TY - JOUR A1 - Yuan, Junxia A1 - Sheng, Guilian A1 - Preick, Michaela A1 - Sun, Boyang A1 - Hou, Xindong A1 - Chen, Shungang A1 - Taron, Ulrike Helene A1 - Barlow, Axel A1 - Wang, Linying A1 - Hu, Jiaming A1 - Deng, Tao A1 - Lai, Xulong A1 - Hofreiter, Michael T1 - Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species. KW - Equus dalianensis KW - Equus przewalskii KW - Pleistocene caballine horses KW - ancient DNA KW - phylogenetic relationship KW - divergence time Y1 - 2020 U6 - https://doi.org/10.1016/j.quascirev.2020.106691 SN - 0277-3791 VL - 250 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Vences, Miguel A1 - Köhler, Jörn A1 - Crottini, Angelica A1 - Hofreiter, Michael A1 - Hutter, Carl R. A1 - du Preez, Louis A1 - Preick, Michaela A1 - Rakotoarison, Andolalao A1 - Rancilhac, Loïs A1 - Raselimanana, Achille P. A1 - Rosa, Gonçalo M. A1 - Scherz, Mark D. A1 - Glaw, Frank T1 - An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar JF - Vertebrate zoology N2 - The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy. KW - Amphibia KW - Anura KW - archival DNA KW - Mantellidae KW - new species KW - phylogeography Y1 - 2022 U6 - https://doi.org/10.3897/vz.72.e78830 SN - 1864-5755 SN - 2625-8498 VL - 72 SP - 271 EP - 309 PB - Senckenberg Gesellschaft für Naturforschung CY - Frankfurt am Main ER - TY - JOUR A1 - Hou, Xindong A1 - Zhao, Jian A1 - Zhang, Hucai A1 - Preick, Michaela A1 - Hu, Jiaming A1 - Xiao, Bo A1 - Wang, Linying A1 - Deng, Miaoxuan A1 - Liu, Sizhao A1 - Chang, Fengqin A1 - Sheng, Guilian A1 - Lai, Xulong A1 - Hofreiter, Michael A1 - Yuan, Junxia T1 - Paleogenomes reveal a complex evolutionary history of late Pleistocene bison in Northeastern China JF - Genes N2 - Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct. KW - ancient DNA KW - most recent common ancestor KW - fossil KW - genetic diversity KW - admixture Y1 - 2022 U6 - https://doi.org/10.3390/genes13101684 SN - 2073-4425 VL - 13 IS - 10 PB - MDPI CY - Basel ER - TY - JOUR A1 - Arnold, Patrick A1 - Hagemann, Justus A1 - Gilissen, Emmanuel A1 - Hofreiter, Michael T1 - Otter shrew mitogenomes (Afrotheria, Potamogalidae) reconstructed from historical museum skins JF - Mitochondrial DNA. Part B N2 - African otter shrews (Potamogalidae) are Afrotherian mammals adapted to a semi-aquatic lifestyle. Given their rareness, genetic data on otter shrews are limited. By applying laboratory methods tuned for the recovery of archival DNA and an iterative mapping approach, we reconstructed whole mitochondrial genomes of the Giant (Potamogale velox) and Ruwenzori pygmy otter shrew (Micropotamogale ruwenzorii) from historical museum skins. Phylogenetic analyses are consistent with previous reports in recovering a sister relationship between African otter shrews and Malagasy tenrecs. The long branches separating both lineages, however, support their recognition as separate families. KW - tenrecs KW - Afrotheria KW - Africa KW - historical DNA Y1 - 2022 U6 - https://doi.org/10.1080/23802359.2022.2122747 SN - 2380-2359 VL - 7 IS - 9 SP - 1699 EP - 1701 PB - Taylor & Francis Group CY - London ER -