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  • 1.
    Dalerum, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. University of Oviedo, Spain; University of Pretoria, South Africa.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Fröjd, Christina
    Lecomte, Nicolas
    Lindgren, Åsa
    Meijer, Tomas
    Stockholm University, Faculty of Science, Department of Zoology.
    Pečnerová, Patrícia
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    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)
    Abstract [en]

    Arctic environments have relatively simple ecosystems. Yet, we still lack knowledge of the spatio-temporal dynamics of many Arctic organisms and how they are affected by local and regional processes. The Arctic hare (Lepus arcticus) is a large lagomorph endemic to high Arctic environments in Canada and Greenland. Current knowledge about this herbivore is scarce and the temporal and spatial dynamics of their populations are poorly understood. Here, we present observations on Arctic hares in two sites on north Greenland (Hall and Washington lands) and one adjacent site on Ellesmere Island (Judge Daly Promontory). We recorded a large range of group sizes from 1 to 135 individuals, as well as a substantial variation in hare densities among the three sites (Hall land: 0 animals/100 km(2), Washington land 14.5-186.7 animals/100 km(2), Judge Daly Promontory 0.18-2.95 animals/100 km(2)). However, pellet counts suggested that both Hall land and Judge Daly Promontory hosted larger populations at other times. We suggest that our results could have been caused by three spatially differentiated populations with asynchronous population fluctuations. With food limitation being a likely driver behind the observed variation, we argue that food limitation likely interacts with predation and competition in shaping the spatial dynamics of Arctic hares in this region.

  • 2.
    Dalerum, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. University of Oviedo, Spain; University of Pretoria, South Africa.
    Freire, S.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Lecomte, N.
    Lindgren, A.
    Meijer, Tomas
    Stockholm University, Faculty of Science, Department of Zoology.
    Pečnerová, Patricia
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Exploring the diet of arctic wolves (Canis lupus arctos) at their northern range limit2018In: Canadian Journal of Zoology, ISSN 0008-4301, E-ISSN 1480-3283, Vol. 96, no 3, p. 277-281Article in journal (Refereed)
    Abstract [en]

    The grey wolf (Canis lupus Linnaeus, 1758) is one of the most widespread large carnivores on Earth, and occurs throughout the Arctic. Although wolf diet is well studied, we have scant information from high Arctic areas. Global warming is expected to increase the importance of predation for ecosystem regulation in Arctic environments. To improve our ability to manage Arctic ecosystems under environmental change, we therefore need knowledge about Arctic predator diets. Prey remains in 54 wolf scats collected at three sites in the high Arctic region surrounding the Hall Basin (Judge Daly Promontory, Ellesmere Island, Canada, and Washington Land and Hall Land, both in northwestern Greenland) pointed to a dietary importance of arctic hare (Lepus arcticus Ross, 1819; 55% frequency of occurrence) and muskoxen (Ovibos moschatus (Zimmermann, 1780); 39% frequency of occurrence), although we observed diet variation among the sites. A literature compilation suggested that arctic wolves (Canis lupus arctos Pocock, 1935) preferentially feed on caribou (Rangifer tarandus (Linnaeus, 1758)) and muskoxen, but can sustain themselves on arctic hares and Greenland collared lemmings (Dicrostonyx groenlandicus (Traill, 1823)) in areas with limited or no ungulate populations. We suggest that climate change may alter the dynamics among wolves, arctic hare, muskoxen, and caribou, and we encourage further studies evaluating how climate change influences predator-prey interactions in high Arctic environments.

  • 3. Koren, Lee
    et al.
    Matas, Devorah
    Pečnerová, Patrícia
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Tikhonov, Alexei
    Gilbert, M. Thomas P.
    Geffen, Eli
    Testosterone in ancient hair from an extinct speciesManuscript (preprint) (Other academic)
  • 4.
    Pečnerová, Patrícia
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History.
    Genomic analysis of the process leading up to the extinction of the woolly mammoth2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Species worldwide are subject to contractions in both abundance and geographical range, and their persistence in a changing environment may thus depend on the ability to survive in small and fragmented populations. Despite the urgent need to understand how extinction works, our knowledge of pre-extinction genetic processes is limited because techniques allowing population and conservation genomics to be studied in wild threatened populations have become available only recently. In this thesis, I used the last surviving population of the woolly mammoth (Mammuthus primigenius) as a model for studying pre-extinction population dynamics. I used ancient DNA as a tool to study microevolutionary processes in real time, analysing genetic changes in response to environmental shifts at the end of the last Ice Age and exploring impacts of genetic drift and inbreeding as woolly mammoths became isolated on Wrangel Island and survived for 6000 years at small population size. Using mitochondrial genomes, I found evidence of a founder effect that decreased the maternal diversity to a single lineage at the time when mammoths became trapped on Wrangel Island (~10,500 years ago). Moreover, a two- to three-fold higher mitochondrial mutation rate in Holocene and a fixed, potentially detrimental mutation in the ATP6 gene encoding for one of the key enzymes of the oxidative phosphorylation pathway, is consistent with the hypothesis that selection is less effective in removing deleterious mutations in small populations. A loss of diversity was also observed in an immunity gene that belongs to the major histocompatibility complex (MHC), even though the MHC is considered to be under balancing selection. Low-coverage genomic data was analysed in order to estimate endogenous DNA content and molecular sex of the mammoth samples. The observation of a male bias (69%) in the sex ratio led to the conclusion that male mammoths were more likely to die in a way that ensured good preservation. Another potential way of getting information about life history strategies of extinct species, which was explored here, is by measuring testosterone levels in mammoth hair shafts in connection with molecular sex inference. Finally, given that previous estimates have suggested a very small Holocene effective population size on Wrangel Island and thus that the population may have been too small to avoid genome erosion, four mammoths were sequenced to a high coverage in order to look for genomic consequences of small population size. When compared to mammoths from the Pleistocene mainland population, Wrangel Island mammoths had lower levels of genome-wide diversity and had a higher proportion of their genomes allocated in runs of homozygosity, which are large fragments completely depleted of diversity. Importantly, genome erosion appears to have accelerated in the last ten generations before the extinction, resulting in the last known woolly mammoth having almost 40% of its genome without any genetic diversity. Overall, these results highlight how genetic drift and inbreeding triggered genomic deterioration in the last surviving woolly mammoth population. Although Wrangel Island was a refugium, where mammoths survived for thousands of years after the last Ice Age, and the causal factors of the final extinction are not yet clear, isolation and small population size without any possibility of new gene flow may have contributed to reduced fitness, and thus to extinction. 

  • 5.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Diez-del-Molino, David
    Vartanyan, Sergey
    Dalén, Love
    Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 25274Article 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.

  • 6.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Díez-Del-Molino, David
    Dussex, Nicolas
    Feuerborn, Tatiana
    von Seth, Johanna
    van der Plicht, Johannes
    Nikolskiy, Pavel
    Tikhonov, Alexei
    Vartanyan, Sergey
    Dalén, Love
    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. 3505-3510.e3Article in journal (Refereed)
    Abstract [en]

    While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. Wehypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.

  • 7.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Díez-Del-Molino, David
    Palkopoulou, Eleftheria
    Skoglund, Pontus
    Tikhonov, Alexei
    Nikolskiy, Pavel
    Vartanyan, Sergey
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Pre-extinction population dynamics and genome erosion in the woolly mammothManuscript (preprint) (Other academic)
  • 8.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Masaryk University, Czech Republic; Academy of Sciences of the Czech Republic, Czech Republic; Swedish Museum of Natural History, Sweden.
    Moravec, Jiri C.
    Martinkova, Natalia
    A Skull Might Lie: Modeling Ancestral Ranges and Diet from Genes and Shape of Tree Squirrels2015In: 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.

  • 9.
    Pečnerová, Patrícia
    et al.
    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; Harvard Medical School, Massachusetts.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Skoglund, Pontus
    Vartanyan, Sergey
    Tikhonov, Alexei
    Nikolskiy, Pavel
    van der Plicht, Johannes
    Díez-del-Molino, David
    Dalén, Love
    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)
    Abstract [en]

    The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high-quality mitogenomes from 21 radiocarbon-dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.

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