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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. |
- 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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- 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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