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  • 1.
    Ersmark, Erik
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History (NRM).
    Large carnivore population turnover and ecological change during the Late Quaternary2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The cave lion (Panthera spelaea), the grey wolf (Canis lupus) and the brown bear (Ursus arctos) all shared an intercontinental distribution across the northern hemisphere during most of the Late Quaternary, and experienced repeated events of climate change. The cave lion went extinct at the end of the Pleistocene and although the wolf and the bear have survived until present day, recent human persecution has caused demographic bottlenecks and local extinctions. In this thesis, mitochondrial and nuclear DNA was analyzed from ancient and modern samples in order to study spatiotemporal changes in genetic diversity in the three species. Mitochondrial sequences analyzed from 48 radiocarbon dated cave lion remains revealed two haplogroups, of which the more genetically diverse seemingly disappeared around 41,000 years BP. Serial coalescent simulations on the data supported a population bottleneck in Beringia between roughly 47-18,000 years BP. Its long duration prevents a specific causal factor to be singled out, but the early onset and overlapping declines of other large mammals in the region suggests that major environmental changes greatly impacted the fauna of Beringia during this time. Using a similar genetic marker, a set of 126 modern wolves and two Siberian wolf remains of Late Pleistocene age were analyzed. The sequences yielded from the latter samples pertained to a basal haplogroup, which contained all Late Pleistocene wolves from previous studies. As data from both modern and ancient wolves were combined, a pattern of decreasing genetic diversity was identified around the Pleistocene-Holocene transition. This decrease was further tested by serial coalescent simulations, which supported a bottleneck in northern North America around this time. Further analyses were applied to one of the ancient wolf remains from Siberia, producing a draft genome sequence and a complete mitochondrial genome. Given the radiocarbon date of the Siberian wolf, a slower mutation rate could be inferred, which pushed back the split between the lineages leading to modern wolves and dogs to at least 27,000 years BP. The Siberian wolf was positioned close to the split but basal to these lineages. A global comparison with modern dogs indicated a closer genetic affiliation between the Siberian wolf and some arctic breeds. For the brown bear, phylogeographic changes in Europe were studied over the last 50,000 years, using radiocarbon dating and mitochondrial sequences. When concatenated and compared with published data, the mtDNA revealed a turnover event just before the LGM, while the dating confirmed a presence of brown bears at relatively high latitudes during this period. Marked shifts in population size were also inferred. Furthermore, data of stable isotope levels confirmed a dietary shift to increasing herbivory around the LGM. Finally, a recent anthropogenic bottleneck among Scandinavian brown bears was studied. While no change in genetic structure could be detected, mitochondrial and microsatellite markers showed a decline in genetic diversity, especially pronounced in the southern subpopulation. ABC simulations supported a bottleneck taking place across all of Scandinavia. Taken together, this thesis have identified and elucidated several impacts on genetic diversity in the past populations of large carnivores. The use of different genetic markers has enabled comparisons with published data, but also revealed their comparatively different benefits and limitations. Overall, the presented studies compose a synthesis of past population dynamics in large carnivores, uniquely revealed by ancient DNA.

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  • 2.
    Ersmark, Erik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Baryshnikov, Gennady
    Higham, Thomas
    Argant, Alain
    Castaños, Pedro
    Döppes, Doris
    Gasparik, Mihaly
    Germonpré, Mietje
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Lipecki, Grzegorz
    Marciszak, Adrian
    Miller, Rebecca
    Moreno-García, Marta
    Pacher, Martina
    Robu, Marius
    Rodriguez-Varela, Ricardo
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Rojo Guerra, Manuel
    Sabol, Martin
    Spassov, Nikolai
    Storå, Jan
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Valdiosera, Christina
    Villaluenga, Aritza
    Stewart, John R.
    Dalén, Love
    Genetic turnovers and northern survival during the last glacial maximum in European brown bears2019In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, no 10, p. 5891-5905Article in journal (Refereed)
    Abstract [en]

    The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

  • 3.
    Ersmark, Erik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Baryshnikov, Gennady
    Higham, Tom
    Argant, Alain
    Döppes, Doris
    Germonpré, Mietje
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Archaeological Research Laboratory.
    Lipecki, Grzegorz
    Marciszak, Adrian
    Pacher, Martina
    Storå, Jan
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory.
    Sabol, Martin
    Valdiosera, Christina
    Villaluenga, Aritza
    Stewart, John
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic revolutions and northern survival during the last glacial maximum in European brown bearsManuscript (preprint) (Other academic)
  • 4.
    Ersmark, Erik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Klütsch, Cornelya
    Chan, Yvonne
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology.
    Sinding-Larsen, Mikkel
    Gilbert, Thomas
    Arvestad, Lars
    Stockholm University, Faculty of Science, Numerical Analysis and Computer Science (NADA).
    Fain, Steven R.
    Illarionova, Natalia
    Oskarsson, Mattias
    Uhlén, Mathias
    Zhang, Ya-Ping
    Savolainen, Peter
    From the past to the present: Wolf phylogeography and demographic history based on the mitochondrial control regionManuscript (preprint) (Other academic)
  • 5.
    Ersmark, Erik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Orlando, Ludovic
    Sandoval-Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Barnes, Ian
    Barnett, Ross
    Stuart, Anthony
    Lister, Adrian
    Dalén, Love
    Swedish Museum of Natural History, Sweden.
    Population demography and genetic diversity in the Pleistocene cave lion2015In: Open Quaternary, ISSN 2055-298X, Vol. 1, no 1, article id 4Article in journal (Refereed)
    Abstract [en]

    With a range that covered most of northern Eurasia and parts of North America, the cave lion (Panthera spelaea) was one of the most widespread carnivores of the Late Pleistocene. Earlier ancient DNA analyses have shown that it is distinct from modern lions, and have suggested a demographic decline in Beringia during marine isotope stage 3 (MIS 3). Here, we further investigate the Late Pleistocene population dynamics in more detail by combining a powerful algorithm that couples MCMC with coalescent simulations under an approximate Bayesian computation framework. We use an ancient DNA dataset of previously published (n = 34) and new radiocarbon dated specimens (n = 14). Phylogenetic and network analyses based on the mitochondrial control region and the ATP8 gene identified two major haplogroups, one of which appears to vanish around 41,000 cal a BP. The approximate Bayesian computation analysis suggested a decline in effective population size (Ne) in Beringia of at least a 2-fold magnitude that began approximately 47,000 cal a BP, followed by an increase in Ne, most likely around 18,000 cal a BP. The cave lion went through a demographic bottleneck during MIS 3, which may have lasted for several tens of thousands of years, and only recovered shortly before the species' extinction. Several other large mammal species display similar declines in genetic diversity in Beringia during MIS 3, suggesting that major environmental changes might have affected megafaunal populations during this time period.

  • 6.
    Palkopoulou, Eleftheria
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Baca, Mateusz
    Abramson, Natalia I.
    Sablin, Mikhail
    Socha, Pawel
    Nadachowski, Adam
    Prost, Stefan
    Germonpre, Mietje
    Kosintsev, Pavel
    Smirnov, Nickolay G.
    Vartanyan, Sergey
    Ponomarev, Dmitry
    Nyström, Johanna
    Nikolskiy, Pavel
    Jass, Christopher N.
    Litvinov, Yuriy N.
    Kalthoff, Daniela C.
    Grigoriev, Semyon
    Fadeeva, Tatyana
    Douka, Aikaterini
    Higham, Thomas F. G.
    Ersmark, Erik
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Pitulko, Vladimir
    Pavlova, Elena
    Stewart, John R.
    Weglenski, Piotr
    Stankovic, Anna
    Dalén, Love
    Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings2016In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 22, no 5, p. 1710-1721Article in journal (Refereed)
    Abstract [en]

    Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.

  • 7.
    Palkopoulou, Eleftheria
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Baca, Mateusz
    Abramson, Natalya
    Socha, Pavel
    Nadakowski, Adam
    Prost, Stefan
    Germonpré, Metje
    Kosintsev, Pavel
    Smirnov, Nickolay
    Vartanyan, Sergey
    Ponomarev, Dmitry
    Nyström, Johanna
    Nikolskiy, Pavel
    Jass, Chris
    Yuriy, Litvinov
    Kalthoff, Daniela
    Grigoriev, Semyon
    Fadeeva, Tatyana
    Higham, Thomas
    Ersmark, Erik
    Stockholm University, Faculty of Science, Department of Zoology.
    Stewart, John
    Weglénski, Piotr
    Stankovic, Anna
    Dalén, Love
    Palaeogenetic analyses reveal wide-spread Pleistocene range fluctuations in the collared lemmingManuscript (preprint) (Other academic)
  • 8.
    Skoglund, Pontus
    et al.
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies. Harvard Medical School, USA; Broad Institute of Harvard and MIT, USA.
    Ersmark, Erik
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Dalen, Love
    Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds2015In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 11, p. 1515-1519Article in journal (Refereed)
    Abstract [en]

    The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000 year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

  • 9.
    Xenikoudakis, Georgios
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Ersmark, Erik
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Tison, J. -L.
    Waits, L.
    Kindberg, J.
    Swenson, J. E.
    Dalén, Love
    Swedish Museum of National History, Sweden.
    Consequences of a demographic bottleneck on geneticstructure and variation in the Scandinavian brown bear2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 13, p. 3441-3454Article in journal (Refereed)
    Abstract [en]

    The Scandinavian brown bear went through a major decline in population size approximately 100years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.

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