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  • 1. Dehasque, Marianne
    et al.
    Pečnerová, Patrícia
    Muller, Héloïse
    Tikhonov, Alexei
    Nikolskiy, Pavel
    Tsigankova, Valeriya I.
    Danilov, Gleb K.
    Díez-del-Molino, David
    Vartanyan, Sergey
    Dalén, Love
    Lister, Adrian M.
    Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia2021Inngår i: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 259, artikkel-id 106913Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago.

  • 2.
    Hein, Catherine L.
    et al.
    Umeå universitet, Institutionen för ekologi, miljö och geovetenskap.
    Öhlund, Gunnar
    Umeå universitet, Institutionen för ekologi, miljö och geovetenskap.
    Englund, Göran
    Umeå universitet, Institutionen för ekologi, miljö och geovetenskap.
    Fish introductions reveal the temperature dependence of species interactions2014Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, nr 1775, s. 20132641-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A major area of current research is to understand how climate change will impact species interactions and ultimately biodiversity. A variety of environmental conditions are rapidly changing owing to climate warming, and these conditions often affect both the strength and outcome of species interactions. We used fish distributions and replicated fish introductions to investigate environmental conditions influencing the coexistence of two fishes in Swedish lakes: brown trout (Salmo trutta) and pike (Esox lucius). A logistic regression model of brown trout and pike coexistence showed that these species coexist in large lakes (more than 4.5 km(2)), but not in small, warm lakes (annual air temperature more than 0.9-1.5 degrees C). We then explored how climate change will alter coexistence by substituting climate scenarios for 2091-2100 into our model. The model predicts that brown trout will be extirpated from approximately half of the lakes where they presently coexist with pike and from nearly all 9100 lakes where pike are predicted to invade. Context dependency was critical for understanding pike-brown trout interactions, and, given the widespread occurrence of context-dependent species interactions, this aspect will probably be critical for accurately predicting climate impacts on biodiversity.

  • 3. Michell, Craig T.
    et al.
    Wagner, Natascha
    Mutanen, Marko
    Lee, Kyung Min
    Nyman, Tommi
    Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies2023Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, nr 7, s. 1791-1809Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

  • 4. Pruisscher, Peter
    et al.
    Nylin, Sören
    Wheat, Christopher West
    Gotthard, Karl
    A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes2021Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 75, nr 2, s. 490-500Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Developmental plasticity describes the capacity of individuals with the same genotype to induce permanent change in a phenotype depending on a specific external input. One well-studied example of adaptive developmental plasticity is the induction of facultative diapause in insects. Studies investigating the inheritance of diapause induction have suggested diverse genetic origins. However, only few studies have performed genome-wide scans to identify genes affecting the induction decision. Here we compare two populations of the butterfly Pieris napi that differ in the propensity to enter diapause, and despite showing a low genome-wide divergence, we identify a few genomic regions that show high divergence between populations. We then identified a single genomic region associated with diapause induction by genotyping diapausing and directly developing siblings from backcrosses of these populations. This region is located on the Z chromosome and contained three circadian clock genes, cycle, clock, and period. Additionally, period harbored the largest number of SNPs showing complete fixation between populations. We conclude that the heritable basis of between-population variation in the plasticity that determines diapause induction resides on the Z chromosome, with the period gene being the prime candidate for the genetic basis of adaptive plasticity.

  • 5. Sarkissian, Clio Der
    et al.
    Moller, Per
    Hofman, Courtney A.
    Ilsoe, Peter
    Rick, Torben C.
    Schiotte, Tom
    Sorensen, Martin Vinther
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Orlando, Ludovic
    Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells2020Inngår i: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 8Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The shells of marine mollusks represent promising metagenomic archives of the past, adding to bones, teeth, hairs, and environmental samples most commonly examined in ancient DNA research. Seminal work has established that DNA recovery from marine mollusk shells depends on their microstructure, preservation and disease state, and that authentic ancient DNA could be retrieved from specimens as old as 7,000 years. Here, we significantly push the temporal limit for shell DNA recovery to >= 100,000 years with the successful genetic characterization of one Portlandia arctica and one Mytilus mussel sample collected within a dated permafrost layer from the Taimyr Peninsula, Russia. We expand the analysis of ancient DNA in carbonate shells to a larger number of genera (Arctica, Cernuella, Crassostrea, Dreissena, Haliotis, Lymnaea, Margaritifera, Pecten, Ruditapes, Venerupis) from marine, freshwater and terrestrial environments. We demonstrate that DNA from ancient shells can provide sufficient resolution for taxonomic, phylogenetic and/or population assignment. Our results confirm mollusk shells as long-term DNA reservoirs, opening new avenues for the investigation of environmental changes, commercial species management, biological invasion, and extinction. This is especially timely in light of modern threats to biodiversity and ecosystems.

  • 6.
    Thibert-Plante, Xavier
    et al.
    Umeå universitet, Institutionen för ekologi, miljö och geovetenskap.
    Praebel, Kim
    Østbye, Kjartan
    Kahilainen, Kimmo K.
    Amundsen, Per-Arne
    Gavrilets, Sergey
    Using mathematical modelling to investigate the adaptive divergence of whitefish in Fennoscandia2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 7394Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Modern speciation theory has greatly benefited from a variety of simple mathematical models focusing on the conditions and patterns of speciation and diversification in the presence of gene flow. Unfortunately the application of general theoretical concepts and tools to specific ecological systems remains a challenge. Here we apply modeling tools to better understand adaptive divergence of whitefish during the postglacial period in lakes of northern Fennoscandia. These lakes harbor up to three different morphs associated with the three major lake habitats: littoral, pelagic, and profundal. Using large-scale individual-based simulations, we aim to identify factors required for in situ emergence of the pelagic and profundal morphs in lakes initially colonized by the littoral morph. The importance of some of the factors we identify and study - sufficiently large levels of initial genetic variation, size- and habitat-specific mating, sufficiently large carrying capacity of the new niche - is already well recognized. In addition, our model also points to two other factors that have been largely disregarded in theoretical studies: fitness-dependent dispersal and strong predation in the ancestral niche coupled with the lack of it in the new niche(s). We use our theoretical results to speculate about the process of diversification of whitefish in Fennoscandia and to identify potentially profitable directions for future empirical research.

    Fulltekst (pdf)
    FULLTEXT01
  • 7.
    van der Valk, Tom
    et al.
    Uppsala universitet, Beräkningsbiologi och bioinformatik.
    Pecnerova, Patricia
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden; Univ Copenhagen, Sect Computat & RNA Biol, Dept Biol, Copenhagen, Denmark.
    Diez-del-Molino, David
    Ctr Palaeogenet, Stockholm, Sweden; Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Bergström, Anders
    Francis Crick Inst, London, England.
    Oppenheimer, Jonas
    Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA.
    Hartmann, Stefanie
    Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany.
    Xenikoudakis, Georgios
    Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany.
    Thomas, Jessica A.
    Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany.
    Dehasque, Marianne
    Ctr Palaeogenet, Stockholm, Sweden; Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Saglican, Ekin
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkey.
    Fidan, Fatma Rabia
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkey.
    Barnes, Ian
    Nat Hist Museum, Dept Earth Sci, London, England.
    Liu, Shanlin
    China Agr Univ, Coll Plant Protect, Beijing, Peoples R China.
    Somel, Mehmet
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkey.
    Heintzman, Peter D.
    UiT Arctic Univ Norway, Arctic Univ Museum Norway, Tromso, Norway.
    Nikolskiy, Pavel
    Russian Acad Sci, Geol Inst, Moscow, Russia.
    Shapiro, Beth
    Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA; Univ Calif Santa Cruz, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA.
    Skoglund, Pontus
    Francis Crick Inst, London, England.
    Hofreiter, Michael
    Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany.
    Lister, Adrian M.
    Nat Hist Museum, Dept Earth Sci, London, England.
    Götherström, Anders
    Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Dalén, Love
    Ctr Palaeogenet, Stockholm, Sweden; Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Million-year-old DNA sheds light on the genomic history of mammoths2021Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 591, nr 7849, s. 265-269Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

  • 8. Wang, Yucheng
    et al.
    Pedersen, Mikkel Winther
    Alsos, Inger Greve
    De Sanctis, Bianca
    Racimo, Fernando
    Prohaska, Ana
    Coissac, Eric
    Owens, Hannah Lois
    Merkel, Marie Kristine Føreid
    Fernandez-Guerra, Antonio
    Rouillard, Alexandra
    Lammers, Youri
    Alberti, Adriana
    Denoeud, France
    Money, Daniel
    Ruter, Anthony H.
    McColl, Hugh
    Larsen, Nicolaj Krog
    Cherezova, Anna A.
    Edwards, Mary E.
    Fedorov, Grigory B.
    Haile, James
    Orlando, Ludovic
    Vinner, Lasse
    Korneliussen, Thorfinn Sand
    Beilman, David W.
    Bjørk, Anders A.
    Cao, Jialu
    Dockter, Christoph
    Esdale, Julie
    Gusarova, Galina
    Kjeldsen, Kristian K.
    Mangerud, Jan
    Rasic, Jeffrey T.
    Skadhauge, Birgitte
    Svendsen, John Inge
    Tikhonov, Alexei
    Wincker, Patrick
    Xing, Yingchun
    Zhang, Yubin
    Froese, Duane G.
    Rahbek, Carsten
    Nogues, David Bravo
    Holden, Philip B.
    Edwards, Neil R.
    Durbin, Richard
    Meltzer, David J.
    Kjær, Kurt H.
    Möller, Per
    Willerslev, Eske
    Late Quaternary dynamics of Arctic biota from ancient environmental genomics2021Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

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