{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:21:08Z","timestamp":1772166068869,"version":"3.50.1"},"reference-count":102,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,11,19]],"date-time":"2021-11-19T00:00:00Z","timestamp":1637280000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,11,19]],"date-time":"2021-11-19T00:00:00Z","timestamp":1637280000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Jackson Laboratory (JAX) Pyewacket Postdoctoral Fellowship Award"},{"name":"Jackson Laboratory (JAX) Scholar Award"},{"name":"NSF CAREER Award","award":["DEB 1942620-01"],"award-info":[{"award-number":["DEB 1942620-01"]}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["R35 GM133415-01"],"award-info":[{"award-number":["R35 GM133415-01"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["R35 GM133415-01"],"award-info":[{"award-number":["R35 GM133415-01"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Through human-aided dispersal over the last ~\u200910,000\u2009years, house mice (\n                      <jats:italic>Mus musculus<\/jats:italic>\n                      ) have recently colonized diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premier mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here, we leveraged 154 whole-genome sequences from diverse wild house mouse populations to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at many genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including\n                      <jats:italic>Mgam<\/jats:italic>\n                      and\n                      <jats:italic>Amy1<\/jats:italic>\n                      . We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Overall, our findings highlight the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work also highlights the biomedical relevance of wild mouse genetic diversity and underscores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12915-021-01165-3","type":"journal-article","created":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T19:03:08Z","timestamp":1637262188000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Selection shapes the landscape of functional variation in wild house mice"],"prefix":"10.1186","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8908-7664","authenticated-orcid":false,"given":"Raman Akinyanju","family":"Lawal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uma P.","family":"Arora","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beth L.","family":"Dumont","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,11,19]]},"reference":[{"issue":"7","key":"1165_CR1","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1038\/ng.847","volume":"43","author":"H Yang","year":"2011","unstructured":"Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, et al. Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet. 2011;43(7):648\u201355. https:\/\/doi.org\/10.1038\/ng.847.","journal-title":"Nat Genet"},{"issue":"9-10","key":"1165_CR2","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1007\/s00335-017-9704-9","volume":"28","author":"PL Chang","year":"2017","unstructured":"Chang PL, Kopania E, Keeble S, Sarver BA, Larson E, Orth A, et al. Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype. Mamm Genome. 2017;28(9-10):416\u201325. https:\/\/doi.org\/10.1007\/s00335-017-9704-9.","journal-title":"Mamm Genome"},{"issue":"8","key":"1165_CR3","doi-asserted-by":"publisher","first-page":"e144","DOI":"10.1371\/journal.pgen.0030144","volume":"3","author":"CC Laurie","year":"2007","unstructured":"Laurie CC, Nickerson DA, Anderson AD, Weir BS, Livingston RJ, Dean MD, et al. Linkage disequilibrium in wild mice. PLoS Genet. 2007;3(8):e144. https:\/\/doi.org\/10.1371\/journal.pgen.0030144.","journal-title":"PLoS Genet"},{"issue":"7","key":"1165_CR4","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1016\/j.tig.2019.04.003","volume":"35","author":"MC Saul","year":"2019","unstructured":"Saul MC, Philip VM, Reinholdt LG, Chesler EJ. High-diversity mouse populations for complex traits. Trends Genet. 2019;35(7):501\u201314. https:\/\/doi.org\/10.1016\/j.tig.2019.04.003.","journal-title":"Trends Genet"},{"issue":"D1","key":"1165_CR5","doi-asserted-by":"publisher","first-page":"D716","DOI":"10.1093\/nar\/gkz1032","volume":"48","author":"MA Bogue","year":"2020","unstructured":"Bogue MA, Philip VM, Walton DO, Grubb SC, Dunn MH, Kolishovski G, et al. Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data. Nucleic Acids Res. 2020;48(D1):D716\u201323. https:\/\/doi.org\/10.1093\/nar\/gkz1032.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"1165_CR6","doi-asserted-by":"publisher","first-page":"e1007672","DOI":"10.1371\/journal.pgen.1007672","volume":"14","author":"M Phifer-Rixey","year":"2018","unstructured":"Phifer-Rixey M, Bi K, Ferris KG, Sheehan MJ, Lin D, Mack KL, et al. The genomic basis of environmental adaptation in house mice. PLoS Genet. 2018;14(9):e1007672. https:\/\/doi.org\/10.1371\/journal.pgen.1007672.","journal-title":"PLoS Genet"},{"issue":"4","key":"1165_CR7","doi-asserted-by":"publisher","first-page":"e1009495","DOI":"10.1371\/journal.pgen.1009495","volume":"17","author":"KG Ferris","year":"2021","unstructured":"Ferris KG, Chavez AS, Suzuki TA, Beckman EJ, Phifer-Rixey M, Bi K, et al. The genomics of rapid climatic adaptation and parallel evolution in North American house mice. PLoS Genet. 2021;17(4):e1009495. https:\/\/doi.org\/10.1371\/journal.pgen.1009495.","journal-title":"PLoS Genet"},{"key":"1165_CR8","doi-asserted-by":"crossref","unstructured":"Rees JS, Castellano S, Andr\u00e9s AM. The genomics of human local adaptation. Trends Genet. 2020;36(6):415\u201328.","DOI":"10.1016\/j.tig.2020.03.006"},{"issue":"9","key":"1165_CR9","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1038\/ng.3620","volume":"48","author":"RL Minster","year":"2016","unstructured":"Minster RL, Hawley NL, Su C-T, Sun G, Kershaw EE, Cheng H, et al. A thrifty variant in CREBRF strongly influences body mass index in Samoans. Nat Genet. 2016;48(9):1049\u201354. https:\/\/doi.org\/10.1038\/ng.3620.","journal-title":"Nat Genet"},{"issue":"2","key":"1165_CR10","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1086\/432519","volume":"77","author":"DP Kwiatkowski","year":"2005","unstructured":"Kwiatkowski DP. How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Genet. 2005;77(2):171\u201392. https:\/\/doi.org\/10.1086\/432519.","journal-title":"Am J Hum Genet"},{"issue":"12","key":"1165_CR11","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1038\/ng.3120","volume":"46","author":"F Antonacci","year":"2014","unstructured":"Antonacci F, Dennis MY, Huddleston J, Sudmant PH, Steinberg KM, Rosenfeld JA, et al. Palindromic GOLGA8 core duplicons promote chromosome 15q13. 3 microdeletion and evolutionary instability. Nat Genet. 2014;46(12):1293.","journal-title":"Nat Genet"},{"issue":"4","key":"1165_CR12","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1016\/j.biopsych.2015.10.009","volume":"80","author":"S Srinivasan","year":"2016","unstructured":"Srinivasan S, Bettella F, Mattingsdal M, Wang Y, Witoelar A, Schork AJ, et al. Genetic markers of human evolution are enriched in schizophrenia. Biol Psychiatry. 2016;80(4):284\u201392. https:\/\/doi.org\/10.1016\/j.biopsych.2015.10.009.","journal-title":"Biol Psychiatry"},{"key":"1165_CR13","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.gde.2016.08.001","volume":"41","author":"MY Dennis","year":"2016","unstructured":"Dennis MY, Eichler EE. Human adaptation and evolution by segmental duplication. Curr Opin Genet Dev. 2016;41:44\u201352. https:\/\/doi.org\/10.1016\/j.gde.2016.08.001.","journal-title":"Curr Opin Genet Dev"},{"issue":"2","key":"1165_CR14","doi-asserted-by":"publisher","first-page":"e1006618","DOI":"10.1371\/journal.pgen.1006618","volume":"13","author":"R Polimanti","year":"2017","unstructured":"Polimanti R, Gelernter J. Widespread signatures of positive selection in common risk alleles associated to autism spectrum disorder. PLoS Genet. 2017;13(2):e1006618. https:\/\/doi.org\/10.1371\/journal.pgen.1006618.","journal-title":"PLoS Genet"},{"issue":"1","key":"1165_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00439-017-1865-9","volume":"137","author":"J Sikela","year":"2018","unstructured":"Sikela J, Quick VS. Genomic trade-offs: are autism and schizophrenia the steep price of the human brain? Hum Genet. 2018;137(1):1\u201313. https:\/\/doi.org\/10.1007\/s00439-017-1865-9.","journal-title":"Hum Genet"},{"issue":"24","key":"1165_CR16","doi-asserted-by":"publisher","first-page":"5349","DOI":"10.1111\/j.1365-294X.2008.04005.x","volume":"17","author":"A Geraldes","year":"2008","unstructured":"Geraldes A, Basset P, Gibson B, Smith KL, Harr B, Yu HT, et al. Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol Ecol. 2008;17(24):5349\u201363. https:\/\/doi.org\/10.1111\/j.1365-294X.2008.04005.x.","journal-title":"Mol Ecol"},{"issue":"1","key":"1165_CR17","doi-asserted-by":"publisher","first-page":"160075","DOI":"10.1038\/sdata.2016.75","volume":"3","author":"B Harr","year":"2016","unstructured":"Harr B, Karakoc E, Neme R, Teschke M, Pfeifle C, Pezer \u017d, et al. Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. Sci Data. 2016;3(1):160075. https:\/\/doi.org\/10.1038\/sdata.2016.75.","journal-title":"Sci Data"},{"key":"1165_CR18","unstructured":"Davies RW. Factors influencing genetic variation in wild mice: PhD thesis. University of Oxford; 2015."},{"issue":"10","key":"1165_CR19","doi-asserted-by":"publisher","first-page":"2949","DOI":"10.1093\/molbev\/mss105","volume":"29","author":"M Phifer-Rixey","year":"2012","unstructured":"Phifer-Rixey M, Bonhomme F, Boursot P, Churchill GA, Pi\u00e1lek J, Tucker PK, et al. Adaptive evolution and effective population size in wild house mice. Mol Biol Evol. 2012;29(10):2949\u201355. https:\/\/doi.org\/10.1093\/molbev\/mss105.","journal-title":"Mol Biol Evol"},{"key":"1165_CR20","doi-asserted-by":"publisher","unstructured":"Fujiwara K, Kawai Y, Moriwaki K, Takada T, Shiroishi T, Saitou N, et al. Insights into Mus musculus subspecies population structure across Eurasia revealed by whole-genome sequence analysis. Biorxiv. 2021. https:\/\/doi.org\/10.1101\/2021.02.05.429881.","DOI":"10.1101\/2021.02.05.429881"},{"issue":"1","key":"1165_CR21","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1146\/annurev.es.24.110193.001003","volume":"24","author":"P Boursot","year":"1993","unstructured":"Boursot P, Auffray J-C, Britton-Davidian J, Bonhomme F. The evolution of house mice. Annu Rev Ecol Syst. 1993;24(1):119\u201352. https:\/\/doi.org\/10.1146\/annurev.es.24.110193.001003.","journal-title":"Annu Rev Ecol Syst"},{"issue":"1","key":"1165_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-64939-9","volume":"10","author":"T Cucchi","year":"2020","unstructured":"Cucchi T, Papayianni K, Cersoy S, Aznar-Cormano L, Zazzo A, Debruyne R, et al. Tracking the Near Eastern origins and European dispersal of the western house mouse. Sci Rep. 2020;10(1):1\u201312. https:\/\/doi.org\/10.1038\/s41598-020-64939-9.","journal-title":"Sci Rep"},{"issue":"1","key":"1165_CR23","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1006\/geno.1997.4775","volume":"43","author":"A Shvarts","year":"1997","unstructured":"Shvarts A, Bazuine M, Dekker P, Ramos YF, Steegenga WT, Merckx G, et al. Isolation and identification of the human homolog of a new p53-binding protein. Mdmx. Genomics. 1997;43(1):34\u201342. https:\/\/doi.org\/10.1006\/geno.1997.4775.","journal-title":"Mdmx. Genomics"},{"issue":"13","key":"1165_CR24","doi-asserted-by":"publisher","first-page":"5835","DOI":"10.1128\/MCB.24.13.5835-5843.2004","volume":"24","author":"D Danovi","year":"2004","unstructured":"Danovi D, Meulmeester E, Pasini D, Migliorini D, Capra M, Frenk R, et al. Amplification of Mdmx (or Mdm4) directly contributes to tumor formation by inhibiting p53 tumor suppressor activity. Mol Cell Biol. 2004;24(13):5835\u201343. https:\/\/doi.org\/10.1128\/MCB.24.13.5835-5843.2004.","journal-title":"Mol Cell Biol"},{"issue":"15","key":"1165_CR25","doi-asserted-by":"publisher","first-page":"5527","DOI":"10.1128\/MCB.22.15.5527-5538.2002","volume":"22","author":"D Migliorini","year":"2002","unstructured":"Migliorini D, Denchi EL, Danovi D, Jochemsen A, Capillo M, Gobbi A, et al. Mdm4 (Mdmx) regulates p53-induced growth arrest and neuronal cell death during early embryonic mouse development. Mol Cell Biol. 2002;22(15):5527\u201338. https:\/\/doi.org\/10.1128\/MCB.22.15.5527-5538.2002.","journal-title":"Mol Cell Biol"},{"issue":"4","key":"1165_CR26","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1042\/BST0330679","volume":"33","author":"JR Sampson","year":"2005","unstructured":"Sampson JR, Jones S, Dolwani S, Cheadle JP. MutYH (MYH) and colorectal cancer. Biochem Soc Trans. 2005;33(4):679\u201383. https:\/\/doi.org\/10.1042\/BST0330679.","journal-title":"Biochem Soc Trans"},{"key":"1165_CR27","doi-asserted-by":"publisher","unstructured":"Sasani TA, Ashbrook DG, Lu L, Palmer AA, Williams RW, Pritchard JK, et al. A wild-derived antimutator drives germline mutation spectrum differences in a genetically diverse murine family. bioRxiv. 2021. https:\/\/doi.org\/10.1101\/2021.03.12.435196.","DOI":"10.1101\/2021.03.12.435196"},{"issue":"1","key":"1165_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/srep04689","volume":"4","author":"M Ohno","year":"2014","unstructured":"Ohno M, Sakumi K, Fukumura R, Furuichi M, Iwasaki Y, Hokama M, et al. 8-oxoguanine causes spontaneous de novo germline mutations in mice. Sci Rep. 2014;4(1):1\u20139. https:\/\/doi.org\/10.1038\/srep04689.","journal-title":"Sci Rep"},{"issue":"2","key":"1165_CR29","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1038\/ng828","volume":"30","author":"N Al-Tassan","year":"2002","unstructured":"Al-Tassan N, Chmiel NH, Maynard J, Fleming N, Livingston AL, Williams GT, et al. Inherited variants of MYH associated with somatic G: C\u2192 T: A mutations in colorectal tumors. Nat Genet. 2002;30(2):227\u201332. https:\/\/doi.org\/10.1038\/ng828.","journal-title":"Nat Genet"},{"issue":"9","key":"1165_CR30","doi-asserted-by":"publisher","first-page":"3096","DOI":"10.1158\/0008-5472.CAN-03-3834","volume":"64","author":"Y Xie","year":"2004","unstructured":"Xie Y, Yang H, Cunanan C, Okamoto K, Shibata D, Pan J, et al. Deficiencies in mouse Myh and Ogg1 result in tumor predisposition and G to T mutations in codon 12 of the K-ras oncogene in lung tumors. Cancer Res. 2004;64(9):3096\u2013102. https:\/\/doi.org\/10.1158\/0008-5472.CAN-03-3834.","journal-title":"Cancer Res"},{"issue":"9","key":"1165_CR31","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1007\/s00335-015-9600-0","volume":"26","author":"JT Eppig","year":"2015","unstructured":"Eppig JT, Motenko H, Richardson JE, Richards-Smith B, Smith CL. The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources. Mamm Genome. 2015;26(9):448\u201355. https:\/\/doi.org\/10.1007\/s00335-015-9600-0.","journal-title":"Mamm Genome"},{"issue":"3","key":"1165_CR32","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.1534\/genetics.104.038224","volume":"170","author":"JD Jensen","year":"2005","unstructured":"Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics. 2005;170(3):1401\u201310. https:\/\/doi.org\/10.1534\/genetics.104.038224.","journal-title":"Genetics"},{"issue":"7288","key":"1165_CR33","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nature08832","volume":"464","author":"C-J Rubin","year":"2010","unstructured":"Rubin C-J, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010;464(7288):587\u201391. https:\/\/doi.org\/10.1038\/nature08832.","journal-title":"Nature"},{"issue":"10","key":"1165_CR34","doi-asserted-by":"publisher","first-page":"5269","DOI":"10.1073\/pnas.76.10.5269","volume":"76","author":"M Nei","year":"1979","unstructured":"Nei M, Li W-H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci. 1979;76(10):5269\u201373. https:\/\/doi.org\/10.1073\/pnas.76.10.5269.","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"1165_CR35","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","volume":"123","author":"F Tajima","year":"1989","unstructured":"Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123(3):585\u201395. https:\/\/doi.org\/10.1093\/genetics\/123.3.585.","journal-title":"Genetics"},{"issue":"6","key":"1165_CR36","doi-asserted-by":"publisher","first-page":"e1000500","DOI":"10.1371\/journal.pgen.1000500","volume":"5","author":"G Coop","year":"2009","unstructured":"Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, et al. The role of geography in human adaptation. PLoS Genet. 2009;5(6):e1000500. https:\/\/doi.org\/10.1371\/journal.pgen.1000500.","journal-title":"PLoS Genet"},{"issue":"7364","key":"1165_CR37","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1038\/nature10432","volume":"477","author":"B Yalcin","year":"2011","unstructured":"Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, et al. Sequence-based characterization of structural variation in the mouse genome. Nature. 2011;477(7364):326\u20139. https:\/\/doi.org\/10.1038\/nature10432.","journal-title":"Nature"},{"issue":"5","key":"1165_CR38","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1038\/ng.108","volume":"40","author":"LM Boyden","year":"2008","unstructured":"Boyden LM, Lewis JM, Barbee SD, Bas A, Girardi M, Hayday AC, et al. Skint1, the prototype of a newly identified immunoglobulin superfamily gene cluster, positively selects epidermal \u03b3\u03b4 T cells. Nat Genet. 2008;40(5):656\u201362. https:\/\/doi.org\/10.1038\/ng.108.","journal-title":"Nat Genet"},{"issue":"8","key":"1165_CR39","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1101\/gr.187187.114","volume":"25","author":"\u017d Pezer","year":"2015","unstructured":"Pezer \u017d, Harr B, Teschke M, Babiker H, Tautz D. Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions. Genome Res. 2015;25(8):1114\u201324. https:\/\/doi.org\/10.1101\/gr.187187.114.","journal-title":"Genome Res"},{"issue":"3","key":"1165_CR40","doi-asserted-by":"publisher","first-page":"e1005851","DOI":"10.1371\/journal.pgen.1005851","volume":"12","author":"AH Freedman","year":"2016","unstructured":"Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, et al. Demographically-based evaluation of genomic regions under selection in domestic dogs. PLoS Genet. 2016;12(3):e1005851. https:\/\/doi.org\/10.1371\/journal.pgen.1005851.","journal-title":"PLoS Genet"},{"issue":"6","key":"1165_CR41","doi-asserted-by":"publisher","first-page":"1417","DOI":"10.3892\/ijo_00000793","volume":"37","author":"N Ohtomo","year":"2010","unstructured":"Ohtomo N, Tomiya T, Tanoue Y, Inoue Y, Nishikawa T, Ikeda H, et al. Expression of \u03b1-taxilin in hepatocellular carcinoma correlates with growth activity and malignant potential of the tumor. Int J Oncol. 2010;37(6):1417\u201323. https:\/\/doi.org\/10.3892\/ijo_00000793.","journal-title":"Int J Oncol"},{"issue":"1","key":"1165_CR42","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/s00439-012-1228-5","volume":"132","author":"M Cardenas-Rodriguez","year":"2013","unstructured":"Cardenas-Rodriguez M, Osborn DP, Irigo\u00edn F, Gra\u00f1a M, Romero H, Beales PL, et al. Characterization of Ccdc28b reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet\u2013Biedl syndrome. Hum Genet. 2013;132(1):91\u2013105. https:\/\/doi.org\/10.1007\/s00439-012-1228-5.","journal-title":"Hum Genet"},{"issue":"2","key":"1165_CR43","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/j.cell.2017.03.027","volume":"169","author":"A Patke","year":"2017","unstructured":"Patke A, Murphy PJ, Onat OE, Krieger AC, \u00d6z\u00e7elik T, Campbell SS, et al. Mutation of the human circadian clock gene CRY1 in familial delayed sleep phase disorder. Cell. 2017;169(2):203\u201315 e213.","journal-title":"Cell"},{"issue":"6","key":"1165_CR44","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1093\/abbs\/gmr035","volume":"43","author":"W Huang","year":"2011","unstructured":"Huang W, Yu M, Jiao Y, Ma J, Ma M, Wang Z, et al. Mitochondrial transcription termination factor 2 binds to entire mitochondrial DNA and negatively regulates mitochondrial gene expression. Acta Biochim Biophys Sin. 2011;43(6):472\u20139. https:\/\/doi.org\/10.1093\/abbs\/gmr035.","journal-title":"Acta Biochim Biophys Sin"},{"issue":"6","key":"1165_CR45","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1093\/hmg\/ddi076","volume":"14","author":"U zur Stadt","year":"2005","unstructured":"zur Stadt U, Schmidt S, Kasper B, Beutel K, Diler AS, Henter J-I, et al. Linkage of familial hemophagocytic lymphohistiocytosis (FHL) type-4 to chromosome 6q24 and identification of mutations in syntaxin 11. Hum Mol Genet. 2005;14(6):827\u201334.","journal-title":"Hum Mol Genet"},{"key":"1165_CR46","doi-asserted-by":"publisher","first-page":"193","DOI":"10.3389\/fgene.2018.00193","volume":"9","author":"Z Wu","year":"2018","unstructured":"Wu Z, Derks MF, Dibbits B, Megens H-J, Groenen MA, Crooijmans RP. A novel loss-of-function variant in transmembrane protein 263 (TMEM263) of autosomal dwarfism in chicken. Front Genet. 2018;9:193. https:\/\/doi.org\/10.3389\/fgene.2018.00193.","journal-title":"Front Genet"},{"issue":"25","key":"1165_CR47","doi-asserted-by":"publisher","first-page":"11459","DOI":"10.1073\/pnas.1002443107","volume":"107","author":"CM Beall","year":"2010","unstructured":"Beall CM, Cavalleri GL, Deng L, Elston RC, Gao Y, Knight J, et al. Natural selection on EPAS1 (HIF2\u03b1) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci. 2010;107(25):11459\u201364. https:\/\/doi.org\/10.1073\/pnas.1002443107.","journal-title":"Proc Natl Acad Sci"},{"issue":"6","key":"1165_CR48","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1038\/s41437-018-0173-z","volume":"122","author":"AM Graham","year":"2019","unstructured":"Graham AM, McCracken KG. Convergent evolution on the hypoxia-inducible factor (HIF) pathway genes EGLN1 and EPAS1 in high-altitude ducks. Heredity. 2019;122(6):819\u201332. https:\/\/doi.org\/10.1038\/s41437-018-0173-z.","journal-title":"Heredity"},{"issue":"8","key":"1165_CR49","doi-asserted-by":"publisher","first-page":"2013","DOI":"10.1038\/emboj.2012.55","volume":"31","author":"K Ask","year":"2012","unstructured":"Ask K, Jasencakova Z, Menard P, Feng Y, Almouzni G, Groth A. Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply. The EMBO journal. 2012;31(8):2013\u201323. https:\/\/doi.org\/10.1038\/emboj.2012.55.","journal-title":"The EMBO journal"},{"issue":"12","key":"1165_CR50","doi-asserted-by":"publisher","first-page":"e1007844","DOI":"10.1371\/journal.pgen.1007844","volume":"14","author":"E Bowie","year":"2018","unstructured":"Bowie E, Norris R, Anderson KV, Goetz SC. Spinocerebellar ataxia type 11-associated alleles of Ttbk2 dominantly interfere with ciliogenesis and cilium stability. PLoS Genet. 2018;14(12):e1007844. https:\/\/doi.org\/10.1371\/journal.pgen.1007844.","journal-title":"PLoS Genet"},{"issue":"6","key":"1165_CR51","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1016\/j.cell.2011.11.020","volume":"147","author":"JZ Torres","year":"2011","unstructured":"Torres JZ, Summers MK, Peterson D, Brauer MJ, Lee J, Senese S, et al. The Stard9\/Kif16a kinesin associates with mitotic microtubules and regulates spindle pole assembly. Cell. 2011;147(6):1309\u201323. https:\/\/doi.org\/10.1016\/j.cell.2011.11.020.","journal-title":"Cell"},{"issue":"7441","key":"1165_CR52","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/nature11837","volume":"495","author":"E Axelsson","year":"2013","unstructured":"Axelsson E, Ratnakumar A, Arendt M-L, Maqbool K, Webster MT, Perloski M, et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013;495(7441):360\u20134. https:\/\/doi.org\/10.1038\/nature11837.","journal-title":"Nature"},{"issue":"11","key":"1165_CR53","doi-asserted-by":"publisher","first-page":"eaau4921","DOI":"10.1126\/sciadv.aau4921","volume":"4","author":"J Lindo","year":"2018","unstructured":"Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo RA, et al. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci Adv. 2018;4(11):eaau4921.","journal-title":"Sci Adv"},{"issue":"3","key":"1165_CR54","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1042\/BJ20051814","volume":"396","author":"Y Nishito","year":"2006","unstructured":"Nishito Y, Hasegawa M, Inohara N, N\u00fa\u00f1ez G. MEX is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis. Biochem J. 2006;396(3):411\u20137. https:\/\/doi.org\/10.1042\/BJ20051814.","journal-title":"Biochem J"},{"issue":"7572","key":"1165_CR55","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/nature15400","volume":"526","author":"Y Usami","year":"2015","unstructured":"Usami Y, Wu Y, G\u00f6ttlinger HG. Serinc3 and Serinc5 restrict HIV-1 infectivity and are counteracted by Nef. Nature. 2015;526(7572):218\u201323. https:\/\/doi.org\/10.1038\/nature15400.","journal-title":"Nature"},{"issue":"1","key":"1165_CR56","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1073\/pnas.0133792100","volume":"100","author":"T Fujino","year":"2003","unstructured":"Fujino T, Asaba H, Kang M-J, Ikeda Y, Sone H, Takada S, et al. Low-density lipoprotein receptor-related protein 5 (LRP5) is essential for normal cholesterol metabolism and glucose-induced insulin secretion. Proc Natl Acad Sci. 2003;100(1):229\u201334. https:\/\/doi.org\/10.1073\/pnas.0133792100.","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"1165_CR57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2350-13-26","volume":"13","author":"J Korvala","year":"2012","unstructured":"Korvala J, J\u00fcppner H, M\u00e4kitie O, Sochett E, Schnabel D, Mora S, et al. Mutations in LRP5 cause primary osteoporosis without features of OI by reducing Wnt signaling activity. BMC Med Genet. 2012;13(1):1\u201310. https:\/\/doi.org\/10.1186\/1471-2350-13-26.","journal-title":"BMC Med Genet"},{"issue":"16","key":"1165_CR58","doi-asserted-by":"publisher","first-page":"10050","DOI":"10.1016\/S0021-9258(18)99185-4","volume":"266","author":"K Hill","year":"1991","unstructured":"Hill K, Lloyd RS, Yang J, Read R, Burk R. The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame. J Biol Chem. 1991;266(16):10050\u20133. https:\/\/doi.org\/10.1016\/S0021-9258(18)99185-4.","journal-title":"J Biol Chem"},{"issue":"8","key":"1165_CR59","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/j.tig.2004.06.010","volume":"20","author":"RA Sturm","year":"2004","unstructured":"Sturm RA, Frudakis TN. Eye colour: portals into pigmentation genes and ancestry. Trends Genet. 2004;20(8):327\u201332. https:\/\/doi.org\/10.1016\/j.tig.2004.06.010.","journal-title":"Trends Genet"},{"issue":"5","key":"1165_CR60","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1007\/s00439-011-1110-x","volume":"131","author":"MP Donnelly","year":"2012","unstructured":"Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Barta C, Lu RB, et al. A global view of the Oca2-Herc2 region and pigmentation. Hum Genet. 2012;131(5):683\u201396. https:\/\/doi.org\/10.1007\/s00439-011-1110-x.","journal-title":"Hum Genet"},{"issue":"2","key":"1165_CR61","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1007\/s10549-008-9927-2","volume":"113","author":"M Thomassen","year":"2009","unstructured":"Thomassen M, Tan Q, Kruse TA. Gene expression meta-analysis identifies chromosomal regions and candidate genes involved in breast cancer metastasis. Breast Cancer Res Treat. 2009;113(2):239\u201349. https:\/\/doi.org\/10.1007\/s10549-008-9927-2.","journal-title":"Breast Cancer Res Treat"},{"issue":"2","key":"1165_CR62","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/79936","volume":"26","author":"C Delettre","year":"2000","unstructured":"Delettre C, Lenaers G, Griffoin J-M, Gigarel N, Lorenzo C, Belenguer P, et al. Nuclear gene OPA1, encoding a mitochondrial dynamin-related protein, is mutated in dominant optic atrophy. Nat Genet. 2000;26(2):207\u201310. https:\/\/doi.org\/10.1038\/79936.","journal-title":"Nat Genet"},{"issue":"18","key":"1165_CR63","doi-asserted-by":"publisher","first-page":"3620","DOI":"10.1093\/hmg\/ddr282","volume":"20","author":"WM Gerding","year":"2011","unstructured":"Gerding WM, Schreiber S, Schulte-Middelmann T, de Castro MA, Atorf J, Akkad DA, et al. Ccdc66 null mutation causes retinal degeneration and dysfunction. Hum Mol Genet. 2011;20(18):3620\u201331. https:\/\/doi.org\/10.1093\/hmg\/ddr282.","journal-title":"Hum Mol Genet"},{"issue":"12","key":"1165_CR64","doi-asserted-by":"publisher","first-page":"e1003995","DOI":"10.1371\/journal.pgen.1003995","volume":"9","author":"DL Halligan","year":"2013","unstructured":"Halligan DL, Kousathanas A, Ness RW, Harr B, E\u00f6ry L, Keane TM, et al. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet. 2013;9(12):e1003995. https:\/\/doi.org\/10.1371\/journal.pgen.1003995.","journal-title":"PLoS Genet"},{"issue":"11","key":"1165_CR65","doi-asserted-by":"publisher","first-page":"1636","DOI":"10.1101\/gr.238998.118","volume":"28","author":"KL Mack","year":"2018","unstructured":"Mack KL, Ballinger MA, Phifer-Rixey M, Nachman MW. Gene regulation underlies environmental adaptation in house mice. Genome Res. 2018;28(11):1636\u201345. https:\/\/doi.org\/10.1101\/gr.238998.118.","journal-title":"Genome Res"},{"issue":"11","key":"1165_CR66","doi-asserted-by":"publisher","first-page":"e1008420","DOI":"10.1371\/journal.pgen.1008420","volume":"15","author":"RM Schweizer","year":"2019","unstructured":"Schweizer RM, Velotta JP, Ivy CM, Jones MR, Muir SM, Bradburd GS, et al. Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice. PLoS Genet. 2019;15(11):e1008420. https:\/\/doi.org\/10.1371\/journal.pgen.1008420.","journal-title":"PLoS Genet"},{"key":"1165_CR67","doi-asserted-by":"publisher","unstructured":"Shultz AJ, Sackton TB. Immune genes are hotspots of shared positive selection across birds and mammals. Elife. 2019;8. https:\/\/doi.org\/10.7554\/eLife.41815.","DOI":"10.7554\/eLife.41815"},{"issue":"5","key":"1165_CR68","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1093\/hmg\/11.5.535","volume":"11","author":"JM Young","year":"2002","unstructured":"Young JM, Friedman C, Williams EM, Ross JA, Tonnes-Priddy L, Trask BJ. Different evolutionary processes shaped the mouse and human olfactory receptor gene families. Hum Mol Genet. 2002;11(5):535\u201346. https:\/\/doi.org\/10.1093\/hmg\/11.5.535.","journal-title":"Hum Mol Genet"},{"issue":"33","key":"1165_CR69","doi-asserted-by":"publisher","first-page":"11597","DOI":"10.1073\/pnas.0801317105","volume":"105","author":"MA Zeder","year":"2008","unstructured":"Zeder MA. Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proc Natl Acad Sci. 2008;105(33):11597\u2013604. https:\/\/doi.org\/10.1073\/pnas.0801317105.","journal-title":"Proc Natl Acad Sci"},{"issue":"6298","key":"1165_CR70","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1126\/science.aaf7943","volume":"353","author":"F Broushaki","year":"2016","unstructured":"Broushaki F, Thomas MG, Link V, L\u00f3pez S, van Dorp L, Kirsanow K, et al. Early Neolithic genomes from the eastern Fertile Crescent. Science. 2016;353(6298):499\u2013503. https:\/\/doi.org\/10.1126\/science.aaf7943.","journal-title":"Science"},{"issue":"1","key":"1165_CR71","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/s12862-015-0306-4","volume":"15","author":"EA Hardouin","year":"2015","unstructured":"Hardouin EA, Orth A, Teschke M, Darvish J, Tautz D, Bonhomme F. Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot. BMC Evol Biol. 2015;15(1):26.","journal-title":"BMC Evol Biol"},{"issue":"2","key":"1165_CR72","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1515\/mammalia-2015-0041","volume":"81","author":"HS Hamid","year":"2017","unstructured":"Hamid HS, Darvish J, Rastegar-Pouyani E, Mahmoudi A. Subspecies differentiation of the house mouse Mus musculus Linnaeus, 1758 in the center and east of the Iranian plateau and Afghanistan. Mammalia. 2017;81(2):147\u201368. https:\/\/doi.org\/10.1515\/mammalia-2015-0041.","journal-title":"Mammalia"},{"issue":"10","key":"1165_CR73","doi-asserted-by":"publisher","first-page":"1256","DOI":"10.1038\/ng2123","volume":"39","author":"GH Perry","year":"2007","unstructured":"Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, et al. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007;39(10):1256\u201360. https:\/\/doi.org\/10.1038\/ng2123.","journal-title":"Nat Genet"},{"issue":"11","key":"1165_CR74","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/j.tree.2013.08.003","volume":"28","author":"PW Messer","year":"2013","unstructured":"Messer PW, Petrov DA. Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol. 2013;28(11):659\u201369. https:\/\/doi.org\/10.1016\/j.tree.2013.08.003.","journal-title":"Trends Ecol Evol"},{"issue":"12","key":"1165_CR75","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1038\/s41576-020-0250-z","volume":"21","author":"N Barghi","year":"2020","unstructured":"Barghi N, Hermisson J, Schl\u00f6tterer C. Polygenic adaptation: a unifying framework to understand positive selection. Nat Rev Genet. 2020;21(12):769\u201381. https:\/\/doi.org\/10.1038\/s41576-020-0250-z.","journal-title":"Nat Rev Genet"},{"issue":"2","key":"1165_CR76","doi-asserted-by":"publisher","first-page":"e1005004","DOI":"10.1371\/journal.pgen.1005004","volume":"11","author":"NR Garud","year":"2015","unstructured":"Garud NR, Messer PW, Buzbas EO, Petrov DA. Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genet. 2015;11(2):e1005004. https:\/\/doi.org\/10.1371\/journal.pgen.1005004.","journal-title":"PLoS Genet"},{"key":"1165_CR77","volume-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997","author":"H Li","year":"2013","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997; 2013."},{"issue":"5","key":"1165_CR78","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with Burrows\u2013Wheeler transform. Bioinformatics. 2010;26(5):589\u201395. https:\/\/doi.org\/10.1093\/bioinformatics\/btp698.","journal-title":"Bioinformatics"},{"issue":"1","key":"1165_CR79","doi-asserted-by":"publisher","first-page":"11.10.11","DOI":"10.1002\/0471250953.bi1110s43","volume":"43","author":"GA Auwera","year":"2013","unstructured":"Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, et al. From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinform. 2013;43(1):11.10.11\u201333. https:\/\/doi.org\/10.1002\/0471250953.bi1110s43.","journal-title":"Curr Protoc Bioinform"},{"issue":"7364","key":"1165_CR80","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1038\/nature10413","volume":"477","author":"TM Keane","year":"2011","unstructured":"Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 2011;477(7364):289\u201394. https:\/\/doi.org\/10.1038\/nature10413.","journal-title":"Nature"},{"issue":"2","key":"1165_CR81","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80\u201392. https:\/\/doi.org\/10.4161\/fly.19695.","journal-title":"Fly"},{"issue":"15","key":"1165_CR82","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/btr330.","journal-title":"Bioinformatics"},{"issue":"1","key":"1165_CR83","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1471-2105-12-35","volume":"12","author":"H Chen","year":"2011","unstructured":"Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics. 2011;12(1):35. https:\/\/doi.org\/10.1186\/1471-2105-12-35.","journal-title":"BMC Bioinformatics"},{"issue":"22","key":"1165_CR84","doi-asserted-by":"publisher","first-page":"2867","DOI":"10.1093\/bioinformatics\/btq559","volume":"26","author":"A Manichaikul","year":"2010","unstructured":"Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen W-M. Robust relationship inference in genome-wide association studies. Bioinformatics. 2010;26(22):2867\u201373. https:\/\/doi.org\/10.1093\/bioinformatics\/btq559.","journal-title":"Bioinformatics"},{"key":"1165_CR85","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant graphics for data analysis","author":"H Wickham","year":"2016","unstructured":"Wickham H. ggplot2: Elegant graphics for data analysis, vol. 35. New York: Springer-Verlag; 2016."},{"issue":"1","key":"1165_CR86","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","volume":"4","author":"CC Chang","year":"2015","unstructured":"Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4(1):7. https:\/\/doi.org\/10.1186\/s13742-015-0047-8.","journal-title":"Gigascience"},{"issue":"5","key":"1165_CR87","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1080\/10635150390235520","volume":"52","author":"S Guindon","year":"2003","unstructured":"Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52(5):696\u2013704. https:\/\/doi.org\/10.1080\/10635150390235520.","journal-title":"Syst Biol"},{"issue":"8","key":"1165_CR88","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/nmeth.2109","volume":"9","author":"D Darriba","year":"2012","unstructured":"Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9(8):772. https:\/\/doi.org\/10.1038\/nmeth.2109.","journal-title":"Nat Methods"},{"issue":"7","key":"1165_CR89","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1093\/molbev\/msw054","volume":"33","author":"S Kumar","year":"2016","unstructured":"Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870\u20134. https:\/\/doi.org\/10.1093\/molbev\/msw054.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"1165_CR90","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1186\/s12859-014-0356-4","volume":"15","author":"TS Korneliussen","year":"2014","unstructured":"Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics. 2014;15(1):356. https:\/\/doi.org\/10.1186\/s12859-014-0356-4.","journal-title":"BMC Bioinformatics"},{"issue":"10","key":"1165_CR91","doi-asserted-by":"publisher","first-page":"e1000695","DOI":"10.1371\/journal.pgen.1000695","volume":"5","author":"RN Gutenkunst","year":"2009","unstructured":"Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009;5(10):e1000695. https:\/\/doi.org\/10.1371\/journal.pgen.1000695.","journal-title":"PLoS Genet"},{"issue":"1","key":"1165_CR92","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/ncomms15183","volume":"8","author":"B Milholland","year":"2017","unstructured":"Milholland B, Dong X, Zhang L, Hao X, Suh Y, Vijg J. Differences between germline and somatic mutation rates in humans and mice. Nat Commun. 2017;8(1):1\u20138. https:\/\/doi.org\/10.1038\/ncomms15183.","journal-title":"Nat Commun"},{"issue":"2","key":"1165_CR93","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","volume":"18","author":"RR Hudson","year":"2002","unstructured":"Hudson RR. Generating samples under a Wright\u2013Fisher neutral model of genetic variation. Bioinformatics. 2002;18(2):337\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/18.2.337.","journal-title":"Bioinformatics"},{"key":"1165_CR94","doi-asserted-by":"publisher","unstructured":"Lawal RA, Al-Atiyat RM, Aljumaah RS, Silva P, Mwacharo JM, Hanotte O. Whole-genome resequencing of red junglefowl and indigenous village chicken reveal new insights on the genome dynamics of the species. Front Genet. 2018;9. https:\/\/doi.org\/10.3389\/fgene.2018.00264.","DOI":"10.3389\/fgene.2018.00264"},{"issue":"5","key":"1165_CR95","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/bioinformatics\/btx699","volume":"34","author":"BS Pedersen","year":"2018","unstructured":"Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018;34(5):867\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/btx699.","journal-title":"Bioinformatics"},{"key":"1165_CR96","doi-asserted-by":"publisher","first-page":"e836","DOI":"10.7717\/peerj.836","volume":"3","author":"SD Smith","year":"2015","unstructured":"Smith SD, Kawash JK, Grigoriev A. GROM-RD: resolving genomic biases to improve read depth detection of copy number variants. PeerJ. 2015;3:e836. https:\/\/doi.org\/10.7717\/peerj.836.","journal-title":"PeerJ"},{"issue":"14","key":"1165_CR97","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1093\/bioinformatics\/bts277","volume":"28","author":"S Neph","year":"2012","unstructured":"Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, et al. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012;28(14):1919\u201320. https:\/\/doi.org\/10.1093\/bioinformatics\/bts277.","journal-title":"Bioinformatics"},{"issue":"6","key":"1165_CR98","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btq033.","journal-title":"Bioinformatics"},{"key":"1165_CR99","doi-asserted-by":"publisher","unstructured":"Kinsella RJ, K\u00e4h\u00e4ri A, Haider S, Zamora J, Proctor G, Spudich G, et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database. 2011;2011(0). https:\/\/doi.org\/10.1093\/database\/bar030.","DOI":"10.1093\/database\/bar030"},{"issue":"1","key":"1165_CR100","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44\u201357. https:\/\/doi.org\/10.1038\/nprot.2008.211.","journal-title":"Nat Protoc"},{"issue":"1","key":"1165_CR101","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139\u201340. https:\/\/doi.org\/10.1093\/bioinformatics\/btp616.","journal-title":"Bioinformatics"},{"issue":"12","key":"1165_CR102","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):1\u201321. https:\/\/doi.org\/10.1186\/s13059-014-0550-8.","journal-title":"Genome Biol"}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-021-01165-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-021-01165-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-021-01165-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T19:05:16Z","timestamp":1637262316000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-021-01165-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,19]]},"references-count":102,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["1165"],"URL":"https:\/\/doi.org\/10.1186\/s12915-021-01165-3","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.12.443838","asserted-by":"object"}]},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,19]]},"assertion":[{"value":"13 May 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 October 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"239"}}