Cited by 578Evolution and Genetic DynamicsGenomics and Phylogenetic StudiesGenetic diversity and population structure

The DOI matches its Crossref record; 95 of the 97 references it cites were found in a registry or an index.

Patterns of Positive Selection in Six Mammalian Genomes

Open access

Kosiol, Carolin, Vinař, Tomáš, da Fonseca, Rute R., Hubisz, Melissa J., Bustamante, Carlos D., Nielsen, Rasmus, Siepel, Adam·2008·PLoS Genetics

DOI 10.1371/journal.pgen.1000144PMC PMC2483296

Open this paper in CoChat — free account Open PDF

Abstract

Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of individual genes. However, previous scans have been limited in power and accuracy owing to small numbers of available genomes. Here we present the most comprehensive examination of mammalian PSGs to date, using the six high-coverage genome assemblies now available for eutherian mammals. The increased phylogenetic depth of this dataset results in substantially improved statistical power, and permits several new lineage- and clade-specific tests to be applied. Of approximately 16,500 human genes with high-confidence orthologs in at least two other species, 400 genes showed significant evidence of positive selection (FDR<0.05), according to a standard likelihood ratio test. An additional 144 genes showed evidence of positive selection on particular lineages or clades. As in previous studies, the identified PSGs were enriched for roles in defense/immunity, chemosensory perception, and reproduction, but enrichments were also evident for more specific functions, such as complement-mediated immunity and taste perception. Several pathways were strongly enriched for PSGs, suggesting possible co-evolution of interacting genes. A novel Bayesian analysis of the possible "selection histories" of each gene indicated that most PSGs have switched multiple times between positive selection and nonselection, suggesting that positive selection is often episodic. A detailed analysis of Affymetrix exon array data indicated that PSGs are expressed at significantly lower levels, and in a more tissue-specific manner, than non-PSGs. Genes that are specifically expressed in the spleen, testes, liver, and breast are significantly enriched for PSGs, but no evidence was found for an enrichment for PSGs among brain-specific genes. This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1371/journal.pgen.1000144

Cites

95 of 95 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
A Simple Sequentially Rejective Multiple Test Procedure
(1979) · Scandinavian Journal of Statistics · doi:10.2307/4615733 · Cited by 21,526
Statistical Methods for Research Workers
Fisher, R. A. (1945) · American Journal of Clinical Pathology · doi:10.1093/ajcp/15.11.552b · Cited by 10,883
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,377
Summaries of Affymetrix GeneChip probe level data
Irizarry, R. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng015 · Cited by 4,837
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441

Flagged first, then by citations

Show all 97 references

2 of the 97 references couldn’t be matched to a known paper.

Research works printed but not linked: 1

JL Thorne, 2007, Population genetics without intraspecific data., Mol Biol Evol, 24, 1667, 10.1093/molbev/msm085 · DOI

Sorted by citations

Items 101–200 of 578

Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms
Greminger, M. P., Stölting, K. N., Nater, A., Goossens, B., Arora, N., Bruggmann, R., Patrignani, A., Nussberger, B., Sharma, R., Kraus, R. H., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-16 · Cited by 91
Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area
Harris, S. E., Munshi‐South, J., Obergfell, C. J., & O'Neill, R. J. W. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074938 · Cited by 91
Pan-mammalian analysis of molecular constraints underlying extended lifespan
Kowalczyk, A., Partha, R., Clark, N. L., & Chikina, M. (2020) · eLife · doi:10.7554/elife.51089 · Cited by 95
Trans genomic capture and sequencing of primate exomes reveals new targets of positive selectionPreprint
George, R. D., McVicker, G., Diederich, R., Ng, S. B. H., MacKenzie, A. P., Swanson, W. J., Shendure, J., & Thomas, J. H. (2011) · Genome Research · doi:10.1101/gr.121327.111 · Cited by 89
Polygenic and directional regulatory evolution across pathways in Saccharomyces
Bullard, J. H., Mostovoy, Y., Dudoit, S., & Brem, R. B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912959107 · Cited by 87
Evidence for Widespread Positive and Purifying Selection Across the European Rabbit (Oryctolagus cuniculus) Genome
Carneiro, M., Albert, F. W., Melo‐Ferreira, J., Galtier, N., Gayral, P., Blanco, J., Villafuerte, R., Nachman, M. W., & Ferrand, N. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss025 · Cited by 89
Evolutionary genetics and implications of small size and twinning in callitrichine primates
Harris, R. A., Tardif, S. D., Vinař, T., Wildman, D. E., Rutherford, J. N., Rogers, J., Worley, K. C., & Aagaard, K. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316037111 · Cited by 84
Self-citation
Looking for Darwin's footprints in the microbial world
Shapiro, B. J., David, L. A., Friedman, J., & Alm, E. J. (2009) · Trends in Microbiology · doi:10.1016/j.tim.2009.02.002 · Cited by 86
SMARCA2 and other genome-wide supported schizophrenia-associated genes: regulation by REST/NRSF, network organization and primate-specific evolution
Loe-Mie, Y., Lepagnol-Bestel, A.-M., Maussion, G., Doron‐Faigenboim, A., Imbeaud, S., Delacroix, H., Aggerbeck, L. P., Pupko, T., Gorwood, P. A. P. M., Simonneau, M., et al. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq184 · Cited by 86
A Comparative Assessment of the Pig, Mouse and Human Genomes
Dawson, H. D. (2011) · CRC Press eBooks · doi:10.1201/b11356-28 · Cited by 82
Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases
da Fonseca, R. R., Johnson, W. E., O’Brien, S. J., Vasconcelos, V. M., & Antunes, A. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-281 · Cited by 77
Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection
Naumenko, S., Logacheva, M. D., Popova, N. V., Klepikova, A. V., Penin, A. A., Bazykin, G. A., Etingova, A. E., Mugue, N. S., Kondrashov, A. S., & Yampolsky, L. Y. (2016) · Molecular Ecology · doi:10.1111/mec.13927 · Cited by 77
Identification and Characterization of Seminal Fluid Proteins in the Asian Tiger Mosquito, Aedes albopictus
Boes, K. E., Ribeiro, J. M. C., Wong, A., Harrington, L. C., Wolfner, M. F., & Sirot, L. K. (2014) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0002946 · Cited by 78
Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis
Blackburne, B. P., & Whelan, S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss256 · Cited by 76
Developmental Gene Expression Differences between Humans and Mammalian Models
Cardoso-Moreira, M., Sarropoulos, I., Velten, B., Mort, M. E., Cooper, D. N., Huber, W. K., & Kaessmann, H. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108308 · Cited by 77
Copy number variation analysis in the great apes reveals species-specific patterns of structural variationPreprint
Gazave, É., Darré, F., Morcillo-Suárez, C., Petit, N., Carreno, A., Marigorta, U. M., Ryder, O. A., Blancher, A., Rocchi, M., Bosch, E., et al. (2011) · Genome Research · doi:10.1101/gr.117242.110 · Cited by 74
New functional and structural insights from updated mutational databases for complement factor H, Factor I, membrane cofactor protein and C3
Rodríguez, E., Rallapalli, P. M., Osborne, A. J., & Perkins, S. J. (2014) · Bioscience Reports · doi:10.1042/bsr20140117 · Cited by 73
Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes
Wang, D., Liu, F., Wang, L., Huang, S., & Yu, J. M. (2011) · Biology Direct · doi:10.1186/1745-6150-6-13 · Cited by 73
Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution
Huang, Y., Temperley, N. D., Ren, L., Smith, J., Li, N., & Burt, D. W. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-149 · Cited by 73
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts
van der Lee, R., Wiel, L., van Dam, T. J. P., & Huynen, M. A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx704 · Cited by 74
Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus CampylobacterPreprint
Tristan, L., & Stanhope, M. J. (2009) · Genome Research · doi:10.1101/gr.089250.108 · Cited by 72
Towards a Liquid Self: How Time, Geography, and Life Experiences Reshape the Biological Identity
Grignolio, A., Mishto, M., Faria, A. M. C., Garagnani, P., Franceschi, C., & Tieri, P. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00153 · Cited by 73
Enhancer Function and Evolutionary Roles of Human Accelerated Regions
Whalen, S., & Pollard, K. S. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-071819-103933 · Cited by 73
Human and Non-Human Primate Genomes Share Hotspots of Positive Selection
Enard, D., Depaulis, F., & Crollius, H. R. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000840 · Cited by 75
Genome-Wide Association Study SNPs in the Human Genome Diversity Project Populations: Does Selection Affect Unlinked SNPs with Shared Trait Associations?
Casto, A. M., & Feldman, M. W. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001266 · Cited by 67
Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides
Chapman, J. R., Hill, T., & Unckless, R. L. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz191 · Cited by 67
Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica
Guo, Y., Liu, J., Zhang, J., Liu, S., & Du, J. (2017) · The Plant Journal · doi:10.1111/tpj.13541 · Cited by 63
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats
Scheben, A., Ramos, O. M., Kramer, M., Goodwin, S., Oppenheim, S. J., Becker, D. J., Schatz, M. C., Simmons, N. B., Siepel, A. C., & McCombie, W. R. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad148 · Cited by 65
Self-citation
K r /K c but not d N /d S correlates positively with body mass in birds, raising implications for inferring lineage-specific selection
Weber, C. C., Nabholz, B., Romiguier, J., & Ellegren, H. (2014) · Genome biology · doi:10.1186/s13059-014-0542-8 · Cited by 63
Sequencing Primate Genomes: What Have We Learned?
Marquès‐Bonet, T., Ryder, O. A., & Eichler, E. E. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164420 · Cited by 65
Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis
Davies, K. T. J., Bennett, N. C., Tsagkogeorga, G., Rossiter, S. J., & Faulkes, C. G. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv175 · Cited by 65
Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
Sun, Y., Zhou, W., Liu, H., Irwin, D. M., Shen, Y., & Zhang, Y. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs123 · Cited by 65
Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
Liu, W. Y., Fang, L., Li, M., Li, S., Guo, S., Luo, R., Feng, Z., Li, B., Zhou, Z., Shao, G., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035698 · Cited by 65
Proteomic profiling of HIV-1 infection of human CD4+ T cells identifies PSGL-1 as an HIV restriction factor
Liu, Y., Fu, Y., Wang, Q., Li, M., Zhou, Z., Dabbagh, D., Fu, C., Zhang, H., Li, S., Zhang, T., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0372-2 · Cited by 64
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans
Daub, J. T., Moretti, S., Davydov, I. I., Excoffier, L., & Robinson‐Rechavi, M. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx083 · Cited by 65
Whole-Genome Positive Selection and Habitat-Driven Evolution in a Shallow and a Deep-Sea Urchin
Oliver, T. A., Garfield, D. A., Manier, M. K., Haygood, R., Wray, G. A., & Palumbi, S. R. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq063 · Cited by 62
Long-lived rodents reveal signatures of positive selection in genes associated with lifespan
Sahm, A., Bens, M., Szafranski, K., Holtze, S., Groth, M., Görlach, M., Calkhoven, C. F., Müller, C., Schwab, M. G., Kraus, J. M., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007272 · Cited by 65
Inference of Gorilla Demographic and Selective History from Whole-Genome Sequence Data
McManus, K. F., Kelley, J. L., Song, S., Veeramah, K. R., Woerner, A. E., Stevison, L. S., Ryder, O. A., Great Ape Genome Project, Kidd, J. M., Wall, J. D., et al. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu394 · Cited by 63
Self-citation
Genomic signatures of diet-related shifts during human origins
Babbitt, C. C., Warner, L., Fedrigo, O. D., Wall, C. E., & Wray, G. A. (2010) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2010.2433 · Cited by 61
Recent Positive Selection Has Acted on Genes Encoding Proteins with More Interactions within the Whole Human Interactome
Luisi, P., Alvarez‐Ponce, D., Pybus, M., Fares, M. A., Bertranpetit, J., & Laayouni, H. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv055 · Cited by 63
Improving Genome-Wide Scans of Positive Selection by Using Protein Isoforms of Similar Length
Villanueva‐Cañas, J. L., Laurie, S., & Albà, M. M. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt017 · Cited by 63
How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome
Nery, M. F., González, D. J., & Opazo, J. C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065491 · Cited by 57
PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes
Sahm, A., Bens, M., Platzer, M., & Szafranski, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx179 · Cited by 58
Molecular Evolution of Freshwater Snails with Contrasting Mating Systems
Burgarella, C., Gayral, P., Ballenghien, M., Bernard, A., David, P., Jarne, P., Correa, A. C., Hurtrez‐Boussès, S., Escobar, J. S., Galtier, N., et al. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv121 · Cited by 59
Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
Guéguen, L., & Duret, L. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx308 · Cited by 55
GWAS of human bitter taste perception identifies new loci and reveals additional complexity of bitter taste genetics
Ledda, M., Kutalik, Z., Destito, M. C. S., de Souza, M. M., Cirillo, C. A., Zamboni, A., Martin, N., Morya, E., Sameshima, K., Beckmann, J. S., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt404 · Cited by 55
Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution
Suzuki, H., Tristan, L., Hubisz, M. J., Bitar, P. P., Lang, P., Siepel, A. C., & Stanhope, M. J. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr006 · Cited by 54
Self-citation
Evolutionary Trajectories of Primate Genes Involved in HIV Pathogenesis
Ortiz, M., Guex, N., Patin, É., Martin, O., Xénarios, I., Ciuffi, A., Quintana‐Murci, L., & Telenti, A. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp197 · Cited by 55
The frequent evolutionary birth and death of functional promoters in mouse and humanPreprint
Young, R. S., Hayashizaki, Y., Andersson, R., Sandelin, A., Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Bickmore, W. A., Forrest, A. R. R., et al. (2015) · Genome Research · doi:10.1101/gr.190546.115 · Cited by 56
Different selective pressures shape the evolution of Toll-like receptors in human and African great ape populations
Quach, H., Wilson, D. J., Laval, G., Patin, É., Manry, J., Guibert, J., Barreiro, L. B., Nerrienet, E., Verschoor, E. J., Gessain, A., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt335 · Cited by 52
A Total Evidence Phylogenetic Analysis of Pinniped Phylogeny and the Possibility of Parallel Evolution Within a Monophyletic Framework
Paterson, R. S., Rybczynski, N., Kohno, N., & Maddin, H. C. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00457 · Cited by 50
Genome-scale analysis of demographic history and adaptive selection
Wu, Q., Zheng, P., Hu, Y., & Wei, F. (2014) · Protein & Cell · doi:10.1007/s13238-013-0004-1 · Cited by 49
Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution
Doyle, J. M., Katzner, T. E., Roemer, G. W., Cain, J. W., Millsap, B. A., McIntyre, C. L., Sonsthagen, S. A., Fernández, N. B., Wheeler, M., Bulut, Z., et al. (2016) · Conservation Genetics · doi:10.1007/s10592-016-0863-0 · Cited by 49
Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants
Kono, T. J. Y., Li, L., Shih, C.-H., Hoffman, P., Morrell, P. L., & Fay, J. C. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200563 · Cited by 52
Host Genetics and HIV-1: The Final Phase?
Fellay, J., Shianna, K. V., Telenti, A., & Goldstein, D. B. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001033 · Cited by 48
Adaptive evolution and divergent expression of heat stress transcription factors in grasses
Yang, Z., Wang, Y., Gao, Y., Zhou, Y., Zhang, E., Hu, Y., Yuan, Y., Liang, G., & Xu, C. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-147 · Cited by 48
TDP-43 facilitates milk lipid secretion by post-transcriptional regulation of Btn1a1 and Xdh
Zhao, L., Hao, K., Xu, H., Wang, G., Zhang, H., Zou, L., Shu, X., Li, M., Li, P., Zhou, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14183-1 · Cited by 48
Evolution in the Genus Homo
Wood, B. A., & Baker, J. L. (2011) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-102209-144653 · Cited by 47
Understanding the evolution of immune genes in jawed vertebrates
Vinkler, M., Fiddaman, S. R., Těšický, M., O'Connor, E. A., Savage, A. E., Lenz, T. L., Smith, A. L., Kaufman, J., Bolnick, D. I., Davies, C. S., et al. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14181 · Cited by 55
Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies
Daane, J. M., Rohner, N., Konstantinidis, P., Djuranović, S., & Harris, M. P. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv208 · Cited by 44
POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes
Hongo, J. A., de Castro, G. M., Cintra, L. C., Zerlotini, A., & Lobo, F. P. (2015) · BMC Genomics · doi:10.1186/s12864-015-1765-0 · Cited by 47
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals
Slodkowicz, G., & Goldman, N. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1916786117 · Cited by 47
A prominent role of KRAB-ZNF transcription factors in mammalian speciation?
Nowick, K., Carneiro, M., & Faria, R. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.11.007 · Cited by 46
Genetic signals of high-altitude adaptation in amphibians: a comparative transcriptome analysis
Yang, W., Qi, Y., & Fu, J. (2016) · BMC Genetics · doi:10.1186/s12863-016-0440-z · Cited by 46
Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates
Zhuang, H., Chien, M., & Matsunami, H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808378106 · Cited by 44
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model
Rodrigue, N., & Lartillot, N. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw220 · Cited by 43
Selective Pressures on Human Cancer Genes along the Evolution of Mammals
Vicens, A., & Posada, D. (2018) · Genes · doi:10.3390/genes9120582 · Cited by 43
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
Näpflin, K., O’Connor, E., Becks, L., Bensch, S., Ellis, V. A., Hafer, N., Hårding, K. C., Lindén, S. K., Olsen, M. T., Roved, J., et al. (2019) · PeerJ · doi:10.7717/peerj.8013 · Cited by 44
A SELECTION MODEL OF MOLECULAR EVOLUTION INCORPORATING THE EFFECTIVE POPULATION SIZE
Ellegren, H. (2009) · Evolution · doi:10.1111/j.1558-5646.2008.00560.x · Cited by 43
Positive selection on apoptosis related genes
da Fonseca, R. R., Kosiol, C., Vinař, T., Siepel, A., & Nielsen, R. (2010) · FEBS Letters · doi:10.1016/j.febslet.2009.12.022 · Cited by 42
Self-citation
Characterization of the porcine nutrient and taste receptor gene repertoire in domestic and wild populations across the globe
da Silva, E. C., de Jager, N., Burgos-Paz, W. O., Reverter, A., Miguel Pérez-enciso, A., & Roura, E. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1057 · Cited by 43
Genetic Evidence of Human Adaptation to a Cooked Diet
Carmody, R. N., Dannemann, M., Briggs, A. W., Nickel, B., Groopman, E., Wrangham, R. W., & Kelso, J. F. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw059 · Cited by 44
Molecular evolution of Odorant-binding proteins gene family in two closely related Anastrepha fruit flies
Campanini, E. B., & de Brito, R. A. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0775-0 · Cited by 46
Selection efficiency and effective population size in Drosophila species
Petit, N., & Barbadilla, A. (2008) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2008.01672.x · Cited by 44
Genetic diversity in humans and non-human primates and its evolutionary consequences
Osada, N. (2015) · Genes & Genetic Systems · doi:10.1266/ggs.90.133 · Cited by 44
Rapid expansion of immune-related gene families in the house fly, Musca domestica
Sackton, T. B., Lazzaro, B. P., & Clark, A. G. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw285 · Cited by 41
Positive Selection Differs between Protein Secondary Structure Elements in Drosophila
Ridout, K. E., Dixon, C. J., & Filatov, D. A. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq008 · Cited by 43
Genome-Wide Scan for Signatures of Human Population Differentiation and Their Relationship with Natural Selection, Functional Pathways and Diseases
Amato, R., Pinelli, M., Monticelli, A., Marino, D., Miele, G., & Cocozza, S. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007927 · Cited by 41
Interaction between Selection and Biased Gene Conversion in Mammalian Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance Analysis
Lartillot, N. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss231 · Cited by 44
Nonhuman Primate Models of Neuropsychiatric Disorders: Influences of Early Rearing, Genetics, and Epigenetics
Dettmer, A. M., & Suomi, S. J. (2014) · ILAR Journal · doi:10.1093/ilar/ilu025 · Cited by 42
Genetic comparisons yield insight into the evolution of enamel thickness during human evolution
Horvath, J. E., Ramachandran, G. L., Fedrigo, O. D., Nielsen, W., Babbitt, C. C., Clair, E. M. S., Pfefferle, L. W., Jernvall, J., Wray, G. A., & Wall, C. E. (2014) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.01.005 · Cited by 42
Convergent Loss of the Necroptosis Pathway in Disparate Mammalian Lineages Shapes Viruses Countermeasures
Águeda-Pinto, A., Alves, L. Q., Neves, F., McFadden, G., Jacobs, B. L., Castro, L. F. C., Rahman, M. M., & Esteves, P. J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.747737 · Cited by 40
Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages
Kostka, D., Holloway, A. K., & Pollard, K. S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy109 · Cited by 32
Natural Selection on Coding and Noncoding DNA Sequences Is Associated with Virulence Genes in a Plant Pathogenic Fungus
Rech, G. E., Sanz‐Martín, J. M., Anisimova, M. O., Sukno, S. A., & Thon, M. R. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu192 · Cited by 39
dbPSHP: a database of recent positive selection across human populations
Li, M. J., Wang, L. Y., Xia, Z., Wong, M. P., Sham, P. C., & Wang, J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1052 · Cited by 41
Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds
Gossmann, T. I., Santure, A. W., Sheldon, B. C., Slate, J., & Zeng, K. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu157 · Cited by 39
Molecular characterization of novel mitochondrial peroxiredoxins from the Antarctic emerald rockcod and their gene expression in response to environmental warming
Tolomeo, A. M., Carraro, A., Bakiu, R., Toppo, S., Garofalo, F., Pellegrino, D., Gerdol, M., Ferro, D., Place, S. P., & Santovito, G. (2019) · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology · doi:10.1016/j.cbpc.2019.108580 · Cited by 39
Variation of the adaptive substitution rate between species and within genomes
Moutinho, A. F., Bataillon, T. M., & Dutheil, J. Y. (2019) · Evolutionary Ecology · doi:10.1007/s10682-019-10026-z · Cited by 42
Lineage-Specific Variation in Intensity of Natural Selection in Mammals
Toll‐Riera, M., Laurie, S., & Albà, M. M. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq206 · Cited by 39
Bacterial symbiont and salivary peptide evolution in the context of leech phylogeny
Siddall, M. E., Min, G., Fontanella, F. M., Phillips, A. J., & Watson, S. C. (2011) · Parasitology · doi:10.1017/s0031182011000539 · Cited by 39
Use with caution: developmental systems divergence and potential pitfalls of animal models.
Lynch, V. J. (2009) · PubMed Central · Cited by 38
Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection
Davydov, I. I., Salamin, N., & Robinson‐Rechavi, M. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz048 · Cited by 38
Detecting and understanding natural selection
Anisimova, M. O., & Liberles, D. A. (2012) · Oxford University Press eBooks · doi:10.1093/acprof:osobl/9780199601165.003.0006 · Cited by 39
Microcephaly genes evolved adaptively throughout the evolution of eutherian mammals
Montgomery, S. H., & Mundy, N. I. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-120 · Cited by 38
Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species
Mugal, C. F., Kutschera, V. E., Botero-Castro, F., Wolf, J. B. W., & Kaj, I. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz203 · Cited by 37
The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence
Flores, H. A., Bubnell, J. E., Aquadro, C. F., & Barbash, D. A. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005453 · Cited by 40
An Evolutionary Analysis of Antigen Processing and Presentation across Different Timescales Reveals Pervasive Selection
Forni, D., Cagliani, R., Tresoldi, C., Pozzoli, U., GIOIA, L. D., Filippi, G., Riva, S., Menozzi, G., Colleoni, M., Biasin, M., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004189 · Cited by 37
Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds
Axelsson, E., Albrechtsen, A., van, A., Li, L., Megens, H., Vereijken, A., Crooijmans, R. P. M. A., Groenen, M. A. M., Ellegren, H., Willerslev, E., et al. (2010) · Heredity · doi:10.1038/hdy.2009.193 · Cited by 37
Self-citation
Virion-incorporated PSGL-1 and CD43 inhibit both cell-free infection and transinfection of HIV-1 by preventing virus–cell binding
Murakami, T., Carmona, N., & Ono, A. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1916055117 · Cited by 36
Rapid evolution fuels transcriptional plasticity to ocean acidification
Kang, J., Nagelkerken, I., Rummer, J. L., Rodolfo‐Metalpa, R., Munday, P. L., Ravasi, T., & Schunter, C. (2022) · Global Change Biology · doi:10.1111/gcb.16119 · Cited by 37

Authors: Kosiol, C., Vinař, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., & Siepel, A.
Affiliations: Cornell University (US)
University of Chicago (US)
University of Copenhagen (DK)
Corresponding author: Siepel, Adam
ORCID: Kosiol, Carolin
Vinař, Tomáš
Hubisz, Melissa J.
Bustamante, Carlos D.
Nielsen, Rasmus
Siepel, Adam
Venue: PLoS Genetics
Publisher: Public Library of Science (PLoS)
Published: 2008-08-01
Volume: 4
Issue: 8
Pages: e1000144
ISSN: 1553-7390 (ISSN-L)
1553-7404
DOI: 10.1371/journal.pgen.1000144
PMC: PMC2483296
OpenAlex: W2154770881
Cited by: 576
References: 97
Citations by year: 2026: 5 · 2025: 15 · 2024: 23 · 2023: 17 · 2022: 19 · 2021: 58 · 2020: 27 · 2019: 27 · 2018: 24 · 2017: 31 · 2016: 25 · 2015: 32 · 2014: 51 · 2013: 55 · 2012: 41
FWCI: 23.75
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS Genetics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Knowledge@UChicago (University of Chicago) (submittedVersion, cc-by-nc-nd)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
eScholarship (California Digital Library) (submittedVersion)
Figshare (submittedVersion, cc-by)
Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
University of Chicago (cc-by)
Funders: National Science Foundation (0644111, 0516310)
Microsoft Research
National Human Genome Research Institute (R01HG003229)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords: positive selection, mammalian evolution, placental mammals, orthologs, lineage-specific selection, immune-related genes, chemosensory perception, reproduction, taste perception, gene coevolution, episodic selection, gene expression, tissue-specific gene expression, spleen, testis, liver, breast
MeSH terms: Animals, Bayes Theorem, Pan troglodytes, Dogs, Humans, Macaca mulatta, Mammals, Phylogeny, Primates, Rodentia, Selection, Genetic, Gene Expression, Likelihood Functions, Sequence Alignment, Genome, Evolution, Molecular, Databases, Genetic, Mice, Rats

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Patterns of Positive Selection in Six Mammalian Genomes

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks