title: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data.
abstract: Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
authors.forename: Hao-Chih
authors.initials: HC
authors.lastname: Kuo
authors.affiliation: Center for General Education, National Taipei University, New Taipei City, 23741, Taiwan.
authors.forename: Shiang-Fan
authors.initials: SF
authors.lastname: Chen
authors.affiliation: Department of Biological Resources, National Chiayi University, Chiayi City, 60004, Taiwan.
authors.forename: Yin-Ping
authors.initials: YP
authors.lastname: Fang
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
authors.forename: James A
authors.initials: JA
authors.lastname: Cotton
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
authors.forename: Joe D
authors.initials: JD
authors.lastname: Parker
authors.affiliation: Department of Zoology, Hungarian Natural History Museum, 1088, Budapest, Hungary.
authors.forename: Gábor
authors.initials: G
authors.lastname: Csorba
authors.affiliation: Department of Natural History, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada.
authors.forename: Burton K
authors.initials: BK
authors.lastname: Lim
authors.affiliation: Department of Natural History, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada.
authors.forename: Judith L
authors.initials: JL
authors.lastname: Eger
authors.affiliation: Shei-Pa National Park Headquarters, Miaoli County, 36443, Taiwan.
authors.forename: Chia-Hong
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Division of Zoology, Endemic Species Research Institute, Nantou County, 552, Taiwan.
authors.forename: Cheng-Han
authors.initials: CH
authors.lastname: Chou
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Rossiter
mesh_terms: D000818:Animals; D002685:Chiroptera / Q000145:classification* / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D051456:Gene Flow; D049810:Genetic Speciation; D005828:Genetics, Population; D062312:Islands; D018895:Microsatellite Repeats; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Murina; Taiwan; gene flow; introgressive hybridization; nonallopatric divergence