| 1. |
- Bergström, Anders, et al.
(författare)
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Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
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Tidskriftsartikel (refereegranskat)abstract
- The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
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| 2. |
- Bergström, Anders, et al.
(författare)
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Origins and genetic legacy of prehistoric dogs
- 2020
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 370:6516, s. 557-563
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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.
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| 3. |
- Cappellini, Enrico, et al.
(författare)
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Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 574:7776, s. 103-
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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.
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| 4. |
- Dalen, Love, et al.
(författare)
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Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:16, s. 6726-6729
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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.
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| 5. |
- Dalén, Love, et al.
(författare)
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Is the endangered Fennoscandian arctic fox (Alopex lagopus) population genetically isolated?
- 2002
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Ingår i: Biological Conservation. - 0006-3207 .- 1873-2917. ; 105:2, s. 171-178
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Tidskriftsartikel (refereegranskat)abstract
- The arctic fox population in Fennoscandia is on the verge of going extinct after not being able to recover from a severe bottleneck at the end of the 19th century. The Siberian arctic fox population, on the other hand, is large and unthreatened. In order to resolve questions regarding gene flow between, and genetic variation within the populations, a 294 bp long part of the mitochondrial hypervariable region 1 was sequenced. This was done for 17 Swedish, 15 Siberian and two farmed foxes. Twelve variable nucleotide sites were observed, which resulted in 10 different haplotypes. Three haplotypes were found in Sweden and seven haplotypes were found in Siberia. An analysis of molecular variance showed a weak, but significant, differentiation between the populations. No difference in haplotype diversity was found between the populations. A phylogenetic analysis revealed that the three Swedish haplotypes were not monophyletic compared to the Siberian haplotypes. These results indicate a certain amount of gene flow between the two populations. both before and after the bottleneck. Restocking the Fennoscandian population with arctic foxes from Siberia might therefore be a viable option.
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| 6. |
- Dalen, Love, et al.
(författare)
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Partial Genetic Turnover in Neandertals : Continuity in the East and Population Replacement in the West
- 2012
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 29:8, s. 1893-1897
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Tidskriftsartikel (refereegranskat)abstract
- Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (< 48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (> 48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region.
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| 7. |
- Dalén, Lové, 1980-, et al.
(författare)
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Recovery of DNA from Footprints in the snow
- 2008
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Ingår i: Canadian field-naturalist. - OTTAWA, Canada : OTTAWA FIELD-NATURALISTS CLUB. - 0008-3550. ; 121:3, s. 321-324
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Tidskriftsartikel (refereegranskat)abstract
- The recovery of trace amounts of DNA has been demonstrated to be a reliable tool in conservation genetics and has become a key component of modern forensic casework. To date, genetic data have been successfully recovered from a variety of sources, including biological fluids, faeces, clothing, and even directly from fingerprints. However, to our knowledge and despite their widespread occurrence and clear potential as a source of DNA, genetic information has not previously been recovered directly from footprints. Here, we extract and amplify mitochondrial DNA from a snow footprint, <48-hours old, made by a Swedish Arctic Fox (Alopex lagopus). Our results demonstrate that it is possible to recover Sufficient DNA from recent footprints to accurately type the source of the print, with implications for conservation biology and forensic science.
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| 8. |
- Dalén, Love, et al.
(författare)
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Recovery of DNA from Footprints in the Snow
- 2007
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Ingår i: Canadian field-naturalist. - 0008-3550. ; 121:3, s. 321-324
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Tidskriftsartikel (refereegranskat)abstract
- The recovery of trace amounts of DNA has been demonstrated to be a reliable tool in conservation genetics and has become a key component of modern forensic casework. To date, genetic data have been successfully recovered from a variety of sources, including biological fluids, faeces, clothing, and even directly from fingerprints. However, to our knowledge and despite their widespread occurrence and clear potential as a source of DNA, genetic information has not previously been recovered directly from footprints. Here, we extract and amplify mitochondrial DNA from a snow footprint, <48-hours old, made by a Swedish Arctic Fox (Alopex lagopus). Our results demonstrate that it is possible to recover Sufficient DNA from recent footprints to accurately type the source of the print, with implications for conservation biology and forensic science.
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| 9. |
- Dehasque, Marianne, et al.
(författare)
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Temporal dynamics of woolly mammoth genome erosion prior to extinction
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A large number of species have recently recovered from near-extinction events. Understanding the genetic consequences of severe population declines followed by demographic recoveries is key to predict the long-term viability of species in order to mitigate future extinction risks. Although these species have avoided the immediate extinction threat, their long-term viability remains questionable due to the genetic consequences of population declines, which are not understood on a time scale beyond a few generations. The woolly mammoth (Mammuthus primigenius) population on Wrangel Island is an excellent model system to investigate long-term genetic consequences of a population bottleneck. Mammoths became isolated on the island in the early Holocene due to rising sea levels, and persisted for over 200 generations (~6,000 years) before becoming extinct ~4,000 years ago. To study the evolutionary processes leading up to the extinction of the woolly mammoth on the island, we analysed 21 Siberian woolly mammoth genomes, including that of one of the last known mammoths. Our results show that the Wrangel Island mammoths recovered quickly from an initially severe bottleneck, and subsequently remained demographically stable during the ensuing 6 millennia. Further, we find that highly deleterious mutations were gradually purged from the population, whereas there was an accumulation of mildly deleterious mutations. The gradual purging of highly deleterious mutations suggests an ongoing inbreeding depression that lasted for hundreds of generations. This time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked present-day populations.
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| 10. |
- Dehasque, Marianne, et al.
(författare)
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Temporal dynamics of woolly mammoth genome erosion prior to extinction
- 2024
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Ingår i: Cell. - 0092-8674. ; 187:14, s. 13-3540
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Tidskriftsartikel (refereegranskat)abstract
- A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths’ extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.
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