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  • 1. Dalerum, Fredrik
    et al.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Frojd, Christina
    Lecomte, Nicolas
    Lindgren, Asa
    Meijer, Tomas
    Pecnerova, Patricia
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Angerbjorn, Anders
    Spatial variation in Arctic hare (Lepus arcticus) populations around the Hall Basin2017In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, no 10, p. 2113-2118Article in journal (Refereed)
  • 2.
    Pecnerova, Patricia
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Diez-del-Molino, David
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dussex, Nicolas
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Feuerborn, Tatiana
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    von Seth, Johanna
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    van der Plicht, Johannes
    Nikolskiy, Pavel
    Tikhonov, Alexei
    Vartanyan, Sergey
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth2017In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, no 22, p. 3505-+Article in journal (Refereed)
  • 3.
    Pecnerova, Patricia
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Moravec, Jiri C.
    Martinkova, Natalia
    A Skull Might Lie: Modeling Ancestral Ranges and Diet from Genes and Shape of Tree Squirrel2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1074-1088Article in journal (Refereed)
    Abstract [en]

    Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology-diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.

  • 4. Pečnerová, Patrícia
    et al.
    Díez-Del-Molino, David
    Vartanyan, Sergey
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6Article in journal (Refereed)
    Abstract [en]

    According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

  • 5.
    Pečnerová, Patrícia
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Palkopoulou, Eleftheria
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Wheat, Christopher W.
    Skoglund, Pontus
    Vartanyan, Sergey
    Tikhonov, Alexei
    Nikolskiy, Pavel
    van der Plicht, Johannes
    Díez-del-Molino, David
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size2017In: Evolution Letters, ISSN 2056-3744, Vol. 1, no 6, p. 292-303Article in journal (Refereed)
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