| 1. |
|
|
| 2. |
|
|
| 3. |
- Feng, Shaohong, et al.
(författare)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
|
|
| 4. |
- Bergström, Anders, et al.
(författare)
-
Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
-
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.
|
|
| 5. |
- Liu, Shanlin, et al.
(författare)
-
Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
- 2021
-
Ingår i: Cell. - : Elsevier. - 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.
|
|
| 6. |
|
|
| 7. |
- Richtman Feuerborn, Tatiana, et al.
(författare)
-
Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal
- 2021
-
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. ; 118:39
-
Tidskriftsartikel (refereegranskat)abstract
- Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Northwest Siberia around 2,000 y ago. It is unclear if the Siberian Arctic dog population was as continuous as the people of the region or if instead admixture occurred, possibly in relation to the influx of material culture from other parts of Eurasia. To address this question, we sequenced and analyzed the genomes of 20 ancient and historical Siberian and Eurasian Steppe dogs. Our analyses indicate that while Siberian dogs were genetically homogenous between 9,500 to 7,000 y ago, later introduction of dogs from the Eurasian Steppe and Europe led to substantial admixture. This is clearly the case in the Iamal-Nenets region (Northwestern Siberia) where dogs from the Iron Age period (∼2,000 y ago) possess substantially less ancestry related to European and Steppe dogs than dogs from the medieval period (∼1,000 y ago). Combined with findings of nonlocal materials recovered from these archaeological sites, including glass beads and metal items, these results indicate that Northwest Siberian communities were connected to a larger trade network through which they acquired genetically distinctive dogs from other regions. These exchanges were part of a series of major societal changes, including the rise of large-scale reindeer pastoralism ∼800 y ago.
|
|
| 8. |
- von Seth, J, et al.
(författare)
-
Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations
- 2021
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
-
Tidskriftsartikel (refereegranskat)abstract
- Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
|
|
| 9. |
- Barnett, Ross, et al.
(författare)
-
Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
- 2020
-
Ingår i: Current Biology. - 0960-9822 .- 1879-0445.
-
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.
|
|
| 10. |
- Biancari, F, et al.
(författare)
-
Preoperative risk stratification of deep sternal wound infection after coronary surgery
- 2020
-
Ingår i: Infection control and hospital epidemiology. - : Cambridge University Press (CUP). - 1559-6834 .- 0899-823X. ; 41:4, s. 444-451
-
Tidskriftsartikel (refereegranskat)abstract
- Objective:To develop a risk score for deep sternal wound infection (DSWI) after isolated coronary artery bypass grafting (CABG).Design:Multicenter, prospective study.Setting:Tertiary-care referral hospitals.Participants:The study included 7,352 patients from the European multicenter coronary artery bypass grafting (E-CABG) registry.Intervention:Isolated CABG.Methods:An additive risk score (the E-CABG DSWI score) was estimated from the derivation data set (66.7% of patients), and its performance was assessed in the validation data set (33.3% of patients).Results:DSWI occurred in 181 (2.5%) patients and increased 1-year mortality (adjusted hazard ratio, 4.275; 95% confidence interval [CI], 2.804–6.517). Female gender (odds ratio [OR], 1.804; 95% CI, 1.161–2.802), body mass index ≥30 kg/m2(OR, 1.729; 95% CI, 1.166–2.562), glomerular filtration rate <45 mL/min/1.73 m2(OR, 2.410; 95% CI, 1.413–4.111), diabetes (OR, 1.741; 95% CI, 1.178–2.573), pulmonary disease (OR, 1.935; 95% CI, 1.178–3.180), atrial fibrillation (OR, 1.854; 95% CI, 1.096–3.138), critical preoperative state (OR, 2.196; 95% CI, 1.209–3.891), and bilateral internal mammary artery grafting (OR, 2.088; 95% CI, 1.422–3.066) were predictors of DSWI (derivation data set). An additive risk score was calculated by assigning 1 point to each of these independent risk factors for DSWI. In the validation data set, the rate of DSWI increased along with the E-CABG DSWI scores (score of 0, 1.0%; score of 1, 1.8%; score of 2, 2.2%; score of 3, 6.9%; score ≥4: 12.1%;P< .0001). Net reclassification improvement, integrated discrimination improvement, and decision curve analysis showed that the E-CABG DSWI score performed better than other risk scores.Conclusions:DSWI is associated with poor outcome after CABG, and its risk can be stratified using the E-CABG DSWI score.Trial registration:clinicaltrials.gov identifier: NCT02319083
|
|
