| 1. |
- 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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| 2. |
- 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. |
- Polme, S., et al.
(författare)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 4. |
- Davies, Thomas G., et al.
(författare)
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Open data and digital morphology.
- 2017
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1852, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.
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| 5. |
- 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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| 6. |
- Gardiner, N.J., et al.
(författare)
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Contrasting Granite Metallogeny through the Zircon Record: A Case Study from Myanmar
- 2017
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Ingår i: Scientific Reports. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Granitoid-hosted mineral deposits are major global sources of a number of economically important metals. The fundamental controls on magma metal fertility are tectonic setting, the nature of source rocks, and magma differentiation. A clearer understanding of these petrogenetic processes has been forged through the accessory mineral zircon, which has considerable potential in metallogenic studies. We present an integrated zircon isotope (U-Pb, Lu-Hf, O) and trace element dataset from the paired Cu-Au (copper) and Sn-W (tin) magmatic belts in Myanmar. Copper arc zircons have juvenile εHf (+7.6 to +11.5) and mantle-like δ18O (5.2–5.5‰), whereas tin belt zircons have low εHf (−7 to −13) and heavier δ18O (6.2–7.7‰). Variations in zircon Hf and U/Yb reaffirm that tin belt magmas contain greater crustal contributions than copper arc rocks. Links between whole-rock Rb/Sr and zircon Eu/Eu* highlight that the latter can monitor magma fractionation in these systems. Zircon Ce/Ce* and Eu/Eu* are sensitive to redox and fractionation respectively, and here are used to evaluate zircon sensitivity to the metallogenic affinity of their host rock. Critical contents of Sn in granitic magmas, which may be required for the development of economic tin deposits, are marked by zircon Eu/Eu* values of ca. ≤0.08.
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| 7. |
- Merle, Renaud E., 1976-, et al.
(författare)
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Pb-Pb ages and initial Pb isotopic composition of lunar meteorites : NWA 773 clan, NWA 4734, and Dhofar 287
- 2020
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Ingår i: Meteoritics and Planetary Science. - : John Wiley & Sons, Ltd. - 1086-9379 .- 1945-5100. ; 55:8
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Constraining the duration of magmatic activity on the Moon is essential to understand how the lunar mantle evolved chemically through time. Determining age and initial isotopic compositions of mafic lunar meteorites is a critical step in defining the periods of magmatic activity that occurred during the history of the Moon and to constrain the chemical characteristics of mantle components involved in the sources of the magmas. We have used the in situ Pb-Pb SIMS technique to investigate eight lunar gabbros and basalts, including six meteorites from the Northwest Africa (NWA) 773 clan (NWA 2727, NWA 2700, NWA 3333, NWA 2977, NWA 773, and NWA 3170), NWA 4734, and Dhofar 287A. These samples have been selected as there is no clear agreement on their age and they are all from the dominant low titanium chemical group. We have obtained ages of 2981 ± 12 Ma for NWA 4734 and 3208 ± 22 Ma for Dhofar 287. For the NWA 773 clan, four samples (the fine-grained basalt NWA 2727 and the three gabbros NWA 773, NWA 2977, NWA 3170) out of six yielded isochron-calculated ages that are identical within uncertainties and yielding an average age of 3086 ± 5 Ma. The age obtained for the fine-grained basalt NWA 2700 is not precise enough for comparison with the other samples. The gabbroic sample NWA 3333 yielded an age of 3038 ± 20 Ma suggesting that two distinct magmatic events may be recorded in the meteorites of the NWA 773 clan. The present study aims to identify and assess all potential issues that are associated with different ways to date lunar rocks using U-Pb?based methods. To achieve this, we have compared the new ages with the previously published data set. The entire age data set from lunar mafic meteorites was also screened to identify data showing analytical issues and evidence of resetting and terrestrial contamination. The data set combining the ages of mafic lunar meteorites and Apollo rocks suggests pulses of magmatic activity with two distinct phases between 3950 and 3575 Ma and between 3375 and 3075 Ma with the two phases separated by a gap of approximately 200 Ma. The evolution of the Pb initial ratios of the low-Ti mare basalts between approximately 3400 and 3100 Ma suggests that these rocks were progressively contaminated by a KREEP-like component.
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| 8. |
- Virtasalo, J.J., et al.
(författare)
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Pyritic event beds and sulfidized Fe (oxyhydr)oxide aggregates in metalliferous black mudstones of the Paleoproterozoic Talvivaara formation, Finland
- 2015
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Ingår i: Earth and Planetary Science Letters. - : Elsevier BV. - 0012-821X .- 1385-013X. ; 432, s. 449-460
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Tidskriftsartikel (refereegranskat)abstract
- The Paleoproterozoic, 2.0–1.9 Ga Talvivaara formation of Finland was deposited during the Shunga Event, a worldwide episode of enhanced accumulation of organic-rich sediments in the aftermath of the Lomagundi–Jatuli carbon isotope excursion. Sulfidic carbonaceous mudstones in the Talvivaara formation contain one of the largest known shale-hosted nickel deposits. In order to gain new insight into this Shungian sedimentary environment, sedimentological, petrographical and in situ S and Fe isotopic microanalyses were carried out on samples representing depositional and early-diagenetic conditions. The event-bedded lithology with tidal signatures in the organic-rich mudstones strongly indicates deposition from predominantly river-delivered mud on a highly-productive coastal area, below storm-wave base. The riverine supply of phosphorus, sulfate and iron supported high primary productivity and resulted in strong lateral and vertical chemical gradients in the nearshore waters with a shallow oxic surface layer underlain by euxinic water. The stratigraphic upper part of the Talvivaara formation contains banded intervals of thin alternating pyrite beds and carbonaceous mudstone beds. The pyrite beds were deposited by seaward excursions of the concentrated, acidic Fe-rich river plume subsequent to droughts or dry seasons, which led to intense pyrite precipitation upon mixing with euxinic waters. δS34 and δFe56 values of the bedded pyrite (median δS34=−10.3‰ and δFe56=−0.79‰) are consistent with the reaction of dissolved Fe(II) with H2S from bacterial sulfate reduction. Organic-rich clayey Fe-monosulfide-bearing granules were transported from the muddy estuary, and enclosed in Fe (oxyhydr)oxide aggregates that were forming by wave and current reworking in nearshore accumulations of river-delivered iron. The isotopic composition of these presently pyrrhotitic inclusions (median δS34=−3.3‰ and δFe56=−1.6‰) indicates microbial iron reduction. The Fe (oxyhydr)oxide aggregates were transported in muddy debris flows to the distal euxinic seafloor. Their Fe (oxyhydr)oxide matrix was replaced by pyrite (median δS34=+5.8‰ and δFe56=+0.81‰) at shallow sediment depths with 34S and 56Fe-enriched porewater. Wavy-crinkly laminae of possible microbial origin developed on the euxinic seafloor during low sedimentation. These results indicate episodic deposition at seasonal to multiannual time scales. δS34 and δFe56 values in the studied Fe-sulfides provide evidence of microbial isotope fractionation processes and syndepositional and early-diagenetic origin, finding no support for the previously proposed local hydrothermal activity in the Talvivaara mudstones.
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| 9. |
- Bellucci, J. J., et al.
(författare)
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Tracing martian surface interactions with the triple O isotope compositions of meteoritic phosphates
- 2020
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Ingår i: Earth and Planetary Science Letters. - : Elsevier BV. - 0012-821X .- 1385-013X. ; 531
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Tidskriftsartikel (refereegranskat)abstract
- The triple oxygen isotope compositions of phosphate grains in six martian meteorites have been measured by Secondary Ion Mass Spectrometry (SIMS) and combined together with their chlorine isotope and halogen concentrations have been used to constrain hydrosphere-lithosphere interactions on Mars. These samples include three enriched shergottites (Zagami, Roberts Massif 04262 and Larkman Nunatak 12011), one depleted shergottite (Tissint), an orthopyroxenite (Allan Hills 84001), and a regolith breccia (Northwest Africa 7533). The phosphates measured here have a range in δ18O [(18O/16O)sample/(18O/16O)Standard-1] × 103] from +1.0 to +6.8‰ and could be a result of indigenous mantle values, mixing with martian water, or replacement reactions taking place on the surface of Mars. Three samples have a Δ17O [δ17O-1000(1 + δ18O /1000)0.528-1] in equilibrium with the martian mantle (ALH 84001, Tissint, and Zagami), while three samples (LAR 12011, RBT 04262, and NWA 7533) have an elevated positive Δ17O outside of analytical uncertainty of the martian fractionation line (MFL). The phosphates in the latter group also have positive and negative δ37Cl [(37Cl/35Cl)sample/(37Cl/35Cl)standard – 1] × 103] and enrichments in halogens not seen in the rest of the sample suite. Perchlorate formation on Earth fractionates Cl in both positive and negative directions and generates a correlated positive Δ17O. Further, perchlorate has been detected in wt% amounts on the martian surface. Thus, these results strongly suggest the presence of multiple Cl isotope reservoirs on the martian surface that have interacted with the samples studied here over the last ca. 2 Ga of geologic time. The weighted average of Δ17O measurements from phosphate grains (n = 13) in NWA 7533, which are the explicit result of exchange reactions on the martian surface, yields a statistically robust mean value of 1.39 ± 0.19‰ (2σ, MSWD = 1.5, p = 0.13). This value likely represents an accurate estimate for an oxidized surface reservoir on Mars.
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| 10. |
- Bollard, J., et al.
(författare)
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Early formation of planetary building blocks inferred from Pb isotopic ages of chondrules.
- 2017
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The most abundant components of primitive meteorites (chondrites) are millimeter-sized glassy spherical chondrules formed by transient melting events in the solar protoplanetary disk. Using Pb-Pb dates of 22 individual chondrules, we show that primary production of chondrules in the early solar system was restricted to the first million years after the formation of the Sun and that these existing chondrules were recycled for the remaining lifetime of the protoplanetary disk. This finding is consistent with a primary chondrule formation episode during the early high-mass accretion phase of the protoplanetary disk that transitions into a longer period of chondrule reworking. An abundance of chondrules at early times provides the precursor material required to drive the efficient and rapid formation of planetary objects via chondrule accretion.
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