| 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. |
- Divakar, Pradeep K., et al.
(författare)
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Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1217-1226
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Tidskriftsartikel (refereegranskat)abstract
- We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
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| 3. |
- 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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| 4. |
- Garcia, Victor B., et al.
(författare)
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The Neoarchean GT-34 Ni deposit, Carajás mineral Province, Brazil : An atypical IOCG-related Ni sulfide mineralization
- 2020
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Ingår i: Ore Geology Reviews. - 0169-1368 .- 1872-7360. ; 127
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Tidskriftsartikel (refereegranskat)abstract
- The GT-34 deposit, located 12 km to the SW of the Sossego copper–gold mine in the Carajás Province, northern Brazil, represents an unusual Ni sulfide mineralization. The deposit occurs along a NE-SW-trending sub-vertical shear zone marked by progressive Mg-alkalic alteration zones, predominantly hosted in granitic and locally in granodioritic to tonalitic orthogneisses. Initial alteration zones result in unique scapolite-orthopyroxene assemblage, which is partially preserved within pervasive hornblende-chlorapatite ± plagioclase replacement zones. Nickel mineralization occurs mainly as matrix-supported breccias characterized by a pentlandite-pyrrhotite-rich matrix and rounded fragments chiefly of hornblende and chlorapatite. Irregular stockworks and net textured veins containing chalcopyrite-pentlandite are less common. Phlogopite ± talc ± actinolite alteration and late-stage veinlets crosscut the previous alteration zones and the mineralization. The phlogopite ± talc ± actinolite alteration occurs as irregular veins and chalcopyrite-pyrrhotite-magnetite are commonly observed where such alteration intersects the Ni mineralization. Late-stage veinlets are represented by K feldspar-epidote-chlorite-calcite and quartz-albite-chlorite-calcite-epidote veins, both containing minor amounts of millerite, pyrite and F-OH-apatite. High-resolution SIMS U-Pb zircon geochronology obtained for the GT-34 deposit revealed an age of 2828 ± 4 Ma for zircon grains inherited from the host orthogneisses. The timing of the mineralization altered zircon grains from the scapolite-orthopyroxene and phlogopite ± talc ± actinolite alteration zones, is attributed to an age interval between 2751 and 2720 Ma. Although poorly constrained, the geochronological data corroborate a Neoarchean age for the GT-34 Ni mineralization, similar to that of other IOCG deposits in the Carajás Province and coeval with the bimodal magmatism in the area. The atypical orthopyroxene-marialite mineral chemistry support a metasomatic crystallization at high temperatures (>700 °C), low aH2O (<0.5) and pressures between 5 and 7 kbar. Hypersaline fluids, as the ones described for the IOCG deposits in Carajás at such PxT conditions, would enable the orthopyroxene-marialite crystallization, as supported by experimental studies available in the literature. Mineralogical and geochemical considerations on the nature of the Ni sulfide mineralization points toward a metasomatic origin, feasible with the predicted P-T-fluid scenario for the hydrothermal alteration. Such conditions raise the initial temperature and pressure estimates of the IOCG metasomatic alteration by at least 200 °C and pressure up to 7 kbar, making it the hottest and probably deepest IOCG-related metasomatic alteration known to date for Carajás.
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