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  • 1. Brace, Selina
    et al.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Dalén, Love
    Lister, Adrian M.
    Miller, Rebecca
    Otte, Marcel
    Germonpre, Mietje
    Blockley, Simon P. E.
    Stewart, John R.
    Barnes, Ian
    Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 50, p. 20532-20536Article in journal (Refereed)
    Abstract [en]

    The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity.

  • 2. Cappellini, Enrico
    et al.
    Gentry, Anthea
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Ishida, Yasuko
    Cram, David
    Roos, Anna-Marie
    Watson, Mick
    Johansson, Ulf S.
    Fernholm, Bo
    Agnelli, Paolo
    Barbagli, Fausto
    Littlewood, D. Tim J.
    Kelstrup, Christian D.
    Olsen, Jesper V.
    Lister, Adrian M.
    Roca, Alfred L.
    Dalén, Love
    Gilbert, M. Thomas P.
    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)2014In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 170, no 1, p. 222-232Article in journal (Refereed)
    Abstract [en]

    The understanding of Earth's biodiversity depends critically on the accurate identification and nomenclature of species. Many species were described centuries ago, and in a surprising number of cases their nomenclature or type material remain unclear or inconsistent. A prime example is provided by Elephas maximus, one of the most iconic and well-known mammalian species, described and named by Linnaeus (1758) and today designating the Asian elephant. We used morphological, ancient DNA (aDNA), and high-throughput ancient proteomic analyses to demonstrate that a widely discussed syntype specimen of E.maximus, a complete foetus preserved in ethanol, is actually an African elephant, genus Loxodonta. We further discovered that an additional E.maximus syntype, mentioned in a description by John Ray (1693) cited by Linnaeus, has been preserved as an almost complete skeleton at the Natural History Museum of the University of Florence. Having confirmed its identity as an Asian elephant through both morphological and ancient DNA analyses, we designate this specimen as the lectotype of E.maximus. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium with the data set identifier PXD000423.

  • 3.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic structure, demographic change and extinction dynamics in the collared lemming and woolly mammoth2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In light of current climate change it is critical to understand how different species have been affected in the past by well-known climatic events. In this thesis, DNA was retrieved from ancient material to study the population dynamics of two cold-adapted taxa that capture the extremes of body size range in mammals: the collared lemming (Dicrostonyx sp.) and the woolly mammoth (Mammuthus primigenius). The aim was to reconstruct their histories to investigate possible associations between past population events and changes in climate. Mitochondrial DNA sequences from collared lemming fossil remains in western Europe suggested that the history of this small mammal was characterized by repeated population extinctions followed by recolonizations, and that these were related to millennial-scale climatic fluctuations. Further genetic sampling of more than 300 mitochondrial DNA sequences, covering a large part of the collared lemming’s historical distribution, showed that these population turnovers were not site-specific but widespread, occurring across Europe and western Russia. Extant populations were found to harbor only a small fraction of the historical genetic diversity demonstrating an extensive loss of genetic variation in this small mammal during the last 50,000 years. For the woolly mammoth, a comprehensive dataset of novel and publicly available mitochondrial DNA sequences was compiled, covering a broad geographical and temporal range. In addition, complete genome sequencing was performed on two mammoth specimens, the first representing one of the last surviving individuals from Wrangel Island and the second representing the ancestral Late Pleistocene Siberian population. Genome-wide as well as mitochondrial DNA data revealed that climatic changes have played a major role in shaping the demographic history of the woolly mammoth. For example, two severe population reductions were identified, with the first one encompassing the last warm interglacial period (~130,000 – 116,000 years ago) and the second coinciding with the end of the last Ice Age (~11,000 years ago). Moreover, climate-driven sea level changes appear to have had considerable impact by enabling increased gene flow across the Bering land bridge, as well as the isolation of mammoths on Wrangel Island. When comparing the two complete genomes, the one from Wrangel Island displayed 20% lower genome-wide diversity and a markedly higher fraction of runs of homozygosity. Consequently, loss of genetic variation and inbreeding may have contributed to the extinction of the woolly mammoth. Overall, the findings presented in this thesis illustrate the power of ancient DNA in providing unique insights into past evolutionary processes.

  • 4.
    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.

  • 5.
    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)
  • 6.
    Palkopoulou, Eleftheria
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Dalén, Love
    Lister, Adrian M.
    Vartanyan, Sergey
    Sablin, Mikhail
    Sher, Andrei
    Nyström Edmark, Veronica
    Brandström, Mikael D.
    Germonpre, Mietje
    Barnes, Ian
    Thomas, Jessica A.
    Holarctic genetic structure and range dynamics in the woolly mammoth2013In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1770, p. 20131910-Article in journal (Refereed)
    Abstract [en]

    Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.

  • 7.
    Palkopoulou, Eleftheria
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Mallick, Swapan
    Skoglund, Pontus
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies. Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
    Enk, Jacob
    Rohland, Nadin
    Li, Heng
    Omrak, Ayca
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Vartanyan, Sergey
    Poinar, Hendrik
    Götherström, Anders
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Reich, David
    Dalen, Love
    Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth2015In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 10, p. 1395-1400Article in journal (Refereed)
    Abstract [en]

    The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding [1]. However, whether such genetic factors have had an impact on species prior to their extinction is unclear [2, 3]; examining this would require a detailed reconstruction of a species' demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage and dates to similar to 4,300 years before present, representing one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from an similar to 44,800-year-old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct.

  • 8.
    Palkopoulou, Eleftheria
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Mallick, Swapan
    Skoglund, Pontus
    Enk, Jacob
    Rohland, Nadin
    Li, Heng
    Omrak, Ayca
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Vartanyan, Sergey
    Poinar, Hendrik
    Götherström, Anders
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Reich, David
    Dalén, Love
    Genome-wide signatures of demographic change and Holocene genetic decline in the extinct woolly mammothManuscript (preprint) (Other academic)
  • 9.
    Sandoval-Castellanos, Edson
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Dalén, Love
    Back to BaySICS: A User-Friendly Program for Bayesian Statistical Inference from Coalescent Simulations2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5, p. e98011-Article in journal (Refereed)
    Abstract [en]

    Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.

  • 10.
    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.

  • 11.
    Tison, Jean-Luc
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Swedish Museum of Natural History, Sweden.
    Blennow, Victor
    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.
    Gustafsson, Petra
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Roos, Anna
    Dalén, Love
    Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden2015In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, no 2, p. 371-384Article in journal (Refereed)
    Abstract [en]

    The Eurasian otter (Lutra lutra) population in Sweden went through a drastic decline in population size between the 1950s and 1980s, caused mostly by anthropogenic factors such as high hunting pressure and the introduction of environmental toxic chemicals into the otter's habitats. However, after the bans of PCBs and DDT in the 1970s, the population began to recover in the 1990s. This study compares microsatellite data across twelve loci from historical and contemporary otter samples to investigate whether there has been a change in population structure and genetic diversity across time in various locations throughout Sweden. The results suggest that otters in the south were more severely affected by the bottleneck, demonstrated by a decline in genetic diversity and a shift in genetic composition. In contrast, the genetic composition in otters from northern Sweden remained mostly unchanged, both in terms of population structure and diversity. This suggests that the decline was not uniform across the country. Moreover, our analyses of historical samples provide an overview of the level of genetic variation and population structure that existed prior to the bottleneck, which may be helpful for the future management and conservation of the species.

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