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 - GEN A1 - Gonzalez-Fortes, Gloria M. A1 - Tassi, Francesca A1 - Ghirotto, Silvia A1 - Henneberger, Kirstin A1 - Hofreiter, Michael A1 - Barbujani, Guido T1 - The Neolithic transition at the Western edge of Europe T2 - American journal of physical anthropology Y1 - 2017 SN - 0002-9483 SN - 1096-8644 VL - 162 SP - 198 EP - 198 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 - 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 - 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 - 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 - 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 -