| 1. |
- Liu, Shanlin, et al.
(författare)
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Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
- 2021
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Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
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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.
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| 2. |
- Ameen, Carly, et al.
(författare)
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Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic
- 2019
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 286:1916
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Tidskriftsartikel (refereegranskat)abstract
- Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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| 3. |
- Angerbjörn, Anders, et al.
(författare)
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Carnivore conservation in practice : replicatedmanagement actions on a large spatial scale
- 2013
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Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 50:1, s. 59-67
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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.
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| 4. |
- Ardalan, Arman, 1976-
(författare)
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Molecular Profiling of the Population Dynamics : Foundation and Expansion of an Archaic Domesticate
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- "An ‘exponential growth of science’ throughout modern history has been frequently boasted by numerous narcissistic accounts of ‘modern humanity.’ Nonetheless, ‘modern science’ seems to have overwhelmingly compromised on its original promises by fitting into an ‘industrial scheme.’ With this concern, ‘molecular phylogeographics with conservational ambitions’ would look an intact ground for research efforts in a ‘school of biotechnology.’ The dog (Canis familiaris) as an earliest domestic animal has a history of conflicts over its origins and dispersal. Having those disputes addressed, valuable knowledge could be acquired on the nature and dynamics of domestication, and of human societies particularly of pre-agricultural ages. We employed two most widely-used genealogical markers, the mitochondrial DNA (mtDNA) and the non-recombining portion of the Y-chromosome (NRY), to address dog demography. Through 582 bps of mtDNA Control Region, complemented with whole mitochondrial genomes, it was established that almost all maternal lineages of the domestic dog worldwide coalesce to a population of at least 51 and perhaps many more female wolves in Asia South of Yangtze River (ASY) approximately 16,000 years before present (BP). This was based on the presence of a maximal diversity in this area, a descending gradient of diversity outward it, and a ubiquitous population structure everywhere in the world. A closer examination of this portrait in Southwest Asia (SwAsia) and the Fertile Crescent (FC), a region which has supplied persuasive evidence on early presence of the domestic dog, retrieved the same information, with implications for backbreeding with the local wolf population. Meanwhile, analyses of mtDNA dispersal showed that dogs took the long way via land to Madagascar Island, and not together with humans via sea. By the other approach, the NRY data in 14,437 bps length supplemented the mtDNA in reporting the height of diversity from ASY with a founding population of at least 13 male wolves, but expectably produced lower inter-regional differentiation by diversity. Screening of NRY by a SNP assay in the dingoes of Australia Island as a population of feral dogs revealed restricted and similar dispersal patterns for sires and dams. Prospects of ancient, multilocus and whole genome assays with the emerging high-throughput technologies has still more to promise on finer elaborations of these issues."
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| 5. |
- Bannikova, Anna A., et al.
(författare)
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Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae) : molecular and morphological analyses with the discussion of tribal affinities
- 2019
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Ingår i: ZooKeys. - : Pensoft Publishers. - 1313-2989 .- 1313-2970. ; :888, s. 133-158
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Tidskriftsartikel (refereegranskat)abstract
- The first genetic study of the holotype of the Gansu short-tailed shrew, Blarinella griselda Thomas, 1912, is presented. The mitochondrial analysis demonstrated that the type specimen of B. griselda is close to several recently collected specimens from southern Gansu, northern Sichuan and Shaanxi, which are highly distinct from the two species of Asiatic short-tailed shrews of southern Sichuan, Yunnan, and Vietnam, B. quadraticauda and B. wardi. Our analysis of four nuclear genes supported the placement of B. griselda as sister to B. quadraticauda / B. wardi, with the level of divergence between these two clades corresponding to that among genera of Soricinae. A new generic name, Parablarinella, is proposed for the Gansu short-tailed shrew. Karyotypes of Parablarinella griselda (2n = 49, NFa = 50) and B. quadraticauda (2n = 49, NFa = 62) from southern Gansu are described. The tribal affinities of Blarinellini and Blarinini are discussed.
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| 6. |
- Barlow, Axel, et al.
(författare)
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Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears
- 2021
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 31:8, s. 1771-1779
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Tidskriftsartikel (refereegranskat)abstract
- Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a 360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals postdivergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
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| 7. |
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| 8. |
- Barnett, Ross, et al.
(författare)
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Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
- 2020
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Ingår i: Current Biology. - 0960-9822 .- 1879-0445.
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Tidskriftsartikel (refereegranskat)abstract
- Summary Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
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| 9. |
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| 10. |
- 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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