Adaptive protein evolution at the Adh locus in Drosophila

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459

Detecting recent positive selection in the human genome from haplotype structure

Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106

Hitchhiking Under Positive Darwinian Selection

Fay, J. C., & Wu, C.-I. (2000) · Genetics · doi:10.1093/genetics/155.3.1405 · Cited by 1,819

Detecting Individual Sites Subject to Episodic Diversifying Selection

Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811

Evolution and functional impact of rare coding variation from deep sequencing of human exomes

Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. (2012) · Science · doi:10.1126/science.1219240 · Cited by 1,613

Positive Natural Selection in the Human Lineage

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T. S., Altshuler, D., & Lander, E. S. (2006) · Science · doi:10.1126/science.1124309 · Cited by 1,157

Genomic variation landscape of the human gut microbiome

Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907

A framework for the interpretation of de novo mutation in human disease

Samocha, K. E., Robinson, E. B., Sanders, S. J., Stevens, C., Sabo, A., McGrath, L. M., Kosmicki, J. A., Rehnström, K., Mallick, S., Kirby, A., et al. (2014) · Nature Genetics · doi:10.1038/ng.3050 · Cited by 979

The Population Genetics of dN/dS

Kryazhimskiy, S., & Plotkin, J. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000304 · Cited by 962

The origin of new genes: Glimpses from the young and old

Long, M., Betrán, E., Thornton, K., & Wang, W. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1204 · Cited by 933

Detecting Natural Selection in Genomic Data

Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation

Tarpey, P. S., Smith, R., Pleasance, E., Whibley, A., Edkins, S., Hardy, C., O'Meara, S., Latimer, C., Dicks, E., Menzies, A., et al. (2009) · Nature Genetics · doi:10.1038/ng.367 · Cited by 603

A population genetic signal of polygenic adaptation

Berg, J. J., & Coop, G. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004412 · Cited by 487

How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles

Morjan, C. L., & Rieseberg, L. H. (2004) · Molecular Ecology · doi:10.1111/j.1365-294x.2004.02164.x · Cited by 479

Natural selection on human microRNA binding sites inferred from SNP data

Chen, K., & Rajewsky, N. (2006) · Nature Genetics · doi:10.1038/ng1910 · Cited by 469

A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation.

Kimura, R., Fujimoto, A., Tokunaga, K., & Ohashi, J. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000286 · Cited by 461

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server

Hardison, R. C., Chui, D. H. K., Giardine, B., Riemer, C., Patrinos, G. P., Anagnou, N., Miller, W., & Wajcman, H. (2002) · Human Mutation · doi:10.1002/humu.10044 · Cited by 439

Genomic signatures of evolutionary transitions from solitary to group living

Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., et al. (2015) · Science · doi:10.1126/science.aaa4788 · Cited by 409

Evidence for Variable Selective Pressures at MC1R

Harding, R. M., Healy, E., Ray, A. J., Ellis, N. S., Flanagan, N., Todd, C., Dixon, C., Sajantila, A., Jackson, I. J., Birch-Machin, M. A., et al. (2000) · The American Journal of Human Genetics · doi:10.1086/302863 · Cited by 389

De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia

Gauthier, J., Champagne, N., Lafrenière, R. G., Xiong, L., Spiegelman, D., Brustein, E., Lapointe, M., Peng, H., Côté, M., Noreau, A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906232107 · Cited by 369

Evolution of primate gene expression

Khaitovich, P., Enard, W., Lachmann, M., & Pääbo, S. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1940 · Cited by 341

Genome-wide scans for footprints of natural selection

Oleksyk, T. K., Smith, M. W., & O'Brien, S. J. (2010) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0219 · Cited by 340

Near-neutrality in evolution of genes and gene regulation

Ohta, T. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252626899 · Cited by 333

A high-coverage Neandertal genome from Chagyrskaya Cave

Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309

New Gene Evolution: Little Did We Know

Long, M., VanKuren, N. W., Chen, S., & Vibranovski, M. D. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133301 · Cited by 307

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin-Orlando, A., Leonardi, M., McCrory Constantz, C., Gamba, C., Al-Rasheid, K. A. S., Albizuri, S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.049 · Cited by 285

Transitions to asexuality result in excess amino acid substitutions

Paland, S., & Lynch, M. (2006) · Science · doi:10.1126/science.1118152 · Cited by 232

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

Golubchik, T., Batty, E. M., Miller, R. R., Farr, H., Young, B. C., Larner-Svensson, H., Fung, R., Godwin, H., Knox, K., Votintseva, A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061319 · Cited by 212

Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans

Cornejo, O. E., Lefébure, T., Pavinski Bitar, P. D., Lang, P., Richards, V. P., Eilertson, K., Do, T., Beighton, D., Zeng, L., Ahn, S.-J., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss278 · Cited by 198

Role of selection in fixation of gene duplications

Kondrashov, F. A., & Kondrashov, A. S. (2006) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.08.033 · Cited by 195

Distinguishing between selective sweeps from standing variation and from a de novo mutation

Peter, B. M., Huerta-Sanchez, E., & Nielsen, R. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003011 · Cited by 193

Evolution at two levels of gene expression in yeast

Artieri, C. G., & Fraser, H. B. (2014) · Genome Research · doi:10.1101/gr.165522.113 · Cited by 138

Accelerated Recruitment of New Brain Development Genes into the Human Genome

Zhang, Y. E., Landback, P., Vibranovski, M. D., & Long, M. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001179 · Cited by 164

Worldwide distribution of NAT2 diversity: Implications for NAT2 evolutionary history

Sabbagh, A., Langaney, A., Darlu, P., Gérard, N., Krishnamoorthy, R., & Poloni, E. S. (2008) · BMC Genetics · doi:10.1186/1471-2156-9-21 · Cited by 147

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Murray, G. G. R., Soares, A. E. R., Novak, B. J., Schaefer, N. K., Cahill, J. A., Baker, A. J., Demboski, J. R., Doll, A., Da Fonseca, R. R., Fulton, T. L., et al. (2017) · Science · doi:10.1126/science.aao0960 · Cited by 132

Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association

Funk, D. J., Wernegreen, J. J., & Moran, N. A. (2001) · Genetics · doi:10.1093/genetics/157.2.477 · Cited by 131

Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species

Wang, W., Yu, H., & Long, M. (2004) · Nature Genetics · doi:10.1038/ng1338 · Cited by 114

Megabase-scale inversion polymorphism in the wild ancestor of maize

Fang, Z., Pyhäjärvi, T., Weber, A. L., Dawe, R. K., Glaubitz, J. C., González, J. D. J. S., Ross-Ibarra, C., Doebley, J., Morrell, P. L., & Ross-Ibarra, J. (2012) · Genetics · doi:10.1534/genetics.112.138578 · Cited by 104

Nocturnal light environments influence color vision and signatures of selection on the OPN1SW opsin gene in nocturnal lemurs

Veilleux, C. C., Louis, E. E., & Bolnick, D. A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst058 · Cited by 103

Evidence for recent positive selection at the human AIM1 locus in a European population

Soejima, M., Tachida, H., Ishida, T., Sano, A., & Koda, Y. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msj018 · Cited by 84

A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences

Wilson, D. J., Hernandez, R. D., Andolfatto, P., & Przeworski, M. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002395 · Cited by 85

DNA Polymorphism and Selection at the Melanocortin‐1 Receptor Gene in Normally Pigmented Southern African Individuals

JOHN, P. R., MAKOVA, K., LI, W., JENKINS, T., & RAMSAY, M. (2003) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2003.tb03193.x · Cited by 72

Locus- and population-specific selection and differentiation between incipient species of Anopheles gambiae

Turner, T. L., & Hahn, M. W. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm143 · Cited by 66

A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL

Herbeck, J. T., Funk, D. J., Degnan, P. H., & Wernegreen, J. J. (2003) · Genetics · doi:10.1093/genetics/165.4.1651 · Cited by 58

De Novo Genes

Zhao, L., Svetec, N., & Begun, D. J. (2024) · Annual Review of Genetics · doi:10.1146/annurev-genet-111523-102413 · Cited by 38

Lack of Self-Averaging in Neutral Evolution of Proteins

Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2002) · Physical Review Letters · doi:10.1103/physrevlett.89.208101 · Cited by 35

Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

(2023) · doi:10.7554/elife.80489 · Cited by 34

PopHuman: the human population genomics browser

Casillas, S., Mulet, R., Villegas-Mirón, P., Hervas, S., Sanz, E., Velasco, D., Bertranpetit, J., Laayouni, H., & Barbadilla, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx943 · Cited by 29

Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD

Librado, P., & Orlando, L. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy053 · Cited by 28

Strong Constraint on Human Genes Escaping X-Inactivation Is Modulated by their Expression Level and Breadth in Both Sexes

Slavney, A., Arbiza, L., Clark, A. G., & Keinan, A. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msv225 · Cited by 26

Regional selection of the brain size regulating gene CASC5 provides new insight into human brain evolution

Shi, L., Hu, E., Wang, Z., Liu, J., Li, J., Li, M., Chen, H., Yu, C., Jiang, T., & Su, B. (2017) · Human Genetics · doi:10.1007/s00439-016-1748-5 · Cited by 20

Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans

Chintalapati, M., Dannemann, M., & Prüfer, K. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1018-8 · Cited by 13

A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites

MacGowan, S. A., Madeira, F., Britto-Borges, T., & Barton, G. J. (2024) · Communications Biology · doi:10.1038/s42003-024-06117-5 · Cited by 8