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  • Kılınç, Gülşah Merve, et al. (författare)
  • Human population dynamics and Yersinia pestis in ancient northeast Asia
  • 2021
  • Ingår i: Science Advances. - : AMER ASSOC ADVANCEMENT SCIENCE. - 2375-2548. ; 7:2
  • Tidskriftsartikel (refereegranskat)abstract
    • We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis. Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.
  • Liu, Shanlin, et al. (författare)
  • Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
  • 2021
  • Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
  • Tidskriftsartikel (refereegranskat)abstract
    • Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (similar to 16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
  • Valdiosera, Cristina, et al. (författare)
  • Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA
  • 2006
  • Ingår i: Biology Letters. - 1744-9561 .- 1744-957X. - 1744-9561 ; 2:4, s. 601-603
  • Tidskriftsartikel (refereegranskat)abstract
    • In this study, we have used a technique designed to target short fragments containing informative mitochondrial substitutions to extend the temporal limits of DNA recovery and study the molecular phylogeny of Ursus deningeri. We present a cladistic analysis using DNA recovered from 400 kyr old U. deningeri remains, which demonstrates U. deningeri's relation to Ursus spelaeus. This study extends the limits of recovery from skeletal remains by almost 300 kyr. Plant material from permafrost environments has yielded DNA of this age in earlier studies, and our data suggest that DNA in teeth from cave environments may be equally well preserved.
  • Angerbjörn, Anders, et al. (författare)
  • Carnivore conservation in practice : replicatedmanagement actions on a large spatial scale
  • 2013
  • Ingår i: Journal of Applied Ecology. - 0021-8901 .- 1365-2664. ; 50:1, s. 59-67
  • Tidskriftsartikel (refereegranskat)abstract
    • More than a quarter of the world’s carnivores are threatened, often due to multiple andcomplex causes. Considerable research efforts are devoted to resolving the mechanisms behindthese threats in order to provide a basis for relevant conservation actions. However, evenwhen the underlying mechanisms are known, specific actions aimed at direct support for carnivoresare difficult to implement and evaluate at efficient spatial and temporal scales.2. We report on a 30-year inventory of the critically endangered Fennoscandian arctic foxVulpes lagopus L., including yearly surveys of 600 fox dens covering 21 000 km2. These surveysshowed that the population was close to extinction in 2000, with 40–60 adult animalsleft. However, the population subsequently showed a fourfold increase in size.3. During this time period, conservation actions through supplementary feeding and predatorremoval were implemented in several regions across Scandinavia, encompassing 79% of thearea. To evaluate these actions, we examined the effect of supplemental winter feeding andred fox control applied at different intensities in 10 regions. A path analysis indicated that47% of the explained variation in population productivity could be attributed to lemmingabundance, whereas winter feeding had a 29% effect and red fox control a 20% effect.4. This confirms that arctic foxes are highly dependent on lemming population fluctuationsbut also shows that red foxes severely impact the viability of arctic foxes. This study also highlightsthe importance of implementing conservation actions on extensive spatial and temporalscales, with geographically dispersed actions to scientifically evaluate the effects. We note thatpopulation recovery was only seen in regions with a high intensity of management actions.5. Synthesis and applications. The present study demonstrates that carnivore populationdeclines may be reversed through extensive actions that target specific threats. Fennoscandianarctic fox is still endangered, due to low population connectivity and expected climate impactson the distribution and dynamics of lemmings and red foxes. Climate warming is expected tocontribute to both more irregular lemming dynamics and red fox appearance in tundra areas;however, the effects of climate change can be mitigated through intensive managementactions such as supplemental feeding and red fox control.
  • Bergström, Anders, et al. (författare)
  • Origins and genetic legacy of prehistoric dogs
  • 2020
  • Ingår i: Science. - 1095-9203 .- 0036-8075. ; 370:6516, s. 557-564
  • Tidskriftsartikel (refereegranskat)abstract
    • Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
  • Brace, Selina, et al. (författare)
  • Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability
  • 2012
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 109:50, s. 20532-20536
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
  • Brealey, Jaelle C., et al. (författare)
  • Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
  • 2020
  • Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 37:10, s. 3003-3022
  • Tidskriftsartikel (refereegranskat)abstract
    • Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
  • Cappellini, Enrico, et al. (författare)
  • Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
  • 2019
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 574:7776, s. 103-
  • Tidskriftsartikel (refereegranskat)abstract
    • The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa(1). However, the irreversible post-mortem degradation(2) of ancient DNA has so far limited its recovery-outside permafrost areasto specimens that are not older than approximately 0.5 million years (Myr)(3). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I-4. and suggested the presence of protein residues in fossils of the Cretaceous period(5)-although with limited phylogenetic use(6). In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch(7-9), using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)(10). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the Glade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates(11), and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
  • Dalén, Love, et al. (författare)
  • Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox
  • 2007
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. - 0027-8424 ; 104:16, s. 6726-6729
  • Tidskriftsartikel (refereegranskat)abstract
    • How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.
  • Dalén, Love, et al. (författare)
  • Identifying Bird Remains Using Ancient DNA Barcoding
  • 2017
  • Ingår i: Genes. - 2073-4425 .- 2073-4425. ; 8:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.
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