Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Open accessAbstract
The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
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KIT is involved in melanocyte differentiation, and evidence points to its importance in selection for coat color, with signals on KIT in Clydesdale horses and Birman cats implicated in their breed-specific coat patterns.
“This gene is involved in melanocyte differentiation, and evidence points to its importance in selection for coat color: Signals occurring on KIT in Clydesdale horses and Birman cats have been implicated in their breed-specific coat patterns (Schubert et al., 2014;Montague et al., 2014).”
From Glutamate receptors in domestication and modern human evolution (2020) · cites this paper as Schubert et al., 2014
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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937 · see citing works
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582 · see citing works
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
Wang, K., Li, M., & Hakonarson, H. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq603 · Cited by 14,380 · see citing works
Median-joining networks for inferring intraspecific phylogenies
Bandelt, H. J., Forster, P., & Rohl, A. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026036 · Cited by 11,742 · see citing works
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss075 · Cited by 9,990 · see citing works
VEGAN, a package of R functions for community ecology
Dixon, P. M. (2003) · Journal of Vegetation Science · doi:10.1111/j.1654-1103.2003.tb02228.x · Cited by 6,783 · see citing works
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280 · 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
Self-citationInference 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
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
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
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906 · see citing works
Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776 · see citing works
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt193 · Cited by 1,669 · see citing works
Self-citationCross-biome metagenomic analyses of soil microbial communities and their functional attributes
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber, C. L., Owens, S. M., Gilbert, J. A., Wall, D. H., & Caporaso, J. G. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215210110 · Cited by 1,636 · see citing works
Robust Demographic Inference from Genomic and SNP Data
Excoffier, L., Dupanloup, I., Huerta‐Sánchez, E., Sousa, V. C., & Foll, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003905 · Cited by 1,485 · see citing works
Self-citationAnalyses of pig genomes provide insight into porcine demography and evolution
Groenen, M. A. M., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Denis Milan, A., Megens, H., et al. (2012) · Nature · doi:10.1038/nature11622 · Cited by 1,386 · see citing works
Testing for ancient admixture between closely related populations
Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr048 · Cited by 1,375 · see citing works
Distribution and intensity of constraint in mammalian genomic sequence
Cooper, G. M., Stone, E. A., Asimenos, G., Green, E. D., Batzoglou, S., & Sidow, A. (2005) · Genome Research · doi:10.1101/gr.3577405 · Cited by 1,359 · see citing works
Patterns of damage in genomic DNA sequences from a neandertal
Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981 · see citing works
Flicek, P., Ahmed, I., Amode, M. R., Barrell, D. G., Beal, K. M., Brent, S., Carvalho‐Silva, D., Clapham, P., Coates, G. M. P., Fairley, S., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1236 · Cited by 869 · see citing works
Ancient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., et al. (2010) · Nature · doi:10.1038/nature08835 · Cited by 849 · see citing works
Self-citationRecalibrating equus evolution using the genome sequence of an early middle pleistocene horse
Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. (2013) · Nature · doi:10.1038/nature12323 · Cited by 841 · see citing works
Self-citationGenome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse
Wade, C. M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., et al. (2009) · Science · doi:10.1126/science.1178158 · Cited by 822 · see citing works
Self-citationThe Earliest Horse Harnessing and Milking
Outram, A. K., Stear, N. A., Bendrey, R., Olsen, S. L., Kasparov, A., Zaibert, V. F., Thorpe, N., & Evershed, R. P. (2009) · Science · doi:10.1126/science.1168594 · Cited by 741 · see citing works
abc: an R package for approximate Bayesian computation (ABC)
Csilléry, K., François, O., & Blum, M. G. B. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00179.x · Cited by 709 · see citing works
The UCSC Genome Browser database: 2014 update
Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1168 · Cited by 670 · see citing works
Strong signatures of selection in the domestic pig genome
Rubin, C.-J., Megens, H.-J., Barrio, A. M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, Ö., Jern, P., Jørgensen, C. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217149109 · Cited by 652 · see citing works
Self-citationScholl, U. I., Goh, G., Stölting, G., de Oliveira, R. C., Choi, M., Overton, J. D., Fonseca, A. L., Korah, R., Starker, L. F., Kunstman, J. W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2695 · Cited by 627 · see citing works
Documenting Domestication. New Genetic and Archaeological Paradigms
Clement, C. R. (2006) · Economic Botany · doi:10.1663/0013-0001(2006)60[398a:ddngaa]2.0.co;2 · Cited by 626 · see citing works
Genome sequencing highlights the dynamic early history of dogs
Freedman, A. H., Gronau, I., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004016 · Cited by 624 · see citing works
Tonkin, E. T., Wang, T.-J., Lisgo, S., Bamshad, M. J., & Strachan, T. (2004) · Nature Genetics · doi:10.1038/ng1363 · Cited by 594 · see citing works
Somatic mutations in ATP1A1 and CACNA1D underlie a common subtype of adrenal hypertension
Azizan, E. A. B., Poulsen, H., Tuluc, P., Zhou, J., Clausen, M. V., Lieb, A., Maniero, C., Garg, S., Bochukova, E. G., Zhao, W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2716 · Cited by 544 · see citing works
Schubert, M., Ermini, L., Sarkissian, C. S. I. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M. E., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.063 · Cited by 515 · see citing works
Self-citationWidespread Origins of Domestic Horse Lineages
Vilà, C., Leonard, J. A., Götherström, A., Marklund, S. L., Sandberg, K., Lidén, K., Wayne, R. K., & Ellegren, H. (2001) · Science · doi:10.1126/science.291.5503.474 · Cited by 510 · see citing works
Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice
Andersson, L. S., Larhammar, M., Memic, F., Wootz, H., Schwochow, D., Rubin, C., Patra, K., Árnason, T., Wellbring, L., Hjälm, G., et al. (2012) · Nature · doi:10.1038/nature11399 · Cited by 431 · see citing works
Self-citationMitochondrial DNA and the origins of the domestic horse
Jansen, T., Forster, P., Levine, M. A., Oelke, H., Hurles, M. E., Renfrew, C., Weber, J., & Olek, K. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.152330099 · Cited by 407 · see citing works
Zeder, M. A. (2012) · Journal of Anthropological Research · doi:10.3998/jar.0521004.0068.201 · Cited by 406 · see citing works
A review of natural vegetation openness in north-western Europe
Svenning, J. (2002) · Biological Conservation · doi:10.1016/s0006-3207(01)00162-8 · Cited by 394 · see citing works
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
Koenig, D., Jiménez‐Gómez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Kumar, R. S., Covington, M. F., Devisetty, U. K., Tat, A. V., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309606110 · Cited by 368 · see citing works
Loss of Cav1.3 (CACNA1D) function in a human channelopathy with bradycardia and congenital deafness
Baig, S. M., Koschak, A., Lieb, A., Gebhart, M., Dafinger, C., Nürnberg, G., Ali, A., Ahmad, I., Sinnegger-Brauns, M. J., Brandt, N., et al. (2010) · Nature Neuroscience · doi:10.1038/nn.2694 · Cited by 318 · see citing works
Coat Color Variation at the Beginning of Horse Domestication
Ludwig, A., Pruvost, M., Reißmann, M., Benecke, N., Brockmann, G. A., Castaños, P., Cieslak, M., Lippold, S., Rodríguez, L. L., Malaspinas, A., et al. (2009) · Science · doi:10.1126/science.1172750 · Cited by 309 · see citing works
Self-citationGenetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data
Petersen, J. L., Mickelson, J. R., Cothran, E. G., Andersson, L. S., Axelsson, J., Bailey, E., Bannasch, D. L., Binns, M. M., Borges, A. S., Brama, P. A. J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054997 · Cited by 278 · see citing works
Self-citationMitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication
Achilli, A., Olivieri, A., Soares, P. A., Lancioni, H., Kashani, B. H., Perego, U. A., Nergadze, S. G., Carossa, V., Santagostino, M., Capomaccio, S., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111637109 · Cited by 268 · see citing works
Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds
Petersen, J. L., Mickelson, J. R., Rendahl, A., Valberg, S. J., Andersson, L. S., Axelsson, J., Bailey, E., Bannasch, D. L., Binns, M. M., Borges, A. S., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003211 · Cited by 268 · see citing works
Self-citationMcCue, M. E., Bannasch, D. L., Petersen, J. L., Gurr, J., Bailey, E., Binns, M. M., Distl, O., Guérin, G., HASEGAWA, T., Hill, E. W., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002451 · Cited by 262 · see citing works
Brotherton, P., Endicott, P., Sánchez, J. J. M., Beaumont, M., Barnett, R., Austin, J. J., & Cooper, A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm588 · Cited by 255 · see citing works
The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication
Lü, J., Tang, T., Tang, H., Huang, J., Shi, S., & Wu, C. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.01.004 · Cited by 248 · see citing works
Prehistoric steppe adaptation and the horse
(2004) · Choice Reviews Online · doi:10.5860/choice.42-1655 · Cited by 235 · see citing works
Classic Selective Sweeps Revealed by Massive Sequencing in Cattle
Qanbari, S., Pausch, H., Jansen, S., Somel, M., Strom, T. M., Fries, R., Nielsen, R., & Simianer, H. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004148 · Cited by 233 · see citing works
Self-citationReconstructing the origin and spread of horse domestication in the Eurasian steppe
Warmuth, V. M., Eriksson, A., Bower, M. A., Barker, G., Barrett, E., Hanks, B. K., Li, S., Lomitashvili, D., Ochir-Goryaeva, M. A., Sizonov, G. V., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111122109 · Cited by 232 · see citing works
A Novel Marker of Tissue Junctions, Collagen XXII
Koch, M., Schulze, J., Hansen, U. J., Ashwodt, T., Keene, D. R., Brunken, W. J., Burgeson, R. E., Brückner, P., & Bruckner‐Tuderman, L. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m400536200 · Cited by 230 · see citing works
Cahill, J. A., Green, R. E., Fulton, T. L., Stiller, M., Jay, F., Ovsyanikov, N., Salamzade, R., St. John, J., Stirling, I., Slatkin, M., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003345 · Cited by 221 · see citing works
Self-citationA Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA
Shapiro, B., & Hofreiter, M. (2014) · Science · doi:10.1126/science.1236573 · Cited by 220 · see citing works
Self-citationComputational approaches to species phylogeny inference and gene tree reconciliation
Nakhleh, L. K. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.09.004 · Cited by 209 · see citing works
Signer‐Hasler, H., Flury, C., Haase, B., Burger, D., Simianer, H., Leeb, T., & Rieder, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037282 · Cited by 209 · see citing works
Limited number of patrilines in horse domestication
Lindgren, G., Backström, N., Swinburne, J. E., Hellborg, L., Einarsson, A., Sandberg, K., Cothran, E. G., Vilà, C., Binns, M. M., & Ellegren, H. (2004) · Nature Genetics · doi:10.1038/ng1326 · Cited by 197 · see citing works
Spinal Muscular Atrophy with Pontocerebellar Hypoplasia Is Caused by a Mutation in the VRK1 Gene
Renbaum, P., Kellerman, E., Jaron, R., et al. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.07.006 · Cited by 194 · see citing works
Origin and History of Mitochondrial DNA Lineages in Domestic Horses
Cieslak, M., Pruvost, M., Benecke, N., Hofreiter, M., Muñiz, A. M., Reißmann, M., & Ludwig, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015311 · Cited by 184 · see citing works
Self-citationCACNA1C (rs1006737) is associated with schizophrenia
Nyegaard, M., Demontis, D., Foldager, L., Hedemand, A., Flint, T. J., Sørensen, K. M., Andersen, P. S., Nordentoft, M., Werge, T., Pedersen, C. B., et al. (2010) · Molecular Psychiatry · doi:10.1038/mp.2009.69 · Cited by 182 · see citing works
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genomePreprint
Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., et al. (2013) · Genome Research · doi:10.1101/gr.163592.113 · Cited by 171 · see citing works
Self-citationThe legacy of domestication: accumulation of deleterious mutations in the dog genome
Cruz, F., Vila, C., & Webster, M. T. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn177 · Cited by 154 · see citing works
Rickard, A. J., Morgan, J., Chrissobolis, S., Miller, A. A., Sobey, C. G., & Young, M. J. (2014) · Hypertension · doi:10.1161/hypertensionaha.113.01803 · Cited by 135 · see citing works
Skeletal muscle α-actin diseases (actinopathies): pathology and mechanisms
Nowak, K. J., Ravenscroft, G., & Laing, N. G. (2012) · Acta Neuropathologica · doi:10.1007/s00401-012-1019-z · Cited by 130 · see citing works
Lippold, S., Matzke, N. J., Reißmann, M., & Hofreiter, M. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-328 · Cited by 119 · see citing works
Self-citationNabholz, B., Sarah, G., Sabot, F., Ruíz, M., Adam, H., Nidelet, S., Ghesquière, A., Santoni, S., David, J., & Glémin, S. (2014) · Molecular Ecology · doi:10.1111/mec.12738 · Cited by 85 · see citing works
Hill, E. W., Gu, J., McGivney, B. A., & MacHugh, D. E. (2010) · Animal Genetics · doi:10.1111/j.1365-2052.2010.02104.x · Cited by 84 · see citing works
Self-citationDiscovery of lost diversity of paternal horse lineages using ancient DNA
Lippold, S., Knapp, M., Kuznetsova, T. V., Leonard, J. A., Benecke, N., Ludwig, A., Rasmussen, M. A., Cooper, A., Weinstock, J., Willerslev, E., et al. (2011) · Nature Communications · doi:10.1038/ncomms1447 · Cited by 82 · see citing works
Self-citationWallner, B., Vogl, C., Shukla, P., Burgstaller, J. P., Druml, T., & Brem, G. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060015 · Cited by 82 · see citing works
Glazov, E. A., Zankl, A., Donskoi, M., Kenna, T., Thomas, G. P., Clark, G. R., Duncan, E. L., & Brown, M. A. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002027 · Cited by 80 · see citing works
NIPBL mutations and genetic heterogeneity in Cornelia de Lange syndrome
Borck, G., Redon, R., Sanlaville, D., Rio, M., Prieur, M., Lyonnet, S., Vekemans, M. J. J., Carter, N. P., Münnich, A., Colleaux, L., et al. (2004) · Journal of Medical Genetics · doi:10.1136/jmg.2004.026666 · Cited by 79 · see citing works
Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
Seguin‐Orlando, A., Schubert, M., Clary, J., Stagegaard, J., Alberdi, M. T., Prado, J. L., I, A. P., Willerslev, E., & Orlando, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078575 · Cited by 72 · see citing works
Self-citationTakeda, Y., Akasaka, K., Lee, S., Kobayashi, S., Kawano, H., Murayama, S., Takahashi, N., Hashimoto, K., Kano, M., Asano, M., et al. (2003) · Journal of Neurobiology · doi:10.1002/neu.10222 · Cited by 71 · see citing works
Goto, H., Ryder, O. A., Fisher, A. R., Schultz, B. M., Pond, S. L. K., Nekrutenko, A., & Makova, K. D. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr067 · Cited by 68 · see citing works
Gu, J., MacHugh, D. E., McGivney, B. A., Park, S. D. E., Katz, L. M., & Hill, E. W. (2010) · Equine Veterinary Journal · doi:10.1111/j.2042-3306.2010.00181.x · Cited by 67 · see citing works
Self-citation(2010) · Choice Reviews Online · doi:10.5860/choice.47-3959 · Cited by 59 · see citing works
Shotgun microbial profiling of fossil remains
Sarkissian, C. S. I. D., Ermini, L., Jónsson, H., Alekseev, A. N., Crubézy, É., Shapiro, B., & Orlando, L. (2014) · Molecular Ecology · doi:10.1111/mec.12690 · Cited by 59 · see citing works
Self-citationCharacterizing DNA preservation in degraded specimens of A mara alpina( C arabidae: C oleoptera)
Heintzman, P. D., Elias, S. A., Moore, K., Paszkiewicz, K. H., & Barnes, I. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12205 · Cited by 49 · see citing works
MSTNgenotype (g.66493737C/T) association with speed indices in Thoroughbred racehorses
Hill, E. W., Fonseca, R. G., McGivney, B. A., Gu, J., MacHugh, D. E., & Katz, L. M. (2011) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00793.2011 · Cited by 47 · see citing works
Self-citationJoubert Syndrome and Related Disorders
Parisi, M. A., & Glass, I. A. (2013) · Cited by 38 · see citing works
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Self-citation
- Authors
- Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., Fumagalli, M., Raghavan, M., Seguin-Orlando, A., Korneliussen, T. S., Velazquez, A. M. V., Stenderup, J., Hoover, C. A., Rubin, C.-J., Alfarhan, A. H., Alquraishi, S. A., Al-Rasheid, K. A. S., MacHugh, D. E., Kalbfleisch, T., MacLeod, J. N., Rubin, E. M., Sicheritz-Ponten, T., Andersson, L., Hofreiter, M., Marques-Bonet, T., Gilbert, M. T. P., Nielsen, R., Excoffier, L., Willerslev, E., Shapiro, B., & Orlando, L.
- Affiliations
- University of Copenhagen (DK)
- University of California, Santa Cruz (US)
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
- University of Bern (CH)
- Technical University of Denmark (DK)
- University College London (GB)
- Joint Genome Institute (US)
- Uppsala University (SE)
- King Saud University (SA)
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
- University College Dublin (IE)
- University of Louisville (US)
- University of Kentucky (US)
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark;
- University of Potsdam (DE)
- Instituticó Catalana de Recerca i Estudis Avançats, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/Consejo Superior de Investigaciones Cientificas), 08003 Barcelona, Spain;
- University of California, Berkeley (US)
- ORCID
- Schubert, Mikkel
- Jónsson, Hákon
- Chang, Dan
- Ermini, Luca
- Ginolhac, Aurélien
- Albrechtsen, Anders
- Dupanloup, Isabelle
- Foucal, Adrien
- Petersen, Bent
- Fumagalli, Matteo
- Raghavan, Maanasa
- Korneliussen, Thorfinn S.
- Velazquez, Amhed M. V.
- Stenderup, Jesper
- Rubin, Carl-Johan
- Alfarhan, Ahmed H.
- Alquraishi, Saleh A.
- MacHugh, David E.
- Kalbfleisch, Ted
- MacLeod, James N.
- Rubin, Edward M.
- Sicheritz-Ponten, Thomas
- Andersson, Leif
- Hofreiter, Michael
- Gilbert, M. Thomas P.
- Nielsen, Rasmus
- Excoffier, Laurent
- Willerslev, Eske
- Shapiro, Beth
- Orlando, Ludovic
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-12-15
- Volume
- 111
- Issue
- 52
- Pages
- E5661-9
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4284583
- OpenAlex
- W2033123297
- Cited by
- 324
- References
- 87
- Citations by year
- 2026: 11 · 2025: 27 · 2024: 33 · 2023: 20 · 2022: 21 · 2021: 31 · 2020: 27 · 2019: 32 · 2018: 39 · 2017: 30 · 2016: 29 · 2015: 24
- FWCI
- 18.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- UKnowledge (University of Kentucky) (submittedVersion)
- BORIS (University Library Bern) (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- eScholarship (California Digital Library) (submittedVersion)
- publish.UP (University of Potsdam) (submittedVersion)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion)
- Unicam Scientific Publications (University of Camerino) (submittedVersion, other-oa)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- Griffith Research Online (submittedVersion)
- Funders
- Villum Fonden (00007171)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (143393)
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R38-2008-3048, R24-2008-2527)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Health Sciences › Veterinary › Equine › Veterinary Equine Medical Research
- Keywords
- horse domestication, Przewalski's horse, positive selection, inbreeding, deleterious mutations, purifying selection, Taymyr
- MeSH terms
- Animals, Animals, Domestic, Cardiovascular System, Dogs, Hindlimb, Horses, Humans, Inbreeding, Russia, Genome, Evolution, Molecular
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 ›
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