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Its original range was from the Black Sea (eastern Mediterranean) to Gambia (western African coast), but was drastically reduced by commercial hunting and human persecution since the early stages of marine exploitation.<\/jats:p><jats:p>We here analyse 42 mitogenomes of Mediterranean monk seals, from across their present and historical geographic ranges to assess the species population dynamics over time. Our data show a decrease in genetic diversity in the last 200 years. Extant individuals presented an almost four-fold reduction in genetic diversity when compared to historical specimens. We also detect, for the first time, a clear segregation between the two North Atlantic populations, Madeira and Cabo Blanco, regardless of their geographical proximity. Moreover, we show the presence of historical gene-flow between the two water basins, the Atlantic Ocean and the Mediterranean Sea, and the presence of at least one extinct maternal lineage in the Mediterranean. Our work demonstrates the advantages of using full mitogenomes in phylogeographic and conservation genomic studies of threatened species.<\/jats:p>","DOI":"10.1093\/zoolinnean\/zlaa084","type":"journal-article","created":{"date-parts":[[2020,6,29]],"date-time":"2020-06-29T19:16:39Z","timestamp":1593458199000},"page":"1147-1159","source":"Crossref","is-referenced-by-count":13,"title":["Mitogenomics of the endangered Mediterranean monk seal (<i>Monachus monachus<\/i>) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations"],"prefix":"10.1093","volume":"191","author":[{"given":"Alba","family":"Rey-Iglesia","sequence":"first","affiliation":[{"name":"Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen , Copenhagen, Denmark"}]},{"given":"Philippe","family":"Gaubert","sequence":"additional","affiliation":[{"name":"Laboratoire Evolution et Diversit\u00e9 Biologique, UPS\/CNRS\/IRD, Universit\u00e9 Paul Sabatier , Toulouse, France"},{"name":"CIIMAR, Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es , Avenida General Norton de Matos, Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5019-9439","authenticated-orcid":false,"given":"Gon\u00e7alo","family":"Espregueira Themudo","sequence":"additional","affiliation":[{"name":"CIIMAR, Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es , Avenida General Norton de Matos, Matosinhos, Portugal"}]},{"given":"Rosa","family":"Pires","sequence":"additional","affiliation":[{"name":"Instituto das Florestas e Conserva\u00e7\u00e3o da Natureza, IP-RAM , Jardim Bot\u00e2nico da Madeira - Eng.\u00ba Rui Vieira, Caminho do Meio, Bom Sucesso, Funchal, Madeira, Portugal"}]},{"given":"Constanza","family":"de la Fuente","sequence":"additional","affiliation":[{"name":"Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen , Copenhagen, Denmark"},{"name":"Department of Human Genetics, University of Chicago , Chicago, USA"}]},{"given":"Lu\u00eds","family":"Freitas","sequence":"additional","affiliation":[{"name":"Museu da Baleia da Madeira , Rua da Pedra D\u2019Eira, Cani\u00e7al, Madeira, Portugal"}]},{"given":"Alex","family":"Aguilar","sequence":"additional","affiliation":[{"name":"IRBio and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona , Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6714-0724","authenticated-orcid":false,"given":"Asunci\u00f3n","family":"Borrell","sequence":"additional","affiliation":[{"name":"IRBio and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona , Barcelona, Spain"}]},{"given":"Tatiana","family":"Krakhmalnaya","sequence":"additional","affiliation":[{"name":"National Museum of Natural History, National Academy of Sciences of Ukraine , Kyiv, Ukraine"}]},{"given":"Raquel","family":"Vasconcelos","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1285-4671","authenticated-orcid":false,"given":"Paula F","family":"Campos","sequence":"additional","affiliation":[{"name":"Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen , Copenhagen, Denmark"},{"name":"CIIMAR, Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es , Avenida General Norton de Matos, Matosinhos, 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