{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T17:14:07Z","timestamp":1791652447222,"version":"4.3.4"},"reference-count":104,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean Zebu in the founder ancestry. Comparative analysis of whole-genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants. Interestingly, the population\u2019s success in the harsh environment can be attributed to preadaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts.<\/jats:p>","DOI":"10.1093\/molbev\/msae121","type":"journal-article","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T14:04:20Z","timestamp":1718719460000},"source":"Crossref","is-referenced-by-count":12,"title":["Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7257-5880","authenticated-orcid":false,"given":"Mathieu","family":"Gautier","sequence":"first","affiliation":[{"name":"CBGP, INRAE, CIRAD, IRD, L\u2019institut Agro, Universit\u00e9 de Montpellier , Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4309-1961","authenticated-orcid":false,"given":"Thierry","family":"Micol","sequence":"additional","affiliation":[{"name":"LPO , Rochefort , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5485-8078","authenticated-orcid":false,"given":"Louise","family":"Camus","sequence":"additional","affiliation":[{"name":"CBGP, INRAE, CIRAD, IRD, L\u2019institut Agro, Universit\u00e9 de Montpellier , Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2860-5418","authenticated-orcid":false,"given":"Katayoun","family":"Moazami-Goudarzi","sequence":"additional","affiliation":[{"name":"GABI, INRAE, AgroParisTech, Universit\u00e9 Paris-Saclay , Jouy-en-Josas , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5574-1509","authenticated-orcid":false,"given":"Michel","family":"Naves","sequence":"additional","affiliation":[{"name":"ASSET, INRAE , Petit-Bourg, Guadeloupe , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0714-3197","authenticated-orcid":false,"given":"Elise","family":"Gu\u00e9ret","sequence":"additional","affiliation":[{"name":"MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM , Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0003-1192","authenticated-orcid":false,"given":"Stefan","family":"Engelen","sequence":"additional","affiliation":[{"name":"Retired, CEA, Institut de biologie Fran\u00e7ois-Jacob, Genoscope, Universit\u00e9 Paris-Saclay , Evry , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaud","family":"Lemainque","sequence":"additional","affiliation":[{"name":"Retired, CEA, Institut de biologie Fran\u00e7ois-Jacob, Genoscope, Universit\u00e9 Paris-Saclay , Evry , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Colas","sequence":"additional","affiliation":[{"name":"Retired , Saint-Paul and Amsterdam District, Terres Australes et Antarctiques Fran\u00e7aises, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7529-8521","authenticated-orcid":false,"given":"Laurence","family":"Flori","sequence":"additional","affiliation":[{"name":"SELMET, INRAE, CIRAD, L\u2019institut Agro, Universit\u00e9 de Montpellier , Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1637-1706","authenticated-orcid":false,"given":"Tom","family":"Druet","sequence":"additional","affiliation":[{"name":"Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge , Li\u00e8ge , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,6,18]]},"reference":[{"issue":"1","key":"2024082222521651100_msae121-B1","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1186\/s13059-016-1090-1","article-title":"Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered iberian lynx","volume":"17","author":"Abascal","year":"2016","journal-title":"Genome Biol"},{"issue":"9","key":"2024082222521651100_msae121-B2","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"issue":"35","key":"2024082222521651100_msae121-B3","doi-asserted-by":"crossref","first-page":"e2122734119","DOI":"10.1073\/pnas.2122734119","article-title":"A single introduction of wild rabbits triggered the biological invasion of Australia","volume":"119","author":"Alves","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"2024082222521651100_msae121-B4","doi-asserted-by":"crossref","first-page":"e1005436","DOI":"10.1371\/journal.pgen.1005436","article-title":"Dominance of deleterious alleles controls the response to a population bottleneck","volume":"11","author":"Balick","year":"2015","journal-title":"PLoS Genet"},{"issue":"7497","key":"2024082222521651100_msae121-B5","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nature13206","article-title":"Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators","volume":"508","author":"Bellott","year":"2014","journal-title":"Nature"},{"issue":"2","key":"2024082222521651100_msae121-B6","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1111\/j.1469-7998.1992.tb04607.x","article-title":"Population studies and reproduction of the feral cattle (Bos taurus) of Amsterdam Island, Indian Ocean","volume":"228","author":"Berteaux","year":"1992","journal-title":"J Zool"},{"issue":"6","key":"2024082222521651100_msae121-B7","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1111\/2041-210X.13167","article-title":"RZooRoH: an R package to characterize individual genomic autozygosity and identify homozygous-by-descent segments","volume":"10","author":"Bertrand","year":"2019","journal-title":"Methods Ecol Evol"},{"issue":"15","key":"2024082222521651100_msae121-B8","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"2024082222521651100_msae121-B9","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1111\/eva.12691","article-title":"Deleterious alleles in the context of domestication, inbreeding, and selection","volume":"12","author":"Bosse","year":"2019","journal-title":"Evol Appl"},{"issue":"3","key":"2024082222521651100_msae121-B10","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/s41588-018-0056-5","article-title":"Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals","volume":"50","author":"Bouwman","year":"2018","journal-title":"Nat Genet"},{"issue":"2","key":"2024082222521651100_msae121-B11","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1007\/s10592-010-0049-0","article-title":"Conservation genetics of population bottlenecks: the role of chance, selection, and history","volume":"11","author":"Bouzat","year":"2010","journal-title":"Conserv Genet"},{"key":"2024082222521651100_msae121-B12","author":"Broad Institute"},{"issue":"10","key":"2024082222521651100_msae121-B13","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","article-title":"Fast two-stage phasing of large-scale sequence data","volume":"108","author":"Browning","year":"2021","journal-title":"Am J Hum Genet"},{"issue":"3","key":"2024082222521651100_msae121-B14","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A one-penny imputed genome from next-generation reference panels","volume":"103","author":"Browning","year":"2018","journal-title":"Am J Hum Genet"},{"issue":"17","key":"2024082222521651100_msae121-B15","doi-asserted-by":"crossref","first-page":"4241","DOI":"10.1111\/mec.12871","article-title":"Inbreeding and inbreeding depression in endangered red wolves (Canis rufus)","volume":"23","author":"Brzeski","year":"2014","journal-title":"Mol Ecol"},{"issue":"1","key":"2024082222521651100_msae121-B16","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1023\/A:1008800423698","article-title":"Delete-m jackknife for unequal m","volume":"9","author":"Busing","year":"1999","journal-title":"Stat Comput"},{"key":"2024082222521651100_msae121-B17","doi-asserted-by":"crossref","first-page":"e13709","DOI":"10.1111\/eva.13709","article-title":"Predicting species invasiveness with genomic data: is Genomic Offset related to establishment probability?","volume":"17","author":"Camus","year":"2024","journal-title":"Evol Appl"},{"issue":"1","key":"2024082222521651100_msae121-B18","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1146\/annurev-ecolsys-020720-042553","article-title":"Genomic prediction of (mal)adaptation across current and future climatic landscapes","volume":"51","author":"Capblancq","year":"2020","journal-title":"Annu Rev Ecol Evol Syst"},{"issue":"10","key":"2024082222521651100_msae121-B19","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1111\/ele.12493","article-title":"The role of life history traits in mammalian invasion success","volume":"18","author":"Capellini","year":"2015","journal-title":"Ecol Lett"},{"issue":"4","key":"2024082222521651100_msae121-B20","doi-asserted-by":"crossref","first-page":"e2005987","DOI":"10.1371\/journal.pbio.2005987","article-title":"Dissecting the null model for biological invasions: a meta-analysis of the propagule pressure effect","volume":"16","author":"Cassey","year":"2018","journal-title":"PLoS Biol"},{"issue":"17","key":"2024082222521651100_msae121-B21","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one fastq preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"issue":"26","key":"2024082222521651100_msae121-B22","first-page":"E3318","article-title":"On some genetic consequences of social structure, mating systems, dispersal, and sampling","volume":"112","author":"Chikhi","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"issue":"11","key":"2024082222521651100_msae121-B23","doi-asserted-by":"crossref","first-page":"2331","DOI":"10.1093\/molbev\/msn177","article-title":"The legacy of domestication: accumulation of deleterious mutations in the dog genome","volume":"25","author":"Cruz","year":"2008","journal-title":"Mol Biol Evol"},{"issue":"8","key":"2024082222521651100_msae121-B24","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1038\/ng.3034","article-title":"Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle","volume":"46","author":"Daetwyler","year":"2014","journal-title":"Nat Genet"},{"issue":"1","key":"2024082222521651100_msae121-B25","first-page":"35","article-title":"Structure sociale de la population de bovins sauvages de l\u2019\u00eele amsterdam, sud de l\u2019oc\u00e9an indien","volume":"45","author":"Daycard","year":"1990","journal-title":"Rev Ecol (La Terre et La Vie)"},{"key":"2024082222521651100_msae121-B26","volume-title":"\u00c9tude sur les races, vari\u00e9t\u00e9s et croisements de l\u2019esp\u00e8ce bovine en France","author":"de Lapparent","year":"1902"},{"issue":"2","key":"2024082222521651100_msae121-B27","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/ng.3186","article-title":"No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans","volume":"47","author":"Do","year":"2015","journal-title":"Nat Genet"},{"issue":"1","key":"2024082222521651100_msae121-B28","doi-asserted-by":"crossref","first-page":"5582","DOI":"10.1038\/s41598-022-09427-y","article-title":"Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle","volume":"12","author":"Dorji","year":"2022","journal-title":"Sci Rep"},{"issue":"4","key":"2024082222521651100_msae121-B29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v022.i04","article-title":"The ade4 package: implementing the duality diagram for ecologists","volume":"22","author":"Dray","year":"2007","journal-title":"J Stat Softw"},{"issue":"20","key":"2024082222521651100_msae121-B30","doi-asserted-by":"crossref","first-page":"5820","DOI":"10.1111\/mec.14324","article-title":"A model-based approach to characterize individual inbreeding at both global and local genomic scales","volume":"26","author":"Druet","year":"2017","journal-title":"Mol Ecol"},{"issue":"1","key":"2024082222521651100_msae121-B31","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.tpb.2022.03.001","article-title":"A hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors","volume":"145","author":"Druet","year":"2022","journal-title":"Theor Popul Biol"},{"issue":"2","key":"2024082222521651100_msae121-B32","first-page":"194","article-title":"Genomic footprints of recovery in the European bison","volume":"111","author":"Druet","year":"2020","journal-title":"J Hered"},{"issue":"1","key":"2024082222521651100_msae121-B33","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1146\/annurev-ecolsys-121415-032116","article-title":"Is there a genetic paradox of biological invasion?","volume":"47","author":"Estoup","year":"2016","journal-title":"Annu Rev Ecol Evol Syst"},{"issue":"14","key":"2024082222521651100_msae121-B34","doi-asserted-by":"crossref","first-page":"3700","DOI":"10.1111\/mec.14141","article-title":"Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: the local score approach","volume":"26","author":"Fariello","year":"2017","journal-title":"Mol Ecol"},{"issue":"6","key":"2024082222521651100_msae121-B35","doi-asserted-by":"crossref","first-page":"msad140","DOI":"10.1093\/molbev\/msad140","article-title":"A quantitative theory for genomic offset statistics","volume":"40","author":"Gain","year":"2023","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2024082222521651100_msae121-B36","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1534\/genetics.115.181453","article-title":"Genome-wide scan for adaptive divergence and association with population-specific covariates","volume":"201","author":"Gautier","year":"2015","journal-title":"Genetics"},{"issue":"1","key":"2024082222521651100_msae121-B37","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/1471-2164-10-550","article-title":"A whole genome Bayesian scan for adaptive genetic divergence in West African cattle","volume":"10","author":"Gautier","year":"2009","journal-title":"BMC Genomics"},{"issue":"1","key":"2024082222521651100_msae121-B38","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1111\/1755-0998.12634","article-title":"rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure","volume":"17","author":"Gautier","year":"2017","journal-title":"Mol Ecol Resour"},{"issue":"9","key":"2024082222521651100_msae121-B39","doi-asserted-by":"crossref","first-page":"e13038","DOI":"10.1371\/journal.pone.0013038","article-title":"Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds","volume":"5","author":"Gautier","year":"2010","journal-title":"PLoS One"},{"issue":"11","key":"2024082222521651100_msae121-B40","doi-asserted-by":"crossref","first-page":"2801","DOI":"10.1093\/molbev\/msw144","article-title":"Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences","volume":"33","author":"Gautier","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2024082222521651100_msae121-B41","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1111\/1755-0998.13557","article-title":"F-statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat","volume":"22","author":"Gautier","year":"2022","journal-title":"Mol Ecol Resour"},{"issue":"12","key":"2024082222521651100_msae121-B42","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1016\/j.tree.2019.07.018","article-title":"Getting back to nature: feralization in animals and plants","volume":"34","author":"Gering","year":"2019","journal-title":"Trends Ecol Evol"},{"issue":"12","key":"2024082222521651100_msae121-B43","first-page":"2678","article-title":"How are deleterious mutations purged? Drift versus nonrandom mating","volume":"57","author":"Gl\u00e9min","year":"2003","journal-title":"Evolution"},{"issue":"1","key":"2024082222521651100_msae121-B44","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/s41467-020-14803-1","article-title":"Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex","volume":"11","author":"Grossen","year":"2020","journal-title":"Nat Commun"},{"key":"2024082222521651100_msae121-B45","doi-asserted-by":"crossref","DOI":"10.1002\/9780470995433","volume-title":"Livestock biodiversity: genetic resources for the farming of the future","author":"Hall","year":"2004"},{"issue":"s1","key":"2024082222521651100_msae121-B46","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1111\/j.1365-294X.2009.04482.x","article-title":"mlRho\u2014a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes","volume":"19","author":"Haubold","year":"2010","journal-title":"Mol Ecol"},{"key":"2024082222521651100_msae121-B47","author":"Hijmans"},{"issue":"1","key":"2024082222521651100_msae121-B48","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1111\/j.1752-4571.2011.00211.x","article-title":"Anthropogenically induced adaptation to invade (AIAI): contemporary adaptation to human-altered habitats within the native range can promote invasions","volume":"5","author":"Hufbauer","year":"2012","journal-title":"Evol Appl"},{"key":"2024082222521651100_msae121-B49","author":"Illumina"},{"key":"2024082222521651100_msae121-B50","author":"Ingenuity Systems, Inc"},{"issue":"22","key":"2024082222521651100_msae121-B51","doi-asserted-by":"crossref","first-page":"9611","DOI":"10.1093\/nar\/15.22.9611","article-title":"A rapid method for the purification of DNA from blood","volume":"15","author":"Jeanpierre","year":"1987","journal-title":"Nucleic Acids Res"},{"key":"2024082222521651100_msae121-B52","article-title":"Data from: climatologies at high resolution for the earth\u2019s land surface areas","author":"Karger","year":"2018","journal-title":"EnviDat"},{"issue":"1","key":"2024082222521651100_msae121-B53","doi-asserted-by":"crossref","first-page":"170122","DOI":"10.1038\/sdata.2017.122","article-title":"Climatologies at high resolution for the Earth\u2019s land surface areas","volume":"4","author":"Karger","year":"2017","journal-title":"Sci Data"},{"issue":"5","key":"2024082222521651100_msae121-B54","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/ng.814","article-title":"Variants modulating the expression of a chromosome domain encompassing plag1 influence bovine stature","volume":"43","author":"Karim","year":"2011","journal-title":"Nat Genet"},{"issue":"5","key":"2024082222521651100_msae121-B55","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/S0169-5347(02)02489-8","article-title":"Inbreeding effects in wild populations","volume":"17","author":"Keller","year":"2002","journal-title":"Trends Ecol Evol"},{"issue":"1","key":"2024082222521651100_msae121-B56","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1186\/1471-2105-12-231","article-title":"Estimation of allele frequency and association mapping using next-generation sequencing data","volume":"12","author":"Kim","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2024082222521651100_msae121-B57","doi-asserted-by":"crossref","first-page":"e0262024","DOI":"10.1371\/journal.pone.0262024","article-title":"Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data","volume":"17","author":"Klassmann","year":"2022","journal-title":"PLoS One"},{"issue":"2","key":"2024082222521651100_msae121-B58","doi-asserted-by":"crossref","first-page":"msad021","DOI":"10.1093\/molbev\/msad021","article-title":"Genomic underpinnings of population persistence in Isle Royale moose","volume":"40","author":"Kyriazis","year":"2023","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2024082222521651100_msae121-B59","doi-asserted-by":"crossref","first-page":"107","DOI":"10.19182\/remvt.7655","article-title":"Etude d\u2019un troupeau de bovins sauvages vivant sur l\u2019\u00eele d\u2019amsterdam","volume":"22","author":"Lesel","year":"1969","journal-title":"Rev \u00c9lev M\u00e9d v\u00e9t Pays trop"},{"key":"2024082222521651100_msae121-B60","author":"Li"},{"issue":"16","key":"2024082222521651100_msae121-B61","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and samtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"6","key":"2024082222521651100_msae121-B62","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1111\/1755-0998.13230","article-title":"Applying F-statistics and admixture graphs: theory and examples","volume":"20","author":"Lipson","year":"2020","journal-title":"Mol Ecol Resour"},{"issue":"5","key":"2024082222521651100_msae121-B63","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.tree.2005.02.004","article-title":"The role of propagule pressure in explaining species invasions","volume":"20","author":"Lockwood","year":"2005","journal-title":"Trends Ecol Evol"},{"issue":"4","key":"2024082222521651100_msae121-B64","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1534\/genetics.112.147330","article-title":"Inferring admixture histories of human populations using linkage disequilibrium","volume":"193","author":"Loh","year":"2013","journal-title":"Genetics"},{"issue":"11","key":"2024082222521651100_msae121-B65","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1093\/molbev\/msn185","article-title":"Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects","volume":"25","author":"Lynch","year":"2008","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2024082222521651100_msae121-B66","doi-asserted-by":"crossref","first-page":"jkac029","DOI":"10.1093\/g3journal\/jkac029","article-title":"The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean","volume":"12","author":"Magnier","year":"2022","journal-title":"G3"},{"issue":"22","key":"2024082222521651100_msae121-B67","doi-asserted-by":"crossref","first-page":"2867","DOI":"10.1093\/bioinformatics\/btq559","article-title":"Robust relationship inference in genome-wide association studies","volume":"26","author":"Manichaikul","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"2024082222521651100_msae121-B68","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1073\/pnas.1512501113","article-title":"Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs","volume":"113","author":"Marsden","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"2024082222521651100_msae121-B69","doi-asserted-by":"crossref","first-page":"e5350","DOI":"10.1371\/journal.pone.0005350","article-title":"Development and characterization of a high density SNP genotyping assay for cattle","volume":"4","author":"Matukumalli","year":"2009","journal-title":"PLoS One"},{"issue":"9","key":"2024082222521651100_msae121-B70","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"issue":"1","key":"2024082222521651100_msae121-B71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"issue":"3","key":"2024082222521651100_msae121-B72","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/0006-3207(94)00109-4","article-title":"Restoration of Amsterdam Island, South Indian Ocean, following control of feral cattle","volume":"73","author":"Micol","year":"1995","journal-title":"Biol Conserv"},{"issue":"1","key":"2024082222521651100_msae121-B73","doi-asserted-by":"crossref","first-page":"msac277","DOI":"10.1093\/molbev\/msac277","article-title":"Long-term small population size, deleterious variation, and altitude adaptation in the Ethiopian wolf, a severely endangered canid","volume":"40","author":"Mooney","year":"2023","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2024082222521651100_msae121-B74","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12711-024-00878-7","article-title":"Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian blue beef cattle","volume":"56","author":"Naji","year":"2024","journal-title":"Genet Sel Evol"},{"issue":"1","key":"2024082222521651100_msae121-B75","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/1471-2164-15-123","article-title":"SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock","volume":"15","author":"Nicolazzi","year":"2014","journal-title":"BMC Genomics"},{"issue":"2","key":"2024082222521651100_msae121-B76","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics"},{"issue":"3","key":"2024082222521651100_msae121-B77","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1534\/genetics.112.145037","article-title":"Ancient admixture in human history","volume":"192","author":"Patterson","year":"2012","journal-title":"Genetics"},{"issue":"12","key":"2024082222521651100_msae121-B78","doi-asserted-by":"crossref","first-page":"e190","DOI":"10.1371\/journal.pgen.0020190","article-title":"Population structure and eigenanalysis","volume":"2","author":"Patterson","year":"2006","journal-title":"PLoS Genet"},{"issue":"5","key":"2024082222521651100_msae121-B79","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1111\/1755-0998.12386","article-title":"DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals","volume":"15","author":"Peng","year":"2015","journal-title":"Mol Ecol Resour"},{"key":"2024082222521651100_msae121-B80","author":"R Core Team"},{"issue":"9","key":"2024082222521651100_msae121-B81","doi-asserted-by":"crossref","first-page":"2273","DOI":"10.1093\/molbev\/msv106","article-title":"The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other compositae crops","volume":"32","author":"Renaut","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2024082222521651100_msae121-B82","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev-animal-080522-093311","article-title":"Deleterious variation in natural populations and implications for conservation genetics","volume":"11","author":"Robinson","year":"2023","journal-title":"Annu Rev Anim Biosci"},{"issue":"9","key":"2024082222521651100_msae121-B83","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1016\/j.cub.2016.02.062","article-title":"Genomic flatlining in the endangered island fox","volume":"26","author":"Robinson","year":"2016","journal-title":"Curr Biol"},{"issue":"5","key":"2024082222521651100_msae121-B84","doi-asserted-by":"crossref","first-page":"eaau0757","DOI":"10.1126\/sciadv.aau0757","article-title":"Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction","volume":"5","author":"Robinson","year":"2019","journal-title":"Sci Adv"},{"issue":"3","key":"2024082222521651100_msae121-B85","doi-asserted-by":"crossref","first-page":"giaa021","DOI":"10.1093\/gigascience\/giaa021","article-title":"De novo assembly of the cattle reference genome with single-molecule sequencing","volume":"9","author":"Rosen","year":"2020","journal-title":"Gigascience"},{"issue":"1","key":"2024082222521651100_msae121-B86","doi-asserted-by":"crossref","first-page":"8820","DOI":"10.1038\/s41598-017-08820-2","article-title":"Rapid dwarfing of an insular mammal\u2014the feral cattle of Amsterdam Island","volume":"7","author":"Rozzi","year":"2017","journal-title":"Sci Rep"},{"issue":"6636","key":"2024082222521651100_msae121-B87","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1126\/science.add8606","article-title":"Dwarfism and gigantism drive human-mediated extinctions on islands","volume":"379","author":"Rozzi","year":"2023","journal-title":"Science"},{"issue":"4","key":"2024082222521651100_msae121-B88","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol Biol Evol"},{"issue":"12","key":"2024082222521651100_msae121-B89","doi-asserted-by":"crossref","first-page":"3642","DOI":"10.1093\/molbev\/msaa169","article-title":"Recent demographic history inferred by high-resolution analysis of linkage disequilibrium","volume":"37","author":"Santiago","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2024082222521651100_msae121-B90","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1186\/s12864-015-2181-1","article-title":"WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle","volume":"16","author":"Semp\u00e9r\u00e9","year":"2015","journal-title":"BMC Genomics"},{"issue":"1","key":"2024082222521651100_msae121-B91","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1146\/annurev.ecolsys.110308.120304","article-title":"The role of propagule pressure in biological invasions","volume":"40","author":"Simberloff","year":"2009","journal-title":"Annu Rev Ecol Evol Syst"},{"issue":"7","key":"2024082222521651100_msae121-B92","doi-asserted-by":"crossref","first-page":"1567","DOI":"10.1111\/mec.16802","article-title":"From high masked to high realized genetic load in inbred Scandinavian wolves","volume":"32","author":"Smeds","year":"2023","journal-title":"Mol Ecol"},{"key":"2024082222521651100_msae121-B93","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/978-3-540-36920-2_8","volume-title":"Biological Invasions. Ecological Studies","author":"Sol","year":"2007"},{"issue":"S1","key":"2024082222521651100_msae121-B94","doi-asserted-by":"crossref","first-page":"S63","DOI":"10.1086\/588304","article-title":"Brain size predicts the success of mammal species introduced into novel environments","volume":"172","author":"Sol","year":"2008","journal-title":"Am Nat"},{"issue":"7","key":"2024082222521651100_msae121-B95","doi-asserted-by":"crossref","first-page":"e171","DOI":"10.1371\/journal.pbio.0050171","article-title":"A new approach for using genome scans to detect recent positive selection in the human genome","volume":"5","author":"Tang","year":"2007","journal-title":"PLoS Biol"},{"issue":"3","key":"2024082222521651100_msae121-B96","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1371\/journal.pbio.0040072","article-title":"A map of recent positive selection in the human genome","volume":"4","author":"Voight","year":"2006","journal-title":"PLoS Biol"},{"issue":"7","key":"2024082222521651100_msae121-B97","doi-asserted-by":"crossref","first-page":"104672","DOI":"10.1016\/j.isci.2022.104672","article-title":"Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations","volume":"25","author":"Ward","year":"2022","journal-title":"Iscience"},{"key":"2024082222521651100_msae121-B98","volume-title":"Genetic data analysis II: methods for discrete population genetic data","author":"Weir","year":"1996"},{"issue":"6","key":"2024082222521651100_msae121-B99","first-page":"1358","article-title":"Estimating F-statistics for the analysis of population structure","volume":"38","author":"Weir","year":"1984","journal-title":"Evolution"},{"issue":"3","key":"2024082222521651100_msae121-B100","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1534\/genetics.114.165423","article-title":"The \u201cdomestication syndrome\u201d in mammals: a unified explanation based on neural crest cell behavior and genetics","volume":"197","author":"Wilkins","year":"2014","journal-title":"Genetics"},{"issue":"1","key":"2024082222521651100_msae121-B101","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41559-018-0746-5","article-title":"Fall webworm genomes yield insights into rapid adaptation of invasive species","volume":"3","author":"Wu","year":"2019","journal-title":"Nat Ecol Evol"},{"issue":"6231","key":"2024082222521651100_msae121-B102","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1126\/science.aaa3952","article-title":"Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding","volume":"348","author":"Xue","year":"2015","journal-title":"Science"},{"issue":"32","key":"2024082222521651100_msae121-B103","doi-asserted-by":"crossref","first-page":"8602","DOI":"10.1073\/pnas.1621096114","article-title":"Detection and quantification of inbreeding depression for complex traits from SNP data","volume":"114","author":"Yengo","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"2024082222521651100_msae121-B104","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/1297-9686-25-4-373","article-title":"Comparison de populations de z\u00e9bu malgache \u00e0 l\u2019aide des distances g\u00e9n\u00e9tiques","volume":"25","author":"Zafindrajaona","year":"1993","journal-title":"Genet Sel Evol"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msae121\/58272179\/msae121.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/41\/7\/msae121\/58888351\/msae121.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/41\/7\/msae121\/58888351\/msae121.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,22]],"date-time":"2024-08-22T19:40:55Z","timestamp":1724355655000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msae121\/7695851"}},"subtitle":[],"editor":[{"given":"Rebekah","family":"Rogers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,6,18]]},"references-count":104,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msae121","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.11.24.568563","asserted-by":"object"}]},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7]]},"published":{"date-parts":[[2024,6,18]]},"article-number":"msae121"}}