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  • 1. Doan, Karolina
    et al.
    Mackiewicz, Pawel
    Sandoval-Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Stefaniak, Krzysztof
    Ridush, Bogdan
    Dalén, Love
    Weglenski, Piotr
    Stankovic, Ana
    The history of Crimean red deer population and Cervus phylogeography in Eurasia2018In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 183, no 1, p. 208-225Article in journal (Refereed)
    Abstract [en]

    The present distribution of many species is a result of climatic changes during the Pleistocene and human activity. The impact of climate has been accompanied by restrictions of populations into refugia during glacial periods, and subsequent expansions during more favourable conditions, whereas human influence has been associated with hunting practices and translocations. One mammalian species that has been subject to such transformations is the red deer, Cervus elaphus, but the exact nature of these changes has been difficult to determine using only modern DNA. In this study, we obtained new cytochrome b sequences from subfossil remains of deer found in the Crimean Peninsula. A comparison of these sequences with the available recent and ancient sequences allowed to us to reconstruct phylogeographic relationships between Cervus lineages and to determine their potential migration routes at both local and Eurasian scales. Our analyses showed that the Crimean Peninsula was not a glacial refugium for red deer, but rather that red deer colonized Crimea in three independent waves from both Western and Eastern red deer populations. The immigrations were related to local extinctions and replacements of native populations.

  • 2.
    Lagerholm, Vendela K.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Sandoval-Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Ehrich, Dorothee
    Abramson, Natalia I.
    Nadachowski, Adam
    Kalthoff, Daniela C.
    Germonpre, Mietje
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Stewart, John R.
    Dalén, Love
    On the origin of the Norwegian lemming2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2060-2071Article in journal (Refereed)
    Abstract [en]

    The Pleistocene glacial cycles resulted in significant changes in species distributions, and it has been discussed whether this caused increased rates of population divergence and speciation. One species that is likely to have evolved during the Pleistocene is the Norwegian lemming (Lemmus lemmus). However, the origin of this species, both in terms of when and from what ancestral taxon it evolved, has been difficult to ascertain. Here, we use ancient DNA recovered from lemming remains from a series of Late Pleistocene and Holocene sites to explore the species' evolutionary history. The results revealed considerable genetic differentiation between glacial and contemporary samples. Moreover, the analyses provided strong support for a divergence time prior to the Last Glacial Maximum (LGM), therefore likely ruling out a postglacial colonization of Scandinavia. Consequently, it appears that the Norwegian lemming evolved from a small population that survived the LGM in an ice-free Scandinavian refugium.

  • 3. Mellows, Andrew
    et al.
    Barnett, Ross
    Dalen, Love
    Sandoval Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Linderholm, Anna
    McGovern, Thomas H.
    Church, Mike J.
    Larson, Greger
    The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox2012In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 279, no 1747, p. 4568-4573Article in journal (Refereed)
    Abstract [en]

    Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.

  • 4.
    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.

  • 5.
    Tison, Jean-Luc
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Swedish Museum of National History, Sweden.
    Nyström Edmark, Veronica
    Sandoval-Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Van Dyck, Hans
    Tammaru, Toomas
    Valimäki, Panu
    Dalén, Love
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Signature of post-glacial expansion and genetic structure at the northern range limit of the speckled wood butterfly2014In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 113, no 1, p. 136-148Article in journal (Refereed)
    Abstract [en]

    The post-glacial recolonisation of northern Europe has left distinct signatures in the genomes of many organisms, both due to random demographic processes and divergent natural selection. However, information on differences in genetic variation in conjunction with patterns of local adaptations along latitudinal gradients is often lacking. In this study, we examine genetic diversity and population structure in the speckled wood butterfly Pararge aegeria in northern Europe to investigate the species post-glacial recolonisation history and discuss how this may have affected its life-history evolution. We collected 209 samples and analysed genetic variation in nine microsatellite loci. The results demonstrated a more pronounced population structure in northern Europe compared with populations further south, as well as an overall decrease in genetic diversity with latitude, likely due to founder effects during the recolonisation process. Coalescent simulations coupled with approximate Bayesian computation suggested that central Scandinavia was colonised from the south, rather than from the east. In contrast to further south, populations at the northern range margin are univoltine expressing only one generation per year. This suggests either that univoltinism evolved independently on each side of the Baltic Sea, or that bivoltinism evolved in the south after northern Europe was recolonised.

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