (Latreille, 1804): from molecules to physiology. J Comp Physiol B (2014) 0.82

Evolution of the correlation between expression divergence and protein divergence in mammals. Genome Biol Evol (2013) 0.82

Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS One (2015) 0.81

Methods to detect selection on noncoding DNA. Methods Mol Biol (2012) 0.81

Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids. Genetica (2011) 0.81

A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees. PLoS One (2012) 0.79

Under-Expression of Chemosensory Genes in Domiciliary Bugs of the Chagas Disease Vector Triatoma brasiliensis. PLoS Negl Trop Dis (2016) 0.75

Articles cited by this

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

The genome sequence of Drosophila melanogaster. Science (2000) 74.32

The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol (1985) 47.78

miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06

The hitch-hiking effect of a favourable gene. Genet Res (1974) 34.74

affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08

Adaptive protein evolution at the Adh locus in Drosophila. Nature (1991) 31.65

The microRNA Registry. Nucleic Acids Res (2004) 29.45

MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell (2003) 14.07

The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol (2003) 7.72

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics (1994) 6.83

Adaptive evolution of non-coding DNA in Drosophila. Nature (2005) 6.68

Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet (2003) 6.60

Highly expressed genes in yeast evolve slowly. Genetics (2001) 6.28

Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A (2005) 6.19

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18

Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science (2003) 5.67

Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature (2006) 4.26

Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol (1996) 3.83

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol (1994) 3.64

A genetic signature of interspecies variations in gene expression. Nat Genet (2006) 3.61

Rapid evolution of male-biased gene expression in Drosophila. Proc Natl Acad Sci U S A (2003) 3.45

A neutral model of transcriptome evolution. PLoS Biol (2004) 3.44

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23

Control of messenger RNA stability in higher eukaryotes. Trends Genet (1996) 2.89

Translational selection and yeast proteome evolution. Genetics (2003) 2.75

Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol (2004) 2.66

Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene (2003) 2.25

Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc Natl Acad Sci U S A (1989) 1.44

Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes. Mol Biol Evol (2003) 1.36

Positive selection on gene expression in the human brain. Curr Biol (2006) 1.14

Adaptive protein evolution and regulatory divergence in Drosophila. Mol Biol Evol (2006) 0.94

Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct. Genetics (2002) 0.89

Articles by these authors

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Extending assembly of short DNA sequences to handle error. Bioinformatics (2007) 14.46

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A (2011) 4.68

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res (2008) 3.41

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00

Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A (2006) 2.84

Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc Natl Acad Sci U S A (2004) 2.65

Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Pathog (2011) 2.50

Genomic variation in natural populations of Drosophila melanogaster. Genetics (2012) 2.33

Practical innovations for high-throughput amplicon sequencing. Nat Methods (2013) 2.25

Gene transposition as a cause of hybrid sterility in Drosophila. Science (2006) 2.18

Natural selection drives Drosophila immune system evolution. Genetics (2003) 2.13

Circulating endothelial microparticles as a measure of early lung destruction in cigarette smokers. Am J Respir Crit Care Med (2011) 2.12

Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet (2012) 2.09

A genome-wide analysis of courting and mating responses in Drosophila melanogaster females. Genome (2004) 1.85

Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics (2010) 1.78

Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics (2007) 1.75

Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics (2008) 1.66

A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis. BMC Bioinformatics (2010) 1.63

Lung adenocarcinoma subtypes based on expression of human airway basal cell genes. Eur Respir J (2013) 1.59

The tardigrade Hypsibius dujardini, a new model for studying the evolution of development. Dev Biol (2007) 1.56

HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathog (2010) 1.47

Parallel evolution of chimeric fusion genes. Proc Natl Acad Sci U S A (2005) 1.45

Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium. Proc Natl Acad Sci U S A (2010) 1.42

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics (2011) 1.41

Four loci explain 83% of size variation in the horse. PLoS One (2012) 1.40

PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Hum Biol (2012) 1.37

Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics (2008) 1.29

RNA-Seq quantification of the human small airway epithelium transcriptome. BMC Genomics (2012) 1.28

Coordinate control of expression of Nrf2-modulated genes in the human small airway epithelium is highly responsive to cigarette smoking. Mol Med (2009) 1.24

Comparative genomics of accessory gland protein genes in Drosophila melanogaster and D. pseudoobscura. Mol Biol Evol (2004) 1.23

Origin and spread of de novo genes in Drosophila melanogaster populations. Science (2014) 1.22

Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics (2004) 1.21

Molecular population genetics of accessory gland protein genes and testis-expressed genes in Drosophila mojavensis and D. arizonae. Genetics (2005) 1.20

Cocaine analog coupled to disrupted adenovirus: a vaccine strategy to evoke high-titer immunity against addictive drugs. Mol Ther (2011) 1.18

Genomic effects of nucleotide substitutions in Drosophila simulans. Genetics (2002) 1.17

Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila. Mol Biol Evol (2004) 1.16

Molecular population genetics of female-expressed mating-induced serine proteases in Drosophila melanogaster. Mol Biol Evol (2007) 1.13

Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes. Mol Biol Evol (2004) 1.12

Protein variation in Drosophila simulans, and comparison of genes from centromeric versus noncentromeric regions of chromosome 3. Mol Biol Evol (2002) 1.11

Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia. Mol Biol Evol (2010) 1.10

Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics (2005) 1.10

Genome of Drosophila suzukii, the spotted wing drosophila. G3 (Bethesda) (2013) 1.08

Linkage disequilibrium and recent selection at three immunity receptor loci in Drosophila simulans. Genetics (2005) 1.08

De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. PLoS Genet (2013) 1.06

A mating plug protein reduces early female remating in Drosophila melanogaster. J Insect Physiol (2010) 1.05

Evolution of gene expression in the Drosophila olfactory system. Mol Biol Evol (2008) 1.01

Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations. BMC Genet (2012) 1.01

Parallel geographic variation in Drosophila melanogaster. Genetics (2014) 1.01

Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster. Genetics (2007) 1.00

PUMA: a unified framework for penalized multiple regression analysis of GWAS data. PLoS Comput Biol (2013) 1.00

An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone-rod dystrophy 9. Mol Vis (2010) 0.99

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res (2008) 0.99

Evolution of an MCM complex in flies that promotes meiotic crossovers by blocking BLM helicase. Science (2012) 0.98

Adaptive evolution of recently duplicated accessory gland protein genes in desert Drosophila. Genetics (2007) 0.97

Next-generation mapping of complex traits with phenotype-based selection and introgression. Genetics (2011) 0.96

Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. BMC Evol Biol (2008) 0.96

Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans. Genetics (2008) 0.94

Airway Basal stem/progenitor cells have diminished capacity to regenerate airway epithelium in chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2014) 0.94

Evolution of a signaling nexus constrained by protein interfaces and conformational States. PLoS Comput Biol (2010) 0.93

Exome sequencing identifies potential risk variants for Mendelian disorders at high prevalence in Qatar. Hum Mutat (2013) 0.92

Relaxed genetic constraint is ancestral to the evolution of phenotypic plasticity. Integr Comp Biol (2012) 0.91

Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control. BMC Bioinformatics (2012) 0.91

Genome reference and sequence variation in the large repetitive central exon of human MUC5AC. Am J Respir Cell Mol Biol (2014) 0.90

Phylogeny of Toll-like receptor signaling: adapting the innate response. PLoS One (2013) 0.90

Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population. PLoS One (2012) 0.89

Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol (2008) 0.89

AAVrh.10-mediated expression of an anti-cocaine antibody mediates persistent passive immunization that suppresses cocaine-induced behavior. Hum Gene Ther (2012) 0.89

Smoking accelerates aging of the small airway epithelium. Respir Res (2014) 0.87

Evidence of spatially varying selection acting on four chromatin-remodeling loci in Drosophila melanogaster. Genetics (2008) 0.87

Evolutionary genomics: codon bias and selection on single genomes. Nature (2005) 0.86

Overcoming redundancy: an RNAi enhancer screen for morphogenesis genes in Caenorhabditis elegans. Genetics (2011) 0.86

A robust method for transcript quantification with RNA-seq data. J Comput Biol (2013) 0.86

A locus in Drosophila sechellia affecting tolerance of a host plant toxin. Genetics (2013) 0.86

Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella. Mol Ecol (2014) 0.86

Persistent suppression of ocular neovascularization with intravitreal administration of AAVrh.10 coding for bevacizumab. Hum Gene Ther (2011) 0.86

Modulation of cystatin A expression in human airway epithelium related to genotype, smoking, COPD, and lung cancer. Cancer Res (2011) 0.85

Comparative population genetics of the immunity gene, Relish: is adaptive evolution idiosyncratic? PLoS One (2007) 0.84

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.). Mol Ecol Resour (2012) 0.83

Patterns of amino acid evolution in the Drosophila ananassae chimeric gene, siren, parallel those of other Adh-derived chimeras. Genetics (2008) 0.83

HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. Bioinformatics (2013) 0.83

Prediction of protein-protein interfaces on G-protein beta subunits reveals a novel phospholipase C beta2 binding domain. J Mol Biol (2009) 0.82

Airway epithelial expression of TLR5 is downregulated in healthy smokers and smokers with chronic obstructive pulmonary disease. J Immunol (2012) 0.82

A QTL analysis of female variation contributing to refractoriness and sperm competition in Drosophila melanogaster. Genet Res (2005) 0.82

Population genomic analysis of base composition evolution in Drosophila melanogaster. Genome Biol Evol (2012) 0.81

Development and use of DNA archives at veterinary teaching hospitals to investigate the genetic basis of disease in dogs. J Am Vet Med Assoc (2009) 0.81

Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genet (2009) 0.81

IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds. Invest Ophthalmol Vis Sci (2013) 0.81

Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers. BMC Med Genomics (2012) 0.81

Comparative genomics of multiple strains of Pseudomonas cannabina pv. alisalensis, a potential model pathogen of both monocots and dicots. PLoS One (2013) 0.80