Testing for ancient selection using cross-population allele frequency differentiation
Open accessPublished version of a preprint
Abstract
A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.
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
Cites
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?
A significant intersection was found with the data from Prüfer et al. [44] (p < 0.05) and with the combined data from Prüfer et al. [44] and Racimo [48] (p < 0.05).
“A significant intersection was found with the data from Prüfer et al. [44] (p < 0.05) and with the combined data from Prüfer et al. [44] and Racimo [48] (p < 0.05).”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [48]
A significant intersection was found with the data in [44] (a = 691, b = 108, v = 9; p < 0.05) and with the combined data from [44] and [48] (a = 691, b = 419, v = 24, p < 0.05).
“A significant intersection was found with the data in [44] (a = 691, b = 108, v = 9; p < 0.05) and with the combined data from [44] and [48] (a = 691, b = 419, v = 24, p < 0.05).”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [48]
One of the most comprehensive studies of regions of the modern human genome associated with selective sweep signals compared to archaics specifically included BAZ1B within the detected portions of the WBSCR.
“(iv) the most comprehensive studies focusing on regions of the modern human genome associated with selective sweep signals compared to Neanderthals/Denisovans (hereafter “archaics”) (13, 14), one of which specifically included BAZ1B within the detected portions of the WBSCR;”
ADSL has been pointed out before as under positive selection.
“which has been pointed out before as under positive selection31,33,34,122.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [34]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183 · see citing works
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works
The hitch-hiking effect of a favourable gene
Smith, J. M., & Haigh, J. (1974) · Genetical Research · doi:10.1017/s0016672300014634 · Cited by 3,415 · see citing works
A Map of Recent Positive Selection in the Human Genome
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,912 · see citing works
Ancient Admixture in Human History
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848 · see citing works
Inference of population splits and mixtures from genome-wide allele frequency data
Pickrell, J. K., & Pritchard, J. K. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002967 · Cited by 2,731 · see citing works
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707 · see citing works
The hitch-hiking effect of a favourable gene
MAYNARD, J., & Haigh, J. (2007) · Genetics Research · doi:10.1017/s0016672308009579 · Cited by 2,663 · see citing works
Inference of human population history from individual whole-genome sequences
Li, H., & Durbin, R. (2011) · Nature · doi:10.1038/nature10231 · Cited by 2,590 · see citing works
The complete genome sequence of a Neanderthal from the Altai Mountains
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254 · see citing works
Self-citationGenome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131 · see citing works
A gene expression atlas of the central nervous system based on bacterial artificial chromosomes
Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., Nowak, N. J., Joyner, A., Leblanc, G., Hatten, M. E., et al. (2003) · Nature · doi:10.1038/nature02033 · Cited by 2,108 · see citing works
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 · see citing works
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
Self-citationGutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · see citing works
Hitchhiking Under Positive Darwinian Selection
Fay, J. C., & Wu, C.-I. (2000) · Genetics · doi:10.1093/genetics/155.3.1405 · Cited by 1,819 · see citing works
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., et al. (2010) · Science · doi:10.1126/science.1190371 · Cited by 1,611 · cited 1× · see citing works
“This and other related statistics have been used to scan the genomes of present-day humans from different populations, so as to detect signals of recent positive selection [Akey et al., 2002, Oleksyk et al., 2008, Weir et al., 2005, Yi et al., 2010].”
MethodMathematical Population Genetics
Ewens, W. J. (2004) · Interdisciplinary applied mathematics · doi:10.1007/978-0-387-21822-9 · Cited by 1,554 · see citing works
Genome-wide patterns of selection in 230 ancient Eurasians
Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S. A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., et al. (2015) · Nature · doi:10.1038/nature16152 · Cited by 1,515 · see citing works
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
Finland, G. O. T. 1. D. I., Todd, J. A., the Wellcome Trust Case Control Consortium, Walker, N. M., Cooper, J. D., Smyth, D. J., Downes, K., Plagnol, V., Bailey, R., Nejentsev, S., et al. (2007) · Nature Genetics · doi:10.1038/ng2068 · Cited by 1,456 · see citing works
Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248 · see citing works
DISTRIBUTION OF GENE FREQUENCY AS A TEST OF THE THEORY OF THE SELECTIVE NEUTRALITY OF POLYMORPHISMS
Lewontin, R. C., & Krakauer, J. (1973) · Genetics · doi:10.1093/genetics/74.1.175 · Cited by 1,181 · see citing works
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works
The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107 · see citing works
The human phenotype ontology: a tool for annotating and analyzing human hereditary disease
Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.09.017 · Cited by 1,034 · see citing works
Genome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023 · see citing works
Interrogating a high-density SNP map for signatures of natural selection.Preprint
Akey, J., Zhang, G., Zhang, K., Jin, L., & Shriver, M. (2002) · Genome Research · doi:10.1101/gr.631202 · Cited by 932 · see citing works
An overview of composite likelihood methods
Varin, C., Reid, N. M., & Firth, D. (2011) · doi:10.82444/warw.33615778 · Cited by 921 · see citing works
Population differentiation as a test for selective sweepsPreprint
Chen, H., Patterson, N. J., & Reich, D. (2010) · Genome Research · doi:10.1101/gr.100545.109 · Cited by 888 · see citing works
Eerola, I., Boon, L. M., Mulliken, J. B., Burrows, P. E., Dompmartin, A., Watanabe, S., Vanwijck, R., & Vikkula, M. (2003) · The American Journal of Human Genetics · doi:10.1086/379793 · Cited by 747 · see citing works
Signals of recent positive selection in a worldwide sample of human populations
Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W., et al. (2009) · Genome Research · doi:10.1101/gr.087577.108 · Cited by 717 · see citing works
Newly identified genetic risk variants for celiac disease related to the immune response
Hunt, K. A., Zhernakova, A., Turner, G., Heap, G., Franke, L., Bruinenberg, M., Romanos, J., Dinesen, L. C., Ryan, A. W., Panesar, D., et al. (2008) · Nature Genetics · doi:10.1038/ng.102 · Cited by 675 · see citing works
Edenberg, H. J., Dick, D. M., Xuei, X., Tian, H., Almasy, L., Bauer, L. O., Crowe, R. R., Goate, A., Hesselbrock, V., Jones, K., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/383283 · Cited by 655 · see citing works
Lindsay, B. G. (1988) · Contemporary mathematics - American Mathematical Society · doi:10.1090/conm/080/999014 · Cited by 555 · see citing works
Identification of Novel Argonaute-Associated Proteins
Meister, G., Landthaler, M., Peters, L., Chen, P., Urlaub, H., Lührmann, R., & Tuschl, T. (2005) · Current Biology · doi:10.1016/j.cub.2005.10.048 · Cited by 554 · see citing works
A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection
Grossman, S. R., Shylakhter, I., Karlsson, E. K., Byrne, E. H., Morales, S., Frieden, G., Hostetter, E., Angelino, E., Garber, M., Zuk, O., et al. (2010) · Science · doi:10.1126/science.1183863 · Cited by 512 · see citing works
Han, J., Kraft, P., Nan, H., Guo, Q., Chen, C., Qureshi, A., Hankinson, S. E., Hu, F. B., Duffy, D. L., Zhao, Z. Z., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000074 · Cited by 499 · see citing works
Molecular Cloning of Two Types of GAP Complementary DNA from Human Placenta
Trahey, M., Wong, G. A., Halenbeck, R., Rubinfeld, B., Martin, G. A., Ladner, M. B., Long, C. M., Crosier, W. J., Watt, K., Koths, K. E., et al. (1988) · Science · doi:10.1126/science.3201259 · Cited by 468 · see citing works
Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
Schlebusch, C. M., Skoglund, P., Sjödin, P., Gattepaille, L. M., Hernandez, D. G., Jay, F., Li, S., de Jongh, M., Singleton, A., Blum, M. G. B., et al. (2012) · Science · doi:10.1126/science.1227721 · Cited by 457 · see citing works
Felsenstein, J. (1981) · Evolution · doi:10.1111/j.1558-5646.1981.tb04991.x · Cited by 456 · see citing works
Reversal of pathological pain through specific spinal GABAA receptor subtypes
Knabl, J., Witschi, R., Hösl, K., Reinold, H., Zeilhofer, U. B., Ahmadi, S., Brockhaus, J., Sergejeva, M., Hess, A., Brune, K., et al. (2008) · Nature · doi:10.1038/nature06493 · Cited by 438 · see citing works
Joe, H., Reid, N. M., Xuekun, P., & Firth, D. (2012) · Cited by 434 · see citing works
FOXG1 Is Responsible for the Congenital Variant of Rett Syndrome
Ariani, F., Hayek, G., Rondinella, D., Artuso, R., Mencarelli, M. A., Rosseto, A. S., Pollazzon, M., Buoni, S., Spiga, O., Ricciardi, S., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.05.015 · Cited by 432 · see citing works
Classic Selective Sweeps Were Rare in Recent Human Evolution
Hernandez, R. D., Kelley, J. L., Elyashiv, E., Melton, S., Auton, A., McVean, G., 1000 Genomes Project, Sella, G., & Przeworski, M. (2011) · Science · doi:10.1126/science.1198878 · Cited by 427 · see citing works
Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer
Guðmundsson, J., Sulem, P., Rafnar, Þ., Bergþorsson, J. Þ., Manolescu, A. R., Gudbjartsson, D. F., Agnarsson, B. A., Sigurðsson, Á., Benediktsdóttir, K. R., Blöndal, T., et al. (2008) · Nature Genetics · doi:10.1038/ng.89 · Cited by 370 · see citing works
Eiberg, H., Troelsen, J., Nielsen, M., Mikkelsen, A., Mengel-From, J., Kjaer, K. W., & Hansen, L. (2008) · Human Genetics · doi:10.1007/s00439-007-0460-x · Cited by 346 · see citing works
Molecular and Functional Diversity of the Expanding GABA‐A Receptor Gene Family
Whiting, P. J., Bonnert, T. P., McKernan, R. M., Farrar, S. J., Bourdellès, B. L., HEAVENS, R. P., SMITH, D. W., Hewson, L., Rigby, M. R., SIRINATHSINGHJI, D. J. S., et al. (1999) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1999.tb11341.x · Cited by 345 · see citing works
Fariello, M. I., Boitard, S., Naya, H., SanCristobal, M., & Servin, B. (2013) · Genetics · doi:10.1534/genetics.112.147231 · Cited by 343 · see citing works
Siddique, H. R., & Saleem, M. (2012) · Stem Cells · doi:10.1002/stem.1035 · Cited by 338 · see citing works
Sapiro, R., Kostetskii, I., Olds‐Clarke, P., Gerton, G. L., Radice, G. L., & Strauss, J. F. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.17.6298-6305.2002 · Cited by 335 · see citing works
Genomic structure in Europeans dating back at least 36,200 years
Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., et al. (2014) · Science · doi:10.1126/science.aaa0114 · Cited by 315 · see citing works
The landscape of recombination in African Americans
Hinch, A. G., Tandon, A., Patterson, N. J., Song, Y., Rohland, N., Palmer, C. D., Chen, G. K., Wang, K., Buxbaum, S. G., Akylbekova, E. L., et al. (2011) · Nature · doi:10.1038/nature10336 · Cited by 311 · see citing works
Measures of human population structure show heterogeneity among genomic regionsPreprint
Weir, B. S., Cardon, L. R., Anderson, A. D., Nielsen, D. M., & Hill, W. G. (2005) · Genome Research · doi:10.1101/gr.4398405 · Cited by 286 · see citing works
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
Rosenbloom, K. R., Dreszer, T. R., Long, J. C., Malladi, V. S., Sloan, C. A., Raney, B. J., Cline, M., Karolchik, D., Barber, G. P., Clawson, H., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1012 · Cited by 258 · see citing works
White, J. A., Ramshaw, H., Taimi, M., Stangle, W., Zhang, A., Everingham, S., Creighton, S., Tam, S.-P., Jones, G., & Petkovich, M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.120161397 · Cited by 248 · see citing works
Patterns of coding variation in the complete exomes of three Neandertals
Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405138111 · Cited by 247 · see citing works
Self-citationA genome-wide association study of metabolic traits in human urine
Suhre, K., Wallaschofski, H., Raffler, J., Friedrich, N., Haring, R., Michael, K., Wasner, C., Krebs, A., Kronenberg, F., Chang, D., et al. (2011) · Nature Genetics · doi:10.1038/ng.837 · Cited by 246 · see citing works
Mercher, T., Coniat, M. L., Monni, R., Mauchauffé, M., Nguyen‐Khac, F., Gressin, L., Mugneret, F., Leblanc, T. M., Dastugue, N., Berger, R., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.101001498 · Cited by 233 · see citing works
Fujimoto, A., Kimura, R., Ohashi, J., Omi, K., Yuliwulandari, R., Batubara, L., Mustofa, M. S., Samakkarn, U., Settheetham-Ishida, W., Ishida, T., et al. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddm355 · Cited by 231 · see citing works
Assessing Population Differentiation and Isolation from Single-Nucleotide Polymorphism Data
Nicholson, G., Smith, A. V., Jónsson, F., Gústafsson, Ó., Stefánsson, K., & Donnelly, P. (2002) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/1467-9868.00357 · Cited by 223 · see citing works
A Common Variation in EDAR Is a Genetic Determinant of Shovel-Shaped Incisors
Kimura, R., Yamaguchi, T., Takeda, M., Kondo, O., Toma, T., Haneji, K., Hanihara, T., Matsukusa, H., Kawamura, S., Maki, K., et al. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.09.006 · Cited by 218 · see citing works
GWASdb: a database for human genetic variants identified by genome-wide association studies
Li, M. J., Wang, P., Liu, X., Lim, E. L., Wang, Z., Yeager, M., Wong, M. P., Sham, P. C., Chanock, S. J., & Wang, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1182 · Cited by 212 · see citing works
A GABAergic system in airway epithelium is essential for mucus overproduction in asthma
Xiang, Y., Wang, S., Liu, M., Hirota, J. A., Li, J., Ju, W. H., Fan, Y., Kelly, M. M., Ye, B., Orser, B. A., et al. (2007) · Nature Medicine · doi:10.1038/nm1604 · Cited by 208 · see citing works
Zhernakova, A., Elbers, C. C., Ferwerda, B., Romanos, J., Trynka, G., Dubois, P. C., de Kovel, C. G. F., Franke, L., Oosting, M., Barisani, D., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.05.004 · Cited by 195 · see citing works
SLiM: Simulating Evolution with Selection and Linkage
Messer, P. W. (2013) · Genetics · doi:10.1534/genetics.113.152181 · Cited by 191 · see citing works
Gao, Q., Srinivasan, S. V., Boyer, S. N., Wazer, D. E., & Band, V. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.1.733 · Cited by 187 · see citing works
Approximating selective sweeps
Durrett, R. T., & Schweinsberg, J. (2004) · Theoretical Population Biology · doi:10.1016/j.tpb.2004.04.002 · Cited by 184 · see citing works
Single-nucleotide evolutionary constraint scores highlight disease-causing mutations
Cooper, G. M., Goode, D. L., Ng, S. B. H., Sidow, A., Bamshad, M. J., Shendure, J., & Nickerson, D. A. (2010) · Nature Methods · doi:10.1038/nmeth0410-250 · Cited by 171 · see citing works
Du, K. L., Chen, M., Li, J., Lepore, J. J., Mericko, P. A., & Parmacek, M. S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m400961200 · Cited by 150 · see citing works
Genome-Wide Association Study of Suicide Attempts in Mood Disorder Patients
Perlis, R. H., Huang, J., Purcell, S., D, M. F. M., Rush, A. J., Sullivan, P. F., Hamilton, S. P., McMahon, F. J., Schulze, T. G., Potash, J. B., et al. (2010) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2010.10040541 · Cited by 147 · see citing works
Murine and human b locus pigmentation genes encode a glycoprotein (gp75) with catalase activity.
Halaban, R., & Moellmann, G. E. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4809 · Cited by 146 · see citing works
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies
Kofler, R., & Schlötterer, C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts315 · Cited by 138 · see citing works
Genome-Wide Population-Based Association Study of Extremely Overweight Young Adults – The GOYA Study
Paternoster, L., Evans, D. M., Nohr, E. A., Holst, C., Gaborieau, V., Brennan, P., Gjesing, A. P., Grarup, N., Witte, D. R., Jørgensen, T., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024303 · Cited by 132 · see citing works
Melanesian Blond Hair Is Caused by an Amino Acid Change in TYRP1
Kenny, E. E., Timpson, N. J., Sikora, M., Yee, M., Moreno‐Estrada, A., Eng, C. S., Huntsman, S., Burchard, E. G., Stoneking, M., Bustamante, C. D., et al. (2012) · Science · doi:10.1126/science.1217849 · Cited by 126 · see citing works
Guilherme, A., Soriano, N. A., Furcinitti, P. S., & Czech, M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m401918200 · Cited by 123 · see citing works
Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow
Lipson, M., Loh, P., Levin, A., Reich, D., Patterson, N. J., & Berger, B. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst099 · Cited by 118 · see citing works
Novel FOXG1 mutations associated with the congenital variant of Rett syndrome
Mencarelli, M. A., Rosseto, A. S., Artuso, R., Rondinella, D., Filippis, R. D., Bahi‐Buisson, N., Nectoux, J., Rubinsztajn, R., Bienvenu, T., Moncla, A., et al. (2009) · Journal of Medical Genetics · doi:10.1136/jmg.2009.067884 · Cited by 111 · see citing works
Comparison of the function and expression of CYP26A1 and CYP26B1, the two retinoic acid hydroxylases
Topletz, A. R., Thatcher, J. E., Zelter, A., Lutz, J. D., Tay, S., Nelson, W. L., & Isoherranen, N. (2011) · Biochemical Pharmacology · doi:10.1016/j.bcp.2011.10.007 · Cited by 109 · see citing works
Branicki, W., Brudnik, U., & Wojas‐Pelc, A. (2009) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2009.00504.x · Cited by 108 · see citing works
RASA1 mutations may cause hereditary capillary malformations without arteriovenous malformations
Hershkovitz, D., Bercovich, D., Sprecher, E., et al. (2008) · British Journal of Dermatology · doi:10.1111/j.1365-2133.2008.08493.x · Cited by 97 · see citing works
Oleksyk, T. K., Zhao, K., Vega, F. M. D. L., Gilbert, D. A., O’Brien, S. J., & Smith, M. W. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001712 · Cited by 95 · see citing works
Kmoch, S. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.10.1501 · Cited by 90 · see citing works
ADJUSTING COMPOSITE LIKELIHOOD RATIO STATISTICS
Pace, L., Salvan, A., & Sartori, N. (2009) · ARCA (Università Ca' Foscari Venezia) · Cited by 76 · see citing works
Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
Race, V. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.14.2159 · Cited by 64 · see citing works
Friedman, E., Gejman, P. V., Martin, G. A., & McCormick, F. P. (1993) · Nature Genetics · doi:10.1038/ng1193-242 · Cited by 61 · see citing works
Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer
Henrion, M., Frampton, M., Scélo, G., et al. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds489 · Cited by 57 · see citing works
Keuren, M. L. V., Hart, I. M., Kao, F., et al. (2008) · Cytogenetics and Cell Genetics · doi:10.1159/000132358 · Cited by 55 · see citing works
Misleading behavioural phenotype with adenylosuccinate lyase deficiency
Gitiaux, C., Ceballos-Picot, I., Marie, S., et al. (2008) · European Journal of Human Genetics · doi:10.1038/ejhg.2008.174 · Cited by 43 · see citing works
Adenylosuccinase deficiency presenting with epilepsy in early infancy
Maaswinkel‐Mooij, P. D., Laan, L. A. E. M., Onkenhout, W., et al. (1997) · Journal of Inherited Metabolic Disease · doi:10.1023/a:1005323512982 · Cited by 40 · see citing works
Edery, P., Chabrier, S., Ceballos-Picot, I., et al. (2003) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.20176 · Cited by 30 · see citing works
A test for ancient selective sweeps and an application to candidate sites in modern humans
Racimo, F., Kuhlwilm, M., & Slatkin, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu255 · Cited by 30 · see citing works
Self-citationCa2+-dependent activator protein for secretion 2 and autistic-like phenotypes
Sadakata, T., & Furuichi, T. (2010) · Neuroscience Research · doi:10.1016/j.neures.2010.03.006 · Cited by 23 · see citing works
Disruption of Apc10/Doc1 in Three Alleles of Oligosyndactylism
Pravtcheva, D. D., & Wise, T. L. (2001) · Genomics · doi:10.1006/geno.2001.6474 · Cited by 17 · see citing works
On Characterizing Adaptive Events Unique to Modern Humans
Crisci, J. L., Wong, A., Good, J. M., & Jensen, J. D. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr075 · Cited by 16 · see citing works
Panagopoulos, I., Lassen, C., Kristoffersson, U., & �man, P. (1999) · Human Mutation · doi:10.1002/(sici)1098-1004(1999)13:3 · Cited by 13 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- Sandrine Marie, Harry Cuppens, Michel Heuterspreute, Martine Jaspers, Eduardo Zambrano Tola, Xiao Xiao Gu, Eric Legius, M Vincent, Jaak Jaeken, Jean-Jacques Cassiman, et al. Mutation anal- ysis in adenylosuccinate lyase deficiency: Eight novel mutations in the re-evaluated full adsl coding sequence. Human mutation, 13(3):197-202, 1999.
- Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Manuel A Rojo Guerra, Johannes Krause, David Anthony, et al. Eight thousand years of natural selection in europe. bioRxiv, page 016477, 2015.
Cited by
Sorted by citations
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584 · see citing works
Self-citationPendleton, A. L., Shen, F., Taravella, A. M., Emery, S., Veeramah, K. R., Boyko, A. R., & Kidd, J. M. (2018) · BMC Biology · doi:10.1186/s12915-018-0535-2 · Cited by 156 · see citing works
Self-domestication in Homo sapiens: Insights from comparative genomics
Theofanopoulou, C., Gastaldon, S., O’Rourke, T., Samuels, B. D., Messner, A., Martins, P. T., Delogu, F., Alamri, S., & Boeckx, C. (2017) · PLOS ONE · doi:10.1371/journal.pone.0185306 · Cited by 174 · see citing works
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108 · see citing works
Zanella, M., Vitriolo, A., Andirko, A., Martins, P. T., Sturm, S., O’Rourke, T., Laugsch, M., Malerba, N., Skaros, A., Trattaro, S., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw7908 · Cited by 101 · see citing works
Detecting ancient positive selection in humans using extended lineage sorting
Peyrégne, S., Boyle, M. J., Dannemann, M., & Prüfer, K. (2017) · Genome Research · doi:10.1101/gr.219493.116 · Cited by 93 · see citing works
Glutamate receptors in domestication and modern human evolution
O’Rourke, T., & Boeckx, C. (2020) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.10.004 · Cited by 50 · see citing works
<i>DLX5/6</i> GABAergic Expression Affects Social Vocalization: Implications for Human Evolution
Levi, G., de Lombares, C., Giuliani, C., Iannuzzi, V., Aouci, R., Garagnani, P., Franceschi, C., Grimaud-Hervé, D., & Narboux-Nême, N. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab181 · Cited by 29 · see citing works
“(Prufer, et al. 2014 ; Racimo, et al. 2014; Racimo 2016; Peyregne, et al. 2017; Hajdinjak, et al. 2018)).”
Background
- Authors
- Racimo, F.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Racimo, Fernando
- ORCID
- Racimo, Fernando
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-20
- Volume
- 202
- Issue
- 2
- Pages
- 733-750
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC4788246
- OpenAlex
- W2953216589
- Cited by
- 96
- References
- 101
- Citations by year
- 2026: 9 · 2025: 9 · 2024: 8 · 2023: 6 · 2022: 12 · 2021: 12 · 2020: 9 · 2019: 10 · 2018: 10 · 2017: 8 · 2016: 3
- FWCI
- 4.81
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM040282, R01‑GM40282)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- selective sweeps, allele frequency differentiation, Neanderthal admixture, functional mutations, 1000 Genomes Project
- MeSH terms
- Algorithms, Alleles, Animals, Computer Simulation, Gene Frequency, Genetics, Population, Humans, Models, Genetic, ROC Curve, Selection, Genetic, Evolution, Molecular, Genomics, White People, Asian People, Genome-Wide Association Study, Neanderthals
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
