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- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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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.
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| 3. |
- Radchuk, Viktoriia, et al.
(författare)
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Adaptive responses of animals to climate change are most likely insufficient
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
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- Sjöström, Jenny K., 1978-, et al.
(författare)
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Late Holocene peat paleodust deposition in south-western Sweden : exploring geochemical properties, local mineral sources and regional aeolian activity
- 2022
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Ingår i: Chemical Geology. - : Elsevier. - 0009-2541 .- 1872-6836. ; 602
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric mineral dust not only interacts with the climate system by scattering incoming solar radiation and affecting atmospheric photochemistry, but also contributes critical nutrients to marine and terrestrial ecosystems. In a high-resolution analysis of paleodust deposition, peat development and soil dust sources, we assess the interplay between dust deposition and bog development of the Davidsmosse bog in south-western Sweden. Analyses of the 5400-year record (458 cm) included radiocarbon dating, bulk density, ash content, chemical and mineralogical composition and carbon stable isotopes, subsequently explored using principal component analysis. Fourteen dust events (DEs) were recorded (cal BP) in the peat sequence: 3580–3490; 3280; 3140; 3010–2840; 2740; 2610; 2480; 2340; 2240–2130; 1690; 1240; 960, 890–760, and 620–360. The majority of the DEs were coupled to increases in peat accumulation rates and increased nutrient content (N, P and K) suggesting that the DEs contributed with nutrients to the bog ecosystem, promoting increased accumulation. We also analyzed the chemical and mineral composition of potential mineral source deposits (separated into 6 grain-size fractions) from sites within a 4 km radius as well as aeolian dunes closer to the coast (25 km). The composition deposited on the present-day bog surface indicates that the bulk of the contemporary minerals have a local origin (<1.5 km), but the DEs may be of a more distant origin. The results also indicate that quartz and plagioclase feldspar content consistently increase with increasing grain-size, both in the source samples as well as in the peat sequence, and that the Si/Al ratio can be used to infer grain size changes in the peat. Two longer phases saw numerous DEs, between 2800 and 2130 cal BP and a stepwise increase from 960 towards 360 cal BP. The episodic character of the events, together with the inferred coarse grain size, suggest that the particles were deposited by (winter) storms. Future studies should include grain size analysis as well as a more in-depth comparison with regional paleo dust and storm records to increase knowledge on both transport processes (creep, saltation, suspension) and the climate processes driving late Holocene dust and storm events in Scandinavia.
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