| 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. |
- Chang, Dan, et al.
(författare)
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The evolutionary and phylogeographic history of woolly mammoths : a comprehensive mitogenomic analysis
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
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| 3. |
- Hempel, Elisabeth, et al.
(författare)
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Blue Turns to Gray : Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus)
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:12
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Tidskriftsartikel (refereegranskat)abstract
- The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
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| 4. |
- Hempel, Elisabeth, et al.
(författare)
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Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:2100
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Tidskriftsartikel (refereegranskat)abstract
- Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the ‘museum population’, possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.
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| 5. |
- Lippold, Sebastian, et al.
(författare)
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Discovery of lost diversity of paternal horse lineages using ancient DNA
- 2011
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 2, s. 450-
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Tidskriftsartikel (refereegranskat)abstract
- Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.
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| 6. |
- Lorenzen, Eline D., et al.
(författare)
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Species-specific responses of Late Quaternary megafauna to climate and humans
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 479:7373, s. 359-364
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Tidskriftsartikel (refereegranskat)abstract
- Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.
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| 7. |
- Westbury, Michael, et al.
(författare)
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Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations
- 2017
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Ingår i: Mitochondrial DNA Part B. - : Informa UK Limited. - 2380-2359. ; 2:1, s. 298-299
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Tidskriftsartikel (refereegranskat)abstract
- The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae.
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| 8. |
- Westbury, Michael V., et al.
(författare)
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Aardwolf population diversity and phylogenetic positioning inferred using complete mitochondrial genomes
- 2019
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Ingår i: African journal of wildlife research. - : Southern African Wildlife Management Association. - 2410-7220 .- 2410-8200. ; 49:1, s. 27-33
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Tidskriftsartikel (refereegranskat)abstract
- The aardwolf (Proteles cristata) is a unique. insectivorous species of the family Hyaenidae. It occupies a disjunct range in eastern and southern Africa and is possibly a remaining member of a historical dog-like hyaena Glade. Although both local and global population status and trends are largely unknown, aardwolves are not uncommon in arid grasslands and the IUCN conservation status of Least Concern appears to be justified. However, they are one of the least studied of the four hyaena species, and we have scarce information about the genetic structure of aardwolf populations. Here, we present the first complete aardwolf mitochondrial genomes and provide novel information about aardwolf evolutionary origins and genetic structure within a single population. Through the investigation of complete mitochondrial genomes from five individuals from a single population within South Africa, we find the mitochondrial diversity of this population to be neither particularly high nor low compared to a number of other mammalian species. Moreover, we also provide additional evidence towards the basal position of the aardwolf within Hyaenidae with a divergence time of 13.0 Ma (95% CI 10.1-16.4 Ma) from all other extant hyaena species.
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| 9. |
- Westbury, Michael V, et al.
(författare)
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Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae
- 2021
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:9, s. 3884-3897
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Tidskriftsartikel (refereegranskat)abstract
- During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
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| 10. |
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