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Pleistocene glaciation has been implicated in shaping the contemporary genetic differentiation between populations of the aquatic snail <jats:italic>Potamopyrgus antipodarum<\/jats:italic>. We investigated whether similar phylogeographic patterns exist for the snail's locally adapted trematode parasite, <jats:italic>Atriophallophorus winterbourni<\/jats:italic>. We found evidence for a barrier to gene\u2010flow in sympatry between cryptic, but ecologically divergent species. When focusing on the most common of these species, disjunct geographic distributions are found for mitochondrial lineages that diverged during the Pleistocene. The boundary between these distributions is found in the central part of the South Island and is reinforced by low cross\u2010alpine migration. Further support for a vicariant origin of the phylogeographic pattern was found when assessing nuclear multilocus SNP data. Nuclear and mitochondrial population differentiation was concordant in pattern, except for populations in a potential secondary contact zone. Additionally, we found larger than expected differentiation between nuclear\u2010 and mitochondrial\u2010based empirical Bayes <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> estimates (global <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>: 0.02 vs. 0.39 for nuclear and mitochondrial data, respectively). Population subdivision is theoretically expected to be stronger for mitochondrial genomes due to a smaller effective population size, but the strong difference here, together with mitonuclear discordance in a putative contact zone, is potentially indicative of divergent gene flow of nuclear and mitochondrial genomes.<\/jats:p>","DOI":"10.1111\/mec.16570","type":"journal-article","created":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T07:59:12Z","timestamp":1655798352000},"page":"4112-4126","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Phylogeography and cryptic species structure of a locally adapted parasite in New Zealand"],"prefix":"10.1111","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5872-8780","authenticated-orcid":false,"given":"Frida","family":"Feijen","sequence":"first","affiliation":[{"name":"Eawag, Swiss Federal Institute of Aquatic Science and Technology  D\u00fcbendorf Switzerland"},{"name":"Department of Environmental Systems Sciences ETH\u2010Zurich, Institute of Integrative Biology  Z\u00fcrich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Zajac","sequence":"additional","affiliation":[{"name":"Eawag, Swiss Federal Institute of Aquatic Science and Technology  D\u00fcbendorf Switzerland"},{"name":"Department of Environmental Systems Sciences ETH\u2010Zurich, Institute of Integrative Biology  Z\u00fcrich Switzerland"},{"name":"Functional Genomics Center Z\u00fcrich ETH Z\u00fcrich\/University of Z\u00fcrich  Z\u00fcrich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Vorburger","sequence":"additional","affiliation":[{"name":"Eawag, Swiss Federal Institute of Aquatic Science and Technology  D\u00fcbendorf Switzerland"},{"name":"Department of Environmental Systems Sciences ETH\u2010Zurich, Institute of Integrative Biology  Z\u00fcrich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Blasco\u2010Costa","sequence":"additional","affiliation":[{"name":"Natural History Museum of Geneva  Geneva 6 Switzerland"},{"name":"Department of Arctic and Marine Biology UiT The Arctic University of Norway  Troms\u00f8 Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jukka","family":"Jokela","sequence":"additional","affiliation":[{"name":"Eawag, Swiss Federal Institute of Aquatic Science and Technology  D\u00fcbendorf Switzerland"},{"name":"Department of Environmental Systems Sciences ETH\u2010Zurich, Institute of Integrative Biology  Z\u00fcrich Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,7,4]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.116.037275"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1130\/0016\u20107606(2000)112<0250:Taotdo>2.3.Co;2"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u2010294X.2005.02766.x"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/121.3.613"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/103.3.513"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182013000784"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0022149X19000993"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2010.08.010"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.3354\/meps09659"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006650"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss086"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12413"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2109"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558\u20105646.1996.tb03615.x"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12686\u2010011\u20109548\u20107"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1755\u20100998.2010.02847.x"},{"key":"e_1_2_9_18_1","volume-title":"Looking\u2010Glass Parasites (PhD)","author":"Feijen F. 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