| 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. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 3. |
- Fontorbe, Guillaume, et al.
(författare)
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Enrichment of dissolved silica in the deep equatorial Pacific during the Eocene-Oligocene
- 2017
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Ingår i: Paleoceanography. - 0883-8305 .- 1944-9186. ; 32, s. 848-863
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Tidskriftsartikel (refereegranskat)abstract
- Silicon isotope ratios (expressed as δ30Si) in marine microfossils can provide insights into silica cycling over geologic time. Here we used δ30Si of sponge spicules and radiolarian tests from the Paleogene Equatorial Transect (Ocean Drilling Program Leg 199) spanning the Eocene and Oligocene (~50–23 Ma) to reconstruct dissolved silica (DSi) concentrations in deep waters and to examine upper ocean δ30Si. The δ30Si values range from 3.16 to +0.18‰ and from 0.07 to +1.42‰ for the sponge and radiolarian records, respectively. Both records show a transition toward lower δ30Si values around 37 Ma. The shift in radiolarian δ30Si is interpreted as a consequence of changes in the δ30Si of source DSi to the region. The decrease in sponge δ30Si is interpreted as a transition from low DSi concentrations to higher DSi concentrations, most likely related to the shift toward a solely Southern Ocean source of deep water in the Pacific during the Paleogene that has been suggested by results from paleoceanographic tracers such as neodymium and carbon isotopes. Sponge δ30Si provides relatively direct information about the nutrient content of deep water and is a useful complement to other tracers of deep water circulation in the oceans of the past.
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| 4. |
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| 5. |
- Field, Daniel J, et al.
(författare)
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Early Evolution of Modern Birds Structured by Global Forest Collapse at the End-Cretaceous Mass Extinction
- 2018
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Ingår i: Current Biology. - Amsterdam : Elsevier. - 0960-9822 .- 1879-0445. ; 28, s. 1825-1831
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Tidskriftsartikel (refereegranskat)abstract
- The fossil record and recent molecular phylogenies support an extraordinary early-Cenozoic radiation of crown birds (Neornithes) after the Cretaceous-Paleogene (K-Pg) mass extinction [1–3 ]. However, questions remain regarding the mechanisms underlying the survival of the deepest lineages within crown birds across the K-Pg boundary, particularly since this global catastrophe eliminated even the closest stem-group relatives of Neornithes [4 ]. Here, ancestral state reconstructions of neornithine ecology reveal a strong bias toward taxa exhibiting predominantly non-arboreal lifestyles across the K-Pg, with multiple convergent transitions toward predominantly arboreal ecologies later in the Paleocene and Eocene. By contrast, ecomorphological inferences indicate predominantly arboreal lifestyles among enantiornithines, the most diverse and widespread Mesozoic avialans [5–7 ]. Global paleobotanical and palynological data show that the K-Pg Chicxulub impact triggered widespread destruction of forests [8, 9 ]. We suggest that ecological filtering due to the temporary loss of significant plant cover across the K-Pg boundary selected against any flying dinosaurs (Avialae [10 ]) committed to arboreal ecologies, resulting in a predominantly non-arboreal postextinction neornithine avifauna composed of totalclade Palaeognathae, Galloanserae, and terrestrial total-clade Neoaves that rapidly diversified into the broad range of avian ecologies familiar today. The explanation proposed here provides a unifying hypothesis for the K-Pg-associated mass extinction of arboreal stem birds, as well as for the post-K-Pg radiation of arboreal crown birds. It also provides a baseline hypothesis to be further refined pending the discovery of additional neornithine fossils from the Latest Cretaceous and earliest Paleogene.
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| 7. |
- Langa, Malose M., et al.
(författare)
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Chromite chemistry of a massive chromitite seam in the northern limb of the Bushveld Igneous Complex, South Africa: correlation with the UG-2 in the eastern and western limbs and evidence of variable assimilation of footwall rocks
- 2021
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Ingår i: Mineralium Deposita. - : Springer Science and Business Media LLC. - 0026-4598 .- 1432-1866. ; 56:1, s. 31-44
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Tidskriftsartikel (refereegranskat)abstract
- The Bushveld Igneous Complex (BIC) is known for its laterally extensive platinum group element–bearing layers, the most famous being the Merensky Reef and the UG-2 chromitite in the eastern and western limbs of the complex. In the northern limb, the Platreef mineralization and a thick chromitite seam below it (referred to as the “UG-2 equivalent” or UG-2E) have been proposed to be the stratigraphic equivalents of the Merensky Reef and the UG-2, respectively. In this study, we compare a suite of UG-2E samples from the Turfspruit project with a UG-2 reference suite from the western limb using petrography, electron probe microanalysis, laser ablation-inductively coupled plasma-mass spectrometry, and Mössbauer spectroscopy. The results show that (a) in Mg# vs. Cr# diagrams, UG-2E chromites have a distinct compositional field; however, when samples of similar chromite modal abundance (≥ 80%) are used, the UG-2E chromites overlap the field that characterizes UG-2 chromites; (b) the UG-2E is more variable in chromite modal abundance than the UG-2; and (c) variations in Mg# and Fe3+/ΣFe in the UG-2E indicate contamination of the magma by metasedimentary rocks of the Duitschland Formation (Transvaal Supergroup) during emplacement, followed by partial re-equilibration of chromite grains with a trapped melt. Thus, we conclude that for chromite modes higher than 80%, the chromite composition retains enough information to allow correlation and that the UG-2E in the northern limb is very likely the UG-2 chromitite.
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