TY - JOUR A1 - Westbury, Michael V. A1 - Dalerumb, Fredrik A1 - Noren, Karin A1 - Hofreiter, Michael T1 - Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations JF - Mitochondrial DNA. Part B N2 - The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae. KW - Phylogenetics KW - mitochondria KW - iterative mapping KW - Canidae Y1 - 2017 U6 - https://doi.org/10.1080/23802359.2017.1331325 SN - 2380-2359 VL - 2 IS - 1 SP - 298 EP - 299 PB - Routledge, Taylor & Francis Group CY - London ER - TY - JOUR A1 - Kehlmaier, Christian A1 - Barlow, Axel A1 - Hastings, Alexander K. A1 - Vamberger, Melita A1 - Paijmans, Johanna L. A. A1 - Steadman, David W. A1 - Albury, Nancy A. A1 - Franz, Richard A1 - Hofreiter, Michael A1 - Fritz, Uwe T1 - Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum JF - Proceedings of the Royal Society of London : Series B, Biological sciences N2 - Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact. KW - Bahamas KW - biogeography KW - extinction KW - palaeontology KW - phylogeny Y1 - 2017 U6 - https://doi.org/10.1098/rspb.2016.2235 SN - 0962-8452 SN - 1471-2954 VL - 284 PB - The Royal Society CY - London ER - TY - JOUR A1 - Siska, Veronika A1 - Jones, Eppie Ruth A1 - Jeon, Sungwon A1 - Bhak, Youngjune A1 - Kim, Hak-Min A1 - Cho, Yun Sung A1 - Kim, Hyunho A1 - Lee, Kyusang A1 - Veselovskaya, Elizaveta A1 - Balueva, Tatiana A1 - Gallego-Llorente, Marcos A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Eriksson, Anders A1 - Pinhasi, Ron A1 - Bhak, Jong A1 - Manica, Andrea T1 - Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago JF - Science Advances N2 - Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe. Y1 - 2017 U6 - https://doi.org/10.1126/sciadv.1601877 SN - 2375-2548 VL - 3 IS - 2 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Mohandesan, Elmira A1 - Speller, Camilla F. A1 - Peters, Joris A1 - Uerpmann, Hans-Peter A1 - Uerpmann, Margarethe A1 - De Cupere, Bea A1 - Hofreiter, Michael A1 - Burger, Pamela A. T1 - Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel JF - Molecular ecology resources N2 - The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens. KW - ancient DNA KW - Camelus dromedarius KW - capture enrichment KW - degraded DNA KW - mitochondrial genome (mtDNA) KW - next-generation sequencing Y1 - 2017 U6 - https://doi.org/10.1111/1755-0998.12551 SN - 1755-098X SN - 1755-0998 VL - 17 IS - 2 SP - 300 EP - 313 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Chang, Dan A1 - Knapp, Michael A1 - Enk, Jacob A1 - Lippold, Sebastian A1 - Kircher, Martin A1 - Lister, Adrian M. A1 - MacPhee, Ross D. E. A1 - Widga, Christopher A1 - Czechowski, Paul A1 - Sommer, Robert A1 - Hodges, Emily A1 - Stümpel, Nikolaus A1 - Barnes, Ian A1 - Dalén, Love A1 - Derevianko, Anatoly A1 - Germonpré, Mietje A1 - Hillebrand-Voiculescu, Alexandra A1 - Constantin, Silviu A1 - Kuznetsova, Tatyana A1 - Mol, Dick A1 - Rathgeber, Thomas A1 - Rosendahl, Wilfried A1 - Tikhonov, Alexey N. A1 - Willerslev, Eske A1 - Hannon, Greg A1 - Lalueza i Fox, Carles A1 - Joger, Ulrich A1 - Poinar, Hendrik N. A1 - Hofreiter, Michael A1 - Shapiro, Beth T1 - The evolutionary and phylogeographic history of woolly mammoths BT - a comprehensive mitogenomic analysis JF - Scientific reports N2 - Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths. Y1 - 2017 U6 - https://doi.org/10.1038/srep44585 SN - 2045-2322 VL - 7 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Thomas, Jessica E. A1 - Carvalho, Gary R. A1 - Haile, James A1 - Martin, Michael D. A1 - Castruita, Jose A. Samaniego A1 - Niemann, Jonas A1 - Sinding, Mikkel-Holger S. A1 - Sandoval-Velasco, Marcela A1 - Rawlence, Nicolas J. A1 - Fuller, Errol A1 - Fjeldsa, Jon A1 - Hofreiter, Michael A1 - Stewart, John R. A1 - Gilbert, M. Thomas P. A1 - Knapp, Michael T1 - An ‛Aukward’ tale BT - a genetic approach to discover the whereabouts of the Last Great Auks JF - Genes N2 - One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds. KW - ancient DNA KW - extinct birds KW - mitochondrial genome KW - museum specimens KW - palaeogenomics Y1 - 2017 U6 - https://doi.org/10.3390/genes8060164 SN - 2073-4425 VL - 8 IS - 6 SP - 164 PB - MDPI CY - Basel ER - TY - JOUR A1 - Dolotovskaya, Sofya A1 - Bordallo, Juan Torroba A1 - Haus, Tanja A1 - Noll, Angela A1 - Hofreiter, Michael A1 - Zinner, Dietmar A1 - Roos, Christian T1 - Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio) JF - Zoological Journal of the Linnean Society N2 - Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west-east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested. KW - African green monkeys KW - baboons KW - mitochondrial genomes KW - phylogeny KW - phylogeography Y1 - 2017 U6 - https://doi.org/10.1093/zoolinnean/zlx001 SN - 0024-4082 SN - 1096-3642 VL - 181 IS - 2 SP - 471 EP - 483 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Librado, Pablo A1 - Gamba, Cristina A1 - Gaunitz, Charleen A1 - Sarkissian, Clio Der A1 - Pruvost, Melanie A1 - Albrechtsen, Anders A1 - Fages, Antoine A1 - Khan, Naveed A1 - Schubert, Mikkel A1 - Jagannathan, Vidhya A1 - Serres-Armero, Aitor A1 - Kuderna, Lukas F. K. A1 - Povolotskaya, Inna S. A1 - Seguin-Orlando, Andaine A1 - Lepetz, Sebastien A1 - Neuditschko, Markus A1 - Theves, Catherine A1 - Alquraishi, Saleh A. A1 - Alfarhan, Ahmed H. A1 - Al-Rasheid, Khaled A. S. A1 - Rieder, Stefan A1 - Samashev, Zainolla A1 - Francfort, Henri-Paul A1 - Benecke, Norbert A1 - Hofreiter, Michael A1 - Ludwig, Arne A1 - Keyser, Christine A1 - Marques-Bonet, Tomas A1 - Ludes, Bertrand A1 - Crubezy, Eric A1 - Leeb, Tosso A1 - Willerslev, Eske A1 - Orlando, Ludovic T1 - Ancient genomic changes associated with domestication of the horse JF - Science N2 - The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between similar to 4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs. Y1 - 2017 U6 - https://doi.org/10.1126/science.aam5298 SN - 0036-8075 SN - 1095-9203 VL - 356 SP - 442 EP - 445 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Elsner, Julia A1 - Hofreiter, Michael A1 - Schibler, Joerg A1 - Schlumbaum, Angela T1 - Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum JF - PLoS one Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0177458 SN - 1932-6203 VL - 12 SP - 17246 EP - 17256 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Meyer, Matthias A1 - Palkopoulou, Eleftheria A1 - Baleka, Sina Isabelle A1 - Stiller, Mathias A1 - Penkman, Kirsty E. H. A1 - Alt, Kurt W. A1 - Ishida, Yasuko A1 - Mania, Dietrich A1 - Mallick, Swapan A1 - Meijer, Tom A1 - Meller, Harald A1 - Nagel, Sarah A1 - Nickel, Birgit A1 - Ostritz, Sven A1 - Rohland, Nadin A1 - Schauer, Karol A1 - Schueler, Tim A1 - Roca, Alfred L. A1 - Reich, David A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution JF - eLife N2 - The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods similar to 120 and similar to 244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision. Y1 - 2017 U6 - https://doi.org/10.7554/eLife.25413 SN - 2050-084X VL - 6 PB - eLife Sciences Publications CY - Cambridge ER -