| 1. |
- 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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| 2. |
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| 3. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 4. |
- Bakker, F. T., et al.
(författare)
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The Global Museum: natural history collections and the future of evolutionary science and public education
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.
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| 5. |
- Fleming, E.J., et al.
(författare)
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Provenance of Triassic sandstones on the southwest Barents Shelf and the implication for sediment dispersal patterns in northwest Pangaea.
- 2016
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Ingår i: Marine and Petroleum Geology. - : Elsevier BV. - 0264-8172 .- 1873-4073. ; 78, s. 516-535
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Tidskriftsartikel (refereegranskat)abstract
- Thick Triassic siliciclastic units form major reservoir targets for hydrocarbon exploration on the Barents Shelf; however, poor reservoir quality, possibly associated with variation in provenance, remains a key risk factor in the area. In this study, sandstone dispersal patterns on the southwest Barents Shelf are investigated through petrographic and heavy mineral analysis, garnet and rutile geochemistry and zircon U-Pb geochronology. The results show that until the Early Norian Maximum Flooding Surface, two contrasting sand types were present: (i) a Caledonian Sand Type, characterised by a high compositional maturity, a heavy mineral assemblage dominated by garnet and low chrome-spinel:zircon (CZi) values, predominantly metapelitic rutiles and mostly Proterozoic and Archaean detrital zircon ages, interpreted to be sourced from the Caledonides, and (ii) a Uralian Sand Type, characterised by a low compositional maturity, high CZi values, predominantly metamafic rutiles and Carboniferous zircon ages, sourced from the Uralian Orogeny. In addition, disparity in detrital zircon ages of the Uralian Sand Type with contiguous strata on the northern Barents Shelf reveals the presence of a Northern Uraloid Sand Type, interpreted to have been sourced from Taimyr and Severnaya Zemlya. As such, a coincidental system is inferred which delivered sand to the Northern Barents Shelf in the late Carnian/early Norian. Following the Early Norian Maximum Flooding Surface, a significant provenance change occurs. In response to Late Triassic/Early Jurassic hinterland rejuvenation, supply from the Uralian Orogen ceased and the northern Scandinavian (Caledonian) source became dominant, extending northwards out on to the southwest Barents Shelf. The data reveal a link between reservoir quality and sand type and illustrate how provenance played an important role in the development of clastic reservoirs within the Triassic of the Barents Shelf.
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| 6. |
- Pointon, Michael A., et al.
(författare)
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A Multi-proxy Provenance Study of Late Carboniferous to Middle Jurassic Sandstones in the Eastern Sverdrup Basin and Its Bearing on Arctic Palaeogeographic Reconstructions
- 2022
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Ingår i: Geosciences. - : MDPI AG. - 2076-3263. ; 13:1, s. 10-10
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Tidskriftsartikel (refereegranskat)abstract
- A multi-proxy provenance study of Late Carboniferous to Middle Jurassic sandstones from the eastern Sverdrup Basin was undertaken employing optical petrography and heavy mineral analysis, chemical analysis of apatite, garnet and rutile grains, as well as detrital zircon U–Pb geochronology and Hf isotope analysis. Late Carboniferous to Middle Jurassic strata on the southern basin margin are inferred as being predominantly reworked from Silurian to Devonian strata within the adjacent Franklinian Basin succession. Higher-grade metamorphic detritus appeared during Middle to Late Triassic times and indicates exhumation and erosion of lower (Neoproterozoic to Cambrian) levels within the Franklinian Basin succession and/or a direct detrital input from the Canadian-Greenland Shield. The provenance of northern-derived sediments is more enigmatic owing to the subsequent opening of the Arctic Ocean. Northern-derived Middle Permian to Early Triassic sediments were likely derived from proximal areas of the Chukotkan part of the Arctic Alaska-Chukotka microplate. Late Triassic northern-derived sediments have different detrital zircon U–Pb age spectra from Middle Permian to Early Triassic ones and were likely derived from the Uralian orogenic belt and/or the Arctic Uralides. The loss of this sand input during latest Triassic times is interpreted to reflect drainage reorganisation farther upstream on the Barents Shelf. Middle Jurassic sands in the northern and axial parts of the basin were largely reworked from local northern-derived Late Triassic strata. This may have been facilitated by rift flank uplift of the northern basin margin in response to rifting in the adjacent proto-Amerasia Basin.
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| 7. |
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| 8. |
- 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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| 9. |
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| 10. |
- 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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