{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T15:55:50Z","timestamp":1765554950798,"version":"3.37.3"},"reference-count":139,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T00:00:00Z","timestamp":1546905600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0210282","type":"journal-article","created":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T18:26:23Z","timestamp":1546971983000},"page":"e0210282","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":36,"title":["Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3633-7217","authenticated-orcid":true,"given":"Jo\u00e3o","family":"Queir\u00f3s","sequence":"first","affiliation":[]},{"given":"Pelayo","family":"Acevedo","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o P. V.","family":"Santos","sequence":"additional","affiliation":[]},{"given":"Jose","family":"Barasona","sequence":"additional","affiliation":[]},{"given":"Beatriz","family":"Beltran-Beck","sequence":"additional","affiliation":[]},{"given":"David","family":"Gonz\u00e1lez-Barrio","sequence":"additional","affiliation":[]},{"given":"Jose A.","family":"Armenteros","sequence":"additional","affiliation":[]},{"given":"Iratxe","family":"Diez-Delgado","sequence":"additional","affiliation":[]},{"given":"Mariana","family":"Boadella","sequence":"additional","affiliation":[]},{"given":"Isabel","family":"Fernand\u00e9z de Mera","sequence":"additional","affiliation":[]},{"given":"Jose F.","family":"Ruiz-Fons","sequence":"additional","affiliation":[]},{"given":"Joaquin","family":"Vicente","sequence":"additional","affiliation":[]},{"given":"Jose","family":"de la Fuente","sequence":"additional","affiliation":[]},{"given":"Christian","family":"Gort\u00e1zar","sequence":"additional","affiliation":[]},{"given":"Jeremy B.","family":"Searle","sequence":"additional","affiliation":[]},{"given":"Paulo C.","family":"Alves","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,1,8]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"e28554","DOI":"10.1371\/journal.pone.0028554","article-title":"Pleistocene climate, phylogeny, and climate envelope models: an integrative approach to better understand species\u2019 response to climate change","volume":"6","author":"AM Lawing","year":"2011","journal-title":"PLoS One"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1111\/j.1466-8238.2011.00686.x","article-title":"Refugia: identifying and understanding safe havens for biodiversity under climate change","volume":"21","author":"G Keppel","year":"2012","journal-title":"Glob Ecol Biogeogr"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1111\/j.1095-8312.1999.tb01160.x","article-title":"Post-glacial re-colonization of European biota","volume":"68","author":"GM Hewitt","year":"1999","journal-title":"Biol J Linn Soc"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1046\/j.1365-294x.1998.00289.x","article-title":"Comparative phylogeography and postglacial colonization routes in Europe","volume":"7","author":"P Taberlet","year":"1998","journal-title":"Mol Ecol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"R584","DOI":"10.1016\/j.cub.2009.06.030","article-title":"Ecological change, range fluctuations and population dynamics during the Pleistocene","volume":"19","author":"M Hofreiter","year":"2009","journal-title":"Curr Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1016\/j.tree.2008.06.010","article-title":"Phylogeographic insights into cryptic glacial refugia","volume":"23","author":"J Provan","year":"2008","journal-title":"Trends Ecol Evol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1742-9994-9-22","article-title":"Extra-Mediterranean refugia: the rule and not the exception","volume":"9","author":"T Schmitt","year":"2012","journal-title":"Front Zool"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"43533","DOI":"10.1038\/srep43533","article-title":"Extra-Mediterranean glacial refugia in a Mediterranean faunal element: the phylogeography of the chalk-hill blue <italic>Polyommatus coridon<\/italic>","volume":"7","author":"G K\u00fchne","year":"2017","journal-title":"Sci Rep"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.quascirev.2014.05.026","article-title":"Origin of British and Irish mammals: disparate post-glacial colonisation and species introductions","volume":"98","author":"WI Montgomery","year":"2014","journal-title":"Quat Sci Rev"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/08912963.2017.1384473","article-title":"Post-glacial colonization of Western Europe brown bears from a cryptic Atlantic refugium out of the Iberian Peninsula","volume":"2963","author":"A Garc\u00eda-V\u00e1zquez","year":"2017","journal-title":"Hist Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"14860","DOI":"10.1073\/pnas.0603237103","article-title":"A northern glacial refugium for bank voles (<italic>Clethrionomys glareolus<\/italic>)","volume":"103","author":"P Kotl\u00edk","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1111\/j.1469-7998.2010.00699.x","article-title":"Phylogeographic signatures of northward post-glacial colonization from high-latitude refugia: a case study of bank voles using museum specimens","volume":"281","author":"JM W\u00f3jcik","year":"2010","journal-title":"J Zool"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1098\/rspb.1998.0423","article-title":"Mediterranean Europe as an area of endemism for small mammals rather than a source for northwards postglacial colonization","volume":"265","author":"DT Bilton","year":"1998","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1098\/rspb.2009.1272","article-title":"Refugia revisited: individualistic responses of species in space and time","volume":"277","author":"JR Stewart","year":"2010","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"4711","DOI":"10.1111\/mec.12420","article-title":"Late-glacial recolonization and phylogeography of European red deer (<italic>Cervus elaphus<\/italic> L.)","volume":"22","author":"M Meiri","year":"2013","journal-title":"Mol Ecol"},{"article-title":"The atlas of European mammals","year":"1999","author":"AJ Mitchell-Jones","key":"ref16"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1111\/j.1365-2907.2010.00177.x","article-title":"Phylogeography, population genetics and conservation of the European red deer <italic>Cervus elaphus<\/italic>","volume":"41","author":"FE Zachos","year":"2011","journal-title":"Mamm Rev"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1016\/j.ympev.2003.10.003","article-title":"Mitochondrial DNA phylogeography of red deer (<italic>Cervus elaphus<\/italic>)","volume":"31","author":"CJ Ludt","year":"2004","journal-title":"Mol Phylogenet Evol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1111\/j.1365-2699.2008.01986.x","article-title":"Phylogeography of red deer (<italic>Cervus elaphus<\/italic>) in Europe","volume":"36","author":"A Skog","year":"2009","journal-title":"J Biogeogr"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1016\/j.ympev.2004.07.013","article-title":"Evolution and phylogeny of Old World deer","volume":"33","author":"C Pitra","year":"2004","journal-title":"Mol Phylogenet Evol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1093\/molbev\/msi145","article-title":"Time dependency of molecular rate estimates and systematic overestimation of recent divergence times","volume":"22","author":"SYW Ho","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"3601","DOI":"10.1098\/rspb.2011.0321","article-title":"Post-glacial partitioning of mitochondrial genetic variation in the field vole","volume":"278","author":"JS Herman","year":"2011","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/j.cub.2013.02.044","article-title":"A revised timescale for human evolution based on ancient mitochondrial genomes","volume":"23","author":"Q Fu","year":"2013","journal-title":"Curr Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"5205","DOI":"10.1111\/mec.12462","article-title":"Divergent evolutionary processes associated with colonization of offshore islands","volume":"22","author":"N Mart\u00ednkov\u00e1","year":"2013","journal-title":"Mol Ecol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.quascirev.2007.11.016","article-title":"Late Quaternary distribution dynamics and phylogeography of the red deer (<italic>Cervus elaphus<\/italic>) in Europe","volume":"27","author":"RS Sommer","year":"2008","journal-title":"Quat Sci Rev"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"20160095","DOI":"10.1098\/rspb.2016.0095","article-title":"Colonization of the Scottish islands via long-distance Neolithic transport of red deer (<italic>Cervus elaphus<\/italic>)","volume":"283","author":"DWG Stanton","year":"2016","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref27","first-page":"155","article-title":"Phylogeography of Southern European Refugia","author":"A G\u00f3mez","year":"2007"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.quaint.2010.04.017","article-title":"Geographical distribution of Pleistocene cold-adapted large mammal faunas in the Iberian Peninsula","volume":"233","author":"DJ \u00c1lvarez-Lao","year":"2011","journal-title":"Quat Int"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1111\/j.1095-8312.1996.tb01434.x","article-title":"Some genetic consequences of ice ages, and their role in divergence and speciation","volume":"58","author":"G Hewitt","year":"1996","journal-title":"Biol J Linn Soc"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1191\/0309133306pp481ra","article-title":"Quaternary glacial history of the Mediterranean mountains","volume":"30","author":"DP Hughes","year":"2006","journal-title":"Prog Phys Geogr"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2034","DOI":"10.1038\/srep02034","article-title":"Early maximum extent of paleoglaciers from Mediterranean mountains during the last glaciation","volume":"3","author":"D Dom\u00ednguez-Villar","year":"2013","journal-title":"Sci Rep"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1111\/mec.13994","article-title":"Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole","volume":"26","author":"S Barbosa","year":"2017","journal-title":"Mol Ecol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S1367943001001019","article-title":"A mitochondrial DNA control region phylogeny of the Cervinae: speciation in <italic>Cervus<\/italic> and implications for conservation","volume":"4","author":"E Randi","year":"2001","journal-title":"Anim Conserv"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/j.1365-2907.2006.00093.x","article-title":"Glacial refugia of mammals in Europe: evidence from fossil records","volume":"36","author":"RS Sommer","year":"2006","journal-title":"Mamm Rev"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1007\/s10531-013-0585-2","article-title":"Mitochondrial D-loop phylogeny signals two native Iberian red deer (<italic>Cervus elaphus)<\/italic> lineages genetically different to Western and Eastern European red deer and infers human-mediated translocations","volume":"23","author":"JL Fern\u00e1ndez-Garc\u00eda","year":"2013","journal-title":"Biodivers Conserv"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1002\/ece3.1836","article-title":"Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity","volume":"6","author":"J Carranza","year":"2016","journal-title":"Ecol Evol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"10690","DOI":"10.1002\/ece3.3553","article-title":"Mitochondrial DNA of pre-last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species","volume":"7","author":"A Rey-Iglesia","year":"2017","journal-title":"Ecol Evol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/S1631-0691(03)00025-8","article-title":"Genetic diversity in European red deer (<italic>Cervus elaphus<\/italic> L.): anthropogenic influences on natural populations","volume":"326","author":"GB Hartl","year":"2003","journal-title":"C R Biol"},{"year":"1968","key":"ref39","article-title":"Mapa Cineg\u00e9tico Nacional"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"39","DOI":"10.5735\/086.046.0105","article-title":"Human-induced range expansion of wild ungulates causes niche overlap between previously allopatric species: red deer and Iberian ibex in mountainous regions of southern Spain","volume":"46","author":"P Acevedo","year":"2009","journal-title":"Ann Zool Fennici"},{"key":"ref41","first-page":"392","article-title":"U","author":"J Vingada","year":"2010"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1111\/bij.12183","article-title":"The impact of management practices and past demographic history on the genetic diversity of red deer (<italic>Cervus elaphus<\/italic>): an assessment of population and individual fitness","volume":"111","author":"J Queir\u00f3s","year":"2014","journal-title":"Biol J Linn Soc"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"3071","DOI":"10.1111\/j.1365-294X.2004.02279.x","article-title":"Phylogeography of roe deer (<italic>Capreolus capreolus<\/italic>) populations: the effects of historical genetic subdivisions and recent nonequilibrium dynamics","volume":"13","author":"E Randi","year":"2004","journal-title":"Mol Ecol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1111\/1755-0998.12349","article-title":"Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications","volume":"15","author":"J Queir\u00f3s","year":"2015","journal-title":"Mol Ecol Resour"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1111\/j.1471-8286.2004.00684.x","article-title":"Micro-checker: software for identifying and correcting genotyping errors in microsatellite data","volume":"4","author":"C Van Oosterhout","year":"2004","journal-title":"Mol Ecol Notes"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1093\/oxfordjournals.jhered.a111573","article-title":"GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism","volume":"86","author":"M Raymond","year":"1995","journal-title":"J Hered"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1111\/j.1558-5646.1989.tb04220.x","article-title":"Analyzing tables of statistical tests","volume":"43","author":"W Rice","year":"1989","journal-title":"Evolution"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1046\/j.1365-294x.1998.00404.x","article-title":"Genetic variation and population structure of the Japanese sika deer (<italic>Cervus nippon<\/italic>) in Hokkaido Island, based on mitochondrial D-loop sequences","volume":"7","author":"J Nagata","year":"1998","journal-title":"Mol Ecol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/bts460","article-title":"GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update","volume":"28","author":"R Peakall","year":"2012","journal-title":"Bioinformatics"},{"key":"ref50","article-title":"FSTAT, a program to estimate and test gene diversities and fixation indices","author":"J Goudet","year":"2001","journal-title":"FSTAT, a program to estimate and test gene diversities and fixation indices"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1093\/genetics\/144.4.2001","article-title":"Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data","volume":"144","author":"JM Cornuet","year":"1996","journal-title":"Genetics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"3166","DOI":"10.1073\/pnas.91.8.3166","article-title":"Mutational processes of simple-sequence repeat loci in human populations","volume":"91","author":"A Di Rienzo","year":"1994","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1046\/j.1523-1739.1998.96388.x","article-title":"Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data","volume":"12","author":"G Luikart","year":"1998","journal-title":"Conserv Biol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1017\/S0016672300013446","article-title":"Mixed self and random mating at two loci","volume":"21","author":"BS Weir","year":"1973","journal-title":"Genet Res"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1093\/genetics\/145.4.1219","article-title":"Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance","volume":"145","author":"F Rousset","year":"1997","journal-title":"Genetics"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"JK Pritchard","year":"2000","journal-title":"Genetics"},{"key":"ref57","article-title":"GENETIX 4.05, logiciel sous Windows TM pour la g\u00e9n\u00e9tique des populations","author":"K Belkhir","year":"2004","journal-title":"GENETIX 4.05, logiciel sous Windows TM pour la g\u00e9n\u00e9tique des populations"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1567","DOI":"10.1093\/genetics\/164.4.1567","article-title":"Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies","volume":"164","author":"D Falush","year":"2003","journal-title":"Genetics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"G Evanno","year":"2005","journal-title":"Mol Ecol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"DA Earl","year":"2011","journal-title":"Conserv Genet Resour"},{"article-title":"Molecular evolutionary genetics","year":"1987","author":"M Nei","key":"ref61"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"5269","DOI":"10.1073\/pnas.76.10.5269","article-title":"Mathematical model for studying genetic variation in terms of restriction endonucleases","volume":"76","author":"M Nei","year":"1979","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: a software for comprehensive analysis of DNA poly-morphism data","volume":"25","author":"P Librado","year":"2009","journal-title":"Bioinformatics"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","article-title":"Statistical method for testing the neutral mutation hypothesis by DNA polymorphism","volume":"123","author":"F Tajima","year":"1989","journal-title":"Genetics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1093\/genetics\/147.2.915","article-title":"Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection","volume":"147","author":"Y-X Fu","year":"1997","journal-title":"Genetics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1111\/j.1755-0998.2010.02847.x","article-title":"Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows","volume":"10","author":"L Excoffier","year":"2010","journal-title":"Mol Ecol Resour"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/j.1469-7998.2006.00123.x","article-title":"Genetic variability and differentiation in red deer (<italic>Cervus elaphus<\/italic>) from Scotland and England","volume":"270","author":"SS Hmwe","year":"2006","journal-title":"J Zool"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.mambio.2009.03.015","article-title":"Genetic structure of, and hybridisation between, red (<italic>Cervus elaphus<\/italic>) and sika (<italic>Cervus nippon<\/italic>) deer in Ireland","volume":"74","author":"AD McDevitt","year":"2009","journal-title":"Mamm Biol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1111\/j.1095-8312.2008.01115.x","article-title":"Genetic structure of the Danish red deer (<italic>Cervus elaphus<\/italic>)","volume":"95","author":"EK Nielsen","year":"2008","journal-title":"Biol J Linn Soc"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/sj.hdy.6800838","article-title":"Genetic consequences of human management in an introduced island population of red deer (<italic>Cervus elaphus<\/italic>)","volume":"97","author":"DH Nussey","year":"2006","journal-title":"Heredity"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/hdy.2008.111","article-title":"Genetic diversity and population structure of Scottish Highland red deer (<italic>Cervus elaphus<\/italic>) populations: a mitochondrial survey","volume":"102","author":"S P\u00e9rez-Espona","year":"2009","journal-title":"Heredity"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/1471-2148-12-191","article-title":"Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA","volume":"12","author":"J Rosvold","year":"2012","journal-title":"BMC Evol Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.mambio.2017.04.005","article-title":"The presence of Balkan and Iberian red deer (<italic>Cervus elaphus<\/italic>) mitochondrial DNA lineages in the Carpathian Basin","volume":"86","author":"K Frank","year":"2017","journal-title":"Mamm Biol"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1093\/jhered\/esv018","article-title":"Admixture of eastern and western European red deer lineages as a result of postglacial recolonization of the Czech Republic (Central Europe)","volume":"106","author":"J Krojerova-Prokesova","year":"2015","journal-title":"J Hered"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0163191","article-title":"Purifying selection, density blocking and unnoticed mitochondrial DNA diversity in the red deer, <italic>Cervus elaphus<\/italic>","volume":"11","author":"Z Borowski","year":"2016","journal-title":"PLoS One"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"e100136","DOI":"10.1371\/journal.pone.0100136","article-title":"Positioning the red deer (<italic>Cervus elaphus<\/italic>) hunted by the Tyrolean Iceman into a mitochondrial DNA phylogeny","volume":"9","author":"C Olivieri","year":"2014","journal-title":"PLoS One"},{"key":"ref77","first-page":"1","article-title":"Genetic diversity, genetic structure and diet of ancient and contemporary red deer (<italic>Cervus elaphus<\/italic> L.) from north-eastern France","volume":"13","author":"A Schnitzler","year":"2018","journal-title":"PLoS One"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/jhered\/esu007","article-title":"Greece: a Balkan subrefuge for a remnant red deer (<italic>Cervus elaphus<\/italic>) population","volume":"105","author":"N Karaiskou","year":"2014","journal-title":"J Hered"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1644\/11-MAMM-A-022.1","article-title":"Hybridization between native and introduced species of deer in Eastern Europe","volume":"93","author":"A Biedrzycka","year":"2012","journal-title":"J Mammal"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.quascirev.2012.02.012","article-title":"Phylogeographic, ancient DNA, fossil and morphometric analyses reveal ancient and modern introductions of a large mammal: the complex case of red deer (<italic>Cervus elaphus<\/italic>) in Ireland","volume":"42","author":"RF Carden","year":"2012","journal-title":"Quat Sci Rev"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.mambio.2011.11.005","article-title":"Crossing the border? structure of the red deer (<italic>Cervus elaphus<\/italic>) population from the Bavarian\u2013Bohemian forest ecosystem","volume":"77","author":"J Fickel","year":"2012","journal-title":"Mamm Biol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1007\/s10592-010-0048-1","article-title":"Consequences for genetic diversity and population performance of introducing continental red deer into the northern distribution range","volume":"11","author":"H Haanes","year":"2010","journal-title":"Conserv Genet"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/oxfordjournals.molbev.a026036","article-title":"Median-joining networks for inferring intraspecific phylogenies","volume":"16","author":"HJ Bandelt","year":"1999","journal-title":"Mol Biol Evol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s13364-010-0002-0","article-title":"Molecular biogeography of red deer <italic>Cervus elaphus<\/italic> from eastern Europe: insights from mitochondrial DNA sequences","volume":"56","author":"M Niedzia\u0142kowska","year":"2011","journal-title":"Acta Theriol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"AJ Drummond","year":"2012","journal-title":"Mol Biol Evol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"D Darriba","year":"2012","journal-title":"Nat Methods"},{"key":"ref87","article-title":"Tracer v1.5","author":"A Rambaut","year":"2007","journal-title":"Tracer v1.5"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1093\/bioinformatics\/btt763","article-title":"DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data","volume":"30","author":"J-M Cornuet","year":"2014","journal-title":"Bioinformatics"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1093\/genetics\/162.4.2025","article-title":"Approximate Bayesian computation in population genetics","volume":"162","author":"MA Beaumont","year":"2002","journal-title":"Genetics"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1111\/j.1365-294X.2010.04690.x","article-title":"ABC as a flexible framework to estimate demography over space and time: some cons, many pros","volume":"19","author":"G Bertorelle","year":"2010","journal-title":"Mol Ecol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"6188","DOI":"10.1111\/mec.13457","article-title":"Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach","volume":"24","author":"J Ortego","year":"2015","journal-title":"Mol Ecol"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"3110","DOI":"10.1002\/ece3.2810","article-title":"Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper","volume":"7","author":"V Noguerales","year":"2017","journal-title":"Ecol Evol"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"2713","DOI":"10.1093\/bioinformatics\/btn514","article-title":"Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation","volume":"24","author":"J-M Cornuet","year":"2008","journal-title":"Bioinformatics"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1186\/1471-2105-11-401","article-title":"Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)","volume":"11","author":"J-M Cornuet","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref95","unstructured":"International Union for Conservation of Nature (2015) IUCN. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.iucn.org\/\" xlink:type=\"simple\">http:\/\/www.iucn.org\/<\/ext-link>."},{"key":"ref96","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1002\/joc.1276","article-title":"Very high resolution interpolated climate surfaces for global land areas","volume":"25","author":"RJ Hijmans","year":"2005","journal-title":"Int J Climatol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"261","DOI":"10.5194\/cp-3-261-2007","article-title":"Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum\u2013Part 1: experiments and large-scale features","volume":"3","author":"P Braconnot","year":"2007","journal-title":"Clim Past"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1126\/science.1120808","article-title":"Simulating Arctic climate warmth and icefield retreat in the last interglaciation","volume":"311","author":"BL Otto-Bliesner","year":"2006","journal-title":"Science"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/j.2041-210X.2009.00001.x","article-title":"A protocol for data exploration to avoid common statistical problems","volume":"1","author":"AF Zuur","year":"2010","journal-title":"Methods Ecol Evol"},{"article-title":"Introduction to linear regression analysis","year":"1992","author":"D Montgomery","key":"ref100"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1111\/geb.12007","article-title":"Discrimination capacity in species distribution models depends on the representativeness of the environmental domain","volume":"22","author":"A Jim\u00e9nez-Valverde","year":"2013","journal-title":"Glob Ecol Biogeogr"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1111\/j.2041-210X.2010.00036.x","article-title":"The art of modelling range-shifting species","volume":"1","author":"J Elith","year":"2010","journal-title":"Methods Ecol Evol"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1111\/j.1600-0587.2008.05742.x","article-title":"BIOMOD\u2013a platform for ensemble forecasting of species distributions","volume":"32","author":"W Thuiller","year":"2009","journal-title":"Ecography"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1111\/j.1365-2699.2010.02456.x","article-title":"Ecological niche conservatism: a time-structured review of evidence","volume":"38","author":"AT Peterson","year":"2011","journal-title":"J Biogeogr"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1111\/ecog.00845","article-title":"What do we gain from simplicity versus complexity in species distribution models?","volume":"37","author":"C Merow","year":"2014","journal-title":"Ecography"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1111\/jbi.12556","article-title":"Range dynamics driven by Quaternary climate oscillations explain the distribution of introgressed mtDNA of <italic>Lepus timidus<\/italic> origin in hares from the Iberian Peninsula","volume":"42","author":"P Acevedo","year":"2015","journal-title":"J Biogeogr"},{"key":"ref107","unstructured":"R Core Team (2014) R: a language and environment for statistical computing. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.r-project.org\/\" xlink:type=\"simple\">http:\/\/www.r-project.org\/<\/ext-link>."},{"key":"ref108","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.2458\/azu_js_rc.55.16947","article-title":"IntCal13 and Marine13 radiocarbon age calibration curves 0\u201350,000 years cal BP","volume":"55","author":"PJ Reimer","year":"2013","journal-title":"Radiocarbon"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.1111\/j.0014-3820.2002.tb01480.x","article-title":"Antler size in red deer: heritability and selection but no evolution","volume":"56","author":"EB Kruuk","year":"2002","journal-title":"Evolution"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1126\/science.1172873","article-title":"The Last Glacial Maximum","volume":"325","author":"PU Clark","year":"2009","journal-title":"Science"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1046\/j.1365-294x.2001.01202.x","article-title":"Speciation, hybrid zones and phylogeography\u2014or seeing genes in space and time","volume":"10","author":"GM Hewitt","year":"2001","journal-title":"Mol Ecol"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nature03905","article-title":"A late Eemian aridity pulse in central Europe during the last glacial inception","volume":"436","author":"F Sirocko","year":"2005","journal-title":"Nature"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1016\/j.quascirev.2003.12.008","article-title":"Late Quaternary ice sheet history of northern Eurasia","volume":"23","author":"JI Svendsen","year":"2004","journal-title":"Quat Sci Rev"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1007\/s00382-010-0870-7","article-title":"The sensitivity of the Late Saalian (140 ka) and LGM (21 ka) Eurasian ice sheets to sea surface conditions","volume":"37","author":"F Colleoni","year":"2011","journal-title":"Clim Dyn"},{"key":"ref115","first-page":"1","article-title":"Phylogeography of the Tyrrhenian red deer (<italic>Cervus elaphus corsicanus<\/italic>) resolved using ancient DNA of radiocarbon-dated subfossils","volume":"7","author":"K Doan","year":"2017","journal-title":"Sci Rep"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"20142605","DOI":"10.1098\/rspb.2014.2605","article-title":"New insights on postglacial colonization in western Europe: the phylogeography of the Leisler\u2019s bat (<italic>Nyctalus leisleri)<\/italic>","volume":"282","author":"ESM Boston","year":"2015","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1002\/ece3.2811","article-title":"Species distribution modeling and molecular markers suggest longitudinal range shifts and cryptic northern refugia of the typical calcareous grassland species <italic>Hippocrepis comosa<\/italic> (horseshoe vetch)","author":"M Leipold","year":"2017","journal-title":"Ecol Evol"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1111\/j.1365-2699.2009.02089.x","article-title":"Ice age distributions of European small mammals: insights from species distribution modelling","volume":"36","author":"C Fl\u00f8jgaard","year":"2009","journal-title":"J Biogeogr"},{"key":"ref119","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511607851","article-title":"Europe\u2019s First Farmers","author":"TD Price","year":"2000"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/hdy.2008.133","article-title":"European phylogeography of the common frog (<italic>Rana temporaria<\/italic>): routes of postglacial colonization into the British Isles, and evidence for an Irish glacial refugium","volume":"102","author":"AGF Teacher","year":"2009","journal-title":"Heredity"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/hdy.2013.17","article-title":"Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (<italic>Salmo salar<\/italic> L.) in Northwest Europe","volume":"111","author":"AK Finnegan","year":"2013","journal-title":"Heredity"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1016\/j.tree.2013.09.001","article-title":"Cryptic or mystic? Glacial tree refugia in northern Europe","volume":"28","author":"PC Tzedakis","year":"2013","journal-title":"Trends Ecol Evol"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"263","DOI":"10.3161\/150811014X687233","article-title":"Further evidence for cryptic north-western refugia in Europe? mitochondrial phylogeography of the sibling species <italic>Pipistrellus pipistrellus<\/italic> and <italic>Pipistrellus pygmaeus<\/italic>","volume":"16","author":"ESM Boston","year":"2014","journal-title":"Acta Chiropterologica"},{"key":"ref124","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1007\/s13364-014-0196-7","article-title":"Genetic variability of central-western European pine marten (<italic>Martes martes<\/italic>) populations","volume":"59","author":"C Pertoldi","year":"2014","journal-title":"Acta Theriol"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1002\/jqs.1212","article-title":"Timing of glaciation in the Mediterranean mountains during the last cold stage","volume":"23","author":"P Hughes","year":"2008","journal-title":"J Quat Sci"},{"key":"ref126","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1002\/jqs.638","article-title":"Sea-level change in the Irish Sea since the Last Glacial Maximum: constraints from isostatic modelling","volume":"16","author":"K Lambeck","year":"2001","journal-title":"J Quat Sci"},{"article-title":"European ungulates and their management in the 21st Century","year":"2010","author":"M Apollonio","key":"ref127"},{"key":"ref128","first-page":"81","article-title":"Game species: extinction hidden by census numbers","volume":"26","author":"J Carranza","year":"2003","journal-title":"Anim Biodivers Conserv"},{"key":"ref129","first-page":"109","article-title":"On the evolution of ice age mammals and its signifcance to an understanding of speciations","volume":"30","author":"V Geist","year":"1983","journal-title":"ASB Bull"},{"key":"ref130","first-page":"85","article-title":"Brief report evaluation of genetic variability in introduced populations of red deer (<italic>Cervus elaphus<\/italic>) using DNA fingerprinting","volume":"89","author":"T Perez","year":"1998","journal-title":"Hereditas"},{"key":"ref131","doi-asserted-by":"crossref","first-page":"3452","DOI":"10.1111\/mec.14806","article-title":"Integrative approaches to guide conservation decisions: using genomics to define conservation units and functional corridors","volume":"27","author":"S Barbosa","year":"2018","journal-title":"Mol Ecol"},{"key":"ref132","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/hdy.2010.165","article-title":"Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (<italic>Salmo salar<\/italic>) population following introgression by farmed escapees","volume":"106","author":"V Bourret","year":"2011","journal-title":"Heredity"},{"key":"ref133","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1111\/eva.12160","article-title":"Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Qu\u00e9bec","volume":"7","author":"E Valiquette","year":"2014","journal-title":"Canada. Evol Appl"},{"key":"ref134","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1093\/jhered\/esq049","article-title":"Low heterozygosity at microsatellite markers in Iberian red deer with small antlers","volume":"101","author":"J P\u00e9rez-Gonz\u00e1lez","year":"2010","journal-title":"J Hered"},{"key":"ref135","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1098\/rspb.1998.0363","article-title":"Birth weight and neonatal survival of harbour seal pups are positively correlated with genetic variation measured by microsatellites","volume":"265","author":"DW Coltman","year":"1998","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref136","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1098\/rspb.2000.1192","article-title":"Inbreeding depression influences lifetime breeding success in a wild population of red deer (<italic>Cervus elaphus<\/italic>)","volume":"267","author":"J Slate","year":"2000","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"ref137","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.meegid.2016.05.031","article-title":"Tuberculosis, genetic diversity and fitness in the red deer, <italic>Cervus elaphus<\/italic>","volume":"43","author":"J Queir\u00f3s","year":"2016","journal-title":"Infect Genet Evol"},{"key":"ref138","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1086\/285684","article-title":"Demographic consequences of inbreeding in remnant populations","volume":"144","author":"LS Mills","year":"1994","journal-title":"Am Nat"},{"key":"ref139","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.pt.2006.02.011","article-title":"Parasite prevalence and sample size: misconceptions and solutions","volume":"22","author":"R Jovani","year":"2006","journal-title":"Trends Parasitol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0210282","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,9]],"date-time":"2022-09-09T21:58:28Z","timestamp":1662760708000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0210282"}},"subtitle":[],"editor":[{"given":"Tzen-Yuh","family":"Chiang","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,8]]},"references-count":139,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,1,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0210282","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2019,1,8]]}}}