TY  - JOUR
A1  - Horn, Susanne
A1  - Prost, Stefan
A1  - Stiller, Mathias
A1  - Makowiecki, Daniel
A1  - Kuznetsova, Tatiana
A1  - Benecke, Norbert
A1  - Pucher, Erich
A1  - Hufthammer, Anne K.
A1  - Schouwenburg, Charles
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe
JF  - Molecular ecology
N2  - After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.
KW  - Conservation Biology
KW  - Phylogeography
KW  - Conservation Genetics
KW  - Population Genetics - Empirical
Y1  - 2014
U6  - https://doi.org/10.1111/mec.12691
SN  - 0962-1083
SN  - 1365-294X
VL  - 23
IS  - 7
SP  - 1717
EP  - 1729
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Alter, S. Elizabeth
A1  - Meyer, Matthias
A1  - Post, Klaas
A1  - Czechowski, Paul
A1  - Gravlund, Peter
A1  - Gaines, Cork
A1  - Rosenbaum, Howard C.
A1  - Kaschner, Kristin
A1  - Turvey, Samuel T.
A1  - van der Plicht, Johannes
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100
JF  - Molecular ecology
N2  - Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.
KW  - ancient DNA
KW  - climate change
KW  - last glacial maximum
KW  - marine mammal
Y1  - 2015
U6  - https://doi.org/10.1111/mec.13121
SN  - 0962-1083
SN  - 1365-294X
VL  - 24
IS  - 7
SP  - 1510
EP  - 1522
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Rawlence, Nicolas J.
A1  - Martin, Michael D.
A1  - Ho, Simon Y. W.
A1  - Sigfusson, Arnor P.
A1  - Josefsson, Vigfus A.
A1  - Frederiksen, Morten
A1  - Linnebjerg, Jannie F.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Soares, Andre E. R.
A1  - Lacy, Robert
A1  - Barilaro, Christina
A1  - Best, Juila
A1  - Brandis, Dirk
A1  - Cavallo, Chiara
A1  - Elorza, Mikelo
A1  - Garrett, Kimball L.
A1  - Groot, Maaike
A1  - Johansson, Friederike
A1  - Lifjeld, Jan T.
A1  - Nilson, Goran
A1  - Serjeanston, Dale
A1  - Sweet, Paul
A1  - Fuller, Errol
A1  - Hufthammer, Anne Karin
A1  - Meldgaard, Morten
A1  - Fjeldsa, Jon
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - Demographic reconstruction from ancient DNA supports rapid extinction of the great auk
JF  - eLife
N2  - The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
Y1  - 2019
U6  - https://doi.org/10.7554/eLife.47509
SN  - 2050-084X
VL  - 8
PB  - eLife Sciences Publications
CY  - Cambridge
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  - 
TY  - JOUR
A1  - Barlow, Axel
A1  - Cahill, James A.
A1  - Hartmann, Stefanie
A1  - Theunert, Christoph
A1  - Xenikoudakis, Georgios
A1  - Gonzalez-Fortes, Gloria M.
A1  - Paijmans, Johanna L. A.
A1  - Rabeder, Gernot
A1  - Frischauf, Christine
A1  - Garcia-Vazquez, Ana
A1  - Murtskhvaladze, Marine
A1  - Saarma, Urmas
A1  - Anijalg, Peeter
A1  - Skrbinsek, Tomaz
A1  - Bertorelle, Giorgio
A1  - Gasparian, Boris
A1  - Bar-Oz, Guy
A1  - Pinhasi, Ron
A1  - Slatkin, Montgomery
A1  - Dalen, Love
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Partial genomic survival of cave bears in living brown bears
JF  - Nature Ecology & Evolution
N2  - Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
Y1  - 2018
U6  - https://doi.org/10.1038/s41559-018-0654-8
SN  - 2397-334X
VL  - 2
IS  - 10
SP  - 1563
EP  - 1570
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Schubert, Mikkel
A1  - Jonsson, Hakon
A1  - Chang, Dan
A1  - Sarkissian, Clio Der
A1  - Ermini, Luca
A1  - Ginolhac, Aurelien
A1  - Albrechtsen, Anders
A1  - Dupanloup, Isabelle
A1  - Foucal, Adrien
A1  - Petersen, Bent Larsen
A1  - Fumagalli, Matteo
A1  - Raghavan, Maanasa
A1  - Seguin-Orlando, Andaine
A1  - Korneliussen, Thorfinn S.
A1  - Velazquez, Amhed M. V.
A1  - Stenderup, Jesper
A1  - Hoover, Cindi A.
A1  - Rubin, Carl-Johan
A1  - Alfarhan, Ahmed H.
A1  - Alquraishi, Saleh A.
A1  - Al-Rasheid, Khaled A. S.
A1  - MacHugh, David E.
A1  - Kalbfleisch, Ted
A1  - MacLeod, James N.
A1  - Rubin, Edward M.
A1  - Sicheritz-Ponten, Thomas
A1  - Andersson, Leif
A1  - Hofreiter, Michael
A1  - Marques-Bonet, Tomas
A1  - Gilbert, M. Thomas P.
A1  - Nielsen, Rasmus
A1  - Excoffier, Laurent
A1  - Willerslev, Eske
A1  - Shapiro, Beth
A1  - Orlando, Ludovic
T1  - Prehistoric genomes reveal the genetic foundation and cost of horse domestication
JF  - Proceedings of the National Academy of Sciences of the United States of America
Y1  - 2014
U6  - https://doi.org/10.1073/pnas.1416991111
SN  - 0027-8424
VL  - 111
IS  - 52
SP  - E5661
EP  - E5669
PB  - National Acad. of Sciences
CY  - Washington
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  - Fages, Antoine
A1  - Hanghoj, Kristian
A1  - Khan, Naveed
A1  - Gaunitz, Charleen
A1  - Seguin-Orlando, Andaine
A1  - Leonardi, Michela
A1  - Constantz, Christian McCrory
A1  - Gamba, Cristina
A1  - Al-Rasheid, Khaled A. S.
A1  - Albizuri, Silvia
A1  - Alfarhan, Ahmed H.
A1  - Allentoft, Morten
A1  - Alquraishi, Saleh
A1  - Anthony, David
A1  - Baimukhanov, Nurbol
A1  - Barrett, James H.
A1  - Bayarsaikhan, Jamsranjav
A1  - Benecke, Norbert
A1  - Bernaldez-Sanchez, Eloisa
A1  - Berrocal-Rangel, Luis
A1  - Biglari, Fereidoun
A1  - Boessenkool, Sanne
A1  - Boldgiv, Bazartseren
A1  - Brem, Gottfried
A1  - Brown, Dorcas
A1  - Burger, Joachim
A1  - Crubezy, Eric
A1  - Daugnora, Linas
A1  - Davoudi, Hossein
A1  - Damgaard, Peter de Barros
A1  - de Chorro y de Villa-Ceballos, Maria de los Angeles
A1  - Deschler-Erb, Sabine
A1  - Detry, Cleia
A1  - Dill, Nadine
A1  - Oom, Maria do Mar
A1  - Dohr, Anna
A1  - Ellingvag, Sturla
A1  - Erdenebaatar, Diimaajav
A1  - Fathi, Homa
A1  - Felkel, Sabine
A1  - Fernandez-Rodriguez, Carlos
A1  - Garcia-Vinas, Esteban
A1  - Germonpre, Mietje
A1  - Granado, Jose D.
A1  - Hallsson, Jon H.
A1  - Hemmer, Helmut
A1  - Hofreiter, Michael
A1  - Kasparov, Aleksei
A1  - Khasanov, Mutalib
A1  - Khazaeli, Roya
A1  - Kosintsev, Pavel
A1  - Kristiansen, Kristian
A1  - Kubatbek, Tabaldiev
A1  - Kuderna, Lukas
A1  - Kuznetsov, Pavel
A1  - Laleh, Haeedeh
A1  - Leonard, Jennifer A.
A1  - Lhuillier, Johanna
A1  - von Lettow-Vorbeck, Corina Liesau
A1  - Logvin, Andrey
A1  - Lougas, Lembi
A1  - Ludwig, Arne
A1  - Luis, Cristina
A1  - Arruda, Ana Margarida
A1  - Marques-Bonet, Tomas
A1  - Silva, Raquel Matoso
A1  - Merz, Victor
A1  - Mijiddorj, Enkhbayar
A1  - Miller, Bryan K.
A1  - Monchalov, Oleg
A1  - Mohaseb, Fatemeh A.
A1  - Morales, Arturo
A1  - Nieto-Espinet, Ariadna
A1  - Nistelberger, Heidi
A1  - Onar, Vedat
A1  - Palsdottir, Albina H.
A1  - Pitulko, Vladimir
A1  - Pitskhelauri, Konstantin
A1  - Pruvost, Melanie
A1  - Sikanjic, Petra Rajic
A1  - Papesa, Anita Rapan
A1  - Roslyakova, Natalia
A1  - Sardari, Alireza
A1  - Sauer, Eberhard
A1  - Schafberg, Renate
A1  - Scheu, Amelie
A1  - Schibler, Jorg
A1  - Schlumbaum, Angela
A1  - Serrand, Nathalie
A1  - Serres-Armero, Aitor
A1  - Shapiro, Beth
A1  - Seno, Shiva Sheikhi
A1  - Shevnina, Irina
A1  - Shidrang, Sonia
A1  - Southon, John
A1  - Star, Bastiaan
A1  - Sykes, Naomi
A1  - Taheri, Kamal
A1  - Taylor, William
A1  - Teegen, Wolf-Rudiger
A1  - Vukicevic, Tajana Trbojevic
A1  - Trixl, Simon
A1  - Tumen, Dashzeveg
A1  - Undrakhbold, Sainbileg
A1  - Usmanova, Emma
A1  - Vahdati, Ali
A1  - Valenzuela-Lamas, Silvia
A1  - Viegas, Catarina
A1  - Wallner, Barbara
A1  - Weinstock, Jaco
A1  - Zaibert, Victor
A1  - Clavel, Benoit
A1  - Lepetz, Sebastien
A1  - Mashkour, Marjan
A1  - Helgason, Agnar
A1  - Stefansson, Kari
A1  - Barrey, Eric
A1  - Willerslev, Eske
A1  - Outram, Alan K.
A1  - Librado, Pablo
A1  - Orlando, Ludovic
T1  - Tracking five millennia of horse management with extensive ancient genome time series
JF  - Cell
N2  - Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.
Y1  - 2019
U6  - https://doi.org/10.1016/j.cell.2019.03.049
SN  - 0092-8674
SN  - 1097-4172
VL  - 177
IS  - 6
SP  - 1419
EP  - 1435
PB  - Cell Press
CY  - Cambridge
ER  -