| 31. |
- Crous, P. W., et al.
(författare)
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Fusarium : more than a node or a foot-shaped basal cell
- 2021
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Ingår i: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
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Tidskriftsartikel (refereegranskat)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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| 32. |
- Dahlin, Peter, 1974-, et al.
(författare)
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Source character, mixing, fractionation and alkali metasomatismin in Palaeoproterozoic greenstone dykes, Dannemora area, NE Bergslagen region, Sweden
- 2013
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Ingår i: Geological Magazine. - Cambridge : Cambridge Academic. - 0016-7568 .- 1469-5081. ; 151:04, s. 573-590
-
Tidskriftsartikel (refereegranskat)abstract
- The geochemical and isotopic characteristics of metamorphosed Svecofennian maficdykes from the Dannemora area in the NE part of the Bergslagen region in central Sweden wereinvestigated and compared to mafic intrusive rocks in their vicinity. The dykes, with an inferred ageof c. 1860–1870 Ma, are calc-alkaline, sub-alkaline and basaltic in composition and have a mixedsubduction and within-plate geochemical affinity. They are the result of mixing of at least three mantlesource components with similar basaltic major element composition, but different concentrations ofincompatible trace elements. Magma M1 is strongly enriched both in Rare Earth Elements (REE)and High-Field-Strength Elements (HFSE); magma M2 is highly enriched in Large-Ion LithophileElements (LILE, except Sr) with only moderate enrichment in HFSE and REE (particularly low inHeavy Rare Earth Elements); and magma M3 is enriched in Sr and has a flat REE profile. MagmaM3 also has a somewhat more positive (depleted) initial εNd value of +1.8, compared to +0.4 to +0.5 for magmas M1 and M2. The magma evolution was controlled by a mixture of fractionation (mainlyaffecting the compatible elements) and mixing, best seen in the incompatible element concentrationsand the Nd isotope data. The basaltic overall composition indicates little or no wholesale contaminationby upper continental crust, but the dykes have undergone later metasomatic changes mainly affectingthe alkali elements.
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| 33. |
- Dalen, Love, et al.
(författare)
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Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:16, s. 6726-6729
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Tidskriftsartikel (refereegranskat)abstract
- How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.
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| 34. |
- Dalen, L, et al.
(författare)
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Identifying species from pieces of faeces
- 2004
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Ingår i: Conservation Genetics. - DORDRECHT : KLUWER ACADEMIC PUBL. - 1566-0621 .- 1572-9737. ; 5:1, s. 109-111
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Tidskriftsartikel (refereegranskat)
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| 35. |
- Dalen, Love, et al.
(författare)
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Partial Genetic Turnover in Neandertals : Continuity in the East and Population Replacement in the West
- 2012
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 29:8, s. 1893-1897
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Tidskriftsartikel (refereegranskat)abstract
- Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (< 48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (> 48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region.
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| 36. |
- Dastoor, Ashu, et al.
(författare)
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Arctic mercury cycling
- 2022
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Ingår i: Nature Reviews Earth & Environment. - : Springer Nature. - 2662-138X. ; 3:4, s. 270-286
-
Forskningsöversikt (refereegranskat)abstract
- Anthropogenic mercury (Hg) emissions have driven marked increases in Arctic Hg levels,which are now being impacted by regional warming, with uncertain ecological consequences. This Review presents a comprehensive assessment of the present-day total Hg mass balance in the Arctic. Over 98% of atmospheric Hg is emitted outside the region and is transported to the Arctic via long-range air and ocean transport. Around two thirds of this Hg is deposited in terrestrial ecosystems, where it predominantly accumulates in soils via vegetation uptake. Rivers and coastal erosion transfer about 80 Mg year−1 of terrestrial Hg to the Arctic Ocean, in approximate balance with modelled net terrestrial Hg deposition in the region. The revised Arctic Ocean Hg mass balance suggests net atmospheric Hg deposition to the ocean and that Hg burial in inner-shelf sediments is underestimated (up to >100%), needing seasonal observations of sediment-oceanHg exchange. Terrestrial Hg mobilization pathways from soils and the cryosphere (permafrost, ice, snow and glaciers) remain uncertain. Improved soil, snowpack and glacial Hg inventories, transfer mechanisms of riverine Hg releases under accelerated glacier and soil thaw, coupled atmosphere– terrestrial modelling and monitoring of Hg in sensitive ecosystems such as fjords can help toanticipate impacts on downstream Arctic ecosystems.
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| 37. |
- de Anca Prado, Violeta, 1996-, et al.
(författare)
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Discovering the world of fossil fungi
- 2020
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Ingår i: Deposits Magazine. - Southwold, UK : UKGE Limited. - 1744-9588. ; 2020, s. 1-7
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- When people think of fossils, they usually picture slabs of rock bristling with bones, or the shells of ammonites or trilobites. Most do not even consider that delicate organisms, such as fungi or bacteria, can even fossilize – they seem too fragile to be preserved as they lack a hard skeleton. In many cases this is true. Microscopic organisms that lack hard parts have fewer chances of being fossilised but, despite the odds, delicate fungi have a fossil record that is more extensive than generally thought.
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| 38. |
- Deegan, Frances, et al.
(författare)
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Boron isotope fractionation in magma via crustal carbonate dissolution.
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Carbon dioxide released by arc volcanoes is widely considered to originate from the mantle and from subducted sediments. Fluids released from upper arc carbonates, however, have recently been proposed to help modulate arc CO2 fluxes. Here we use boron as a tracer, which substitutes for carbon in limestone, to further investigate crustal carbonate degassing in volcanic arcs. We performed laboratory experiments replicating limestone assimilation into magma at crustal pressure-temperature conditions and analysed boron isotope ratios in the resulting experimental glasses. Limestone dissolution and assimilation generates CaO-enriched glass near the reaction site and a CO2-dominated vapour phase. The CaO-rich glasses have extremely low δ11B values down to −41.5‰, reflecting preferential partitioning of 10B into the assimilating melt. Loss of 11B from the reaction site occurs via the CO2 vapour phase generated during carbonate dissolution, which transports 11B away from the reaction site as a boron-rich fluid phase. Our results demonstrate the efficacy of boron isotope fractionation during crustal carbonate assimilation and suggest that low δ11B melt values in arc magmas could flag shallow-level additions to the subduction cycle.
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| 39. |
- Deegan, Frances M., et al.
(författare)
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Pyroxene standards for SIMS oxygen isotope analysis and their application to Merapi volcano, Sunda arc, Indonesia
- 2016
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Ingår i: Chemical Geology. - : Elsevier BV. - 0009-2541 .- 1872-6836. ; 447, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Measurement of oxygen isotope ratios in common silicate minerals such as olivine, pyroxene, feldspar, garnet, and quartz is increasingly performed by Secondary Ion Mass Spectrometry (SIMS). However, certain mineral groups exhibit solid solution series, and the large compositional spectrum of these mineral phases will result in matrix effects during SIMS analysis. These matrix effects must be corrected through repeated analysis of compositionally similar standards to ensure accurate results. In order to widen the current applicability of SIMS to solid solution mineral groups in common igneous rocks, we performed SIMS homogeneity tests on new augite (NRM-AG-1) and enstatite (NRM-EN-2) reference materials sourced from Stromboli, Italy and Webster, North Carolina, respectively. Aliquots of the standard minerals were analysed by laser fluorination (LF) to establish their δ18O values. Repeated SIMS measurements were then performed on randomly oriented fragments of the same pyroxene crystals, which yielded a range in δ18O less than ± 0.42 and ± 0.58‰ (2σ) for NRM-AG-1 and NRM-EN-2, respectively. Homogeneity tests verified that NRM-AG-1 and NRM-EN-2 do not show any crystallographic orientation bias and that they are sufficiently homogeneous on the 20 μm scale to be used as routine mineral standards for SIMS δ18O analysis. We subsequently tested our new standard materials on recently erupted pyroxene crystals from Merapi volcano, Indonesia. The δ18O values for Merapi pyroxene obtained by SIMS (n = 204) agree within error with the LF-derived δ18O values for Merapi pyroxene but differ from bulk mineral and whole-rock data obtained by conventional fluorination. The bulk samples are offset to higher δ18O values as a result of incorporation of mineral and glass inclusions that in part reflects crustal contamination processes. The Merapi pyroxene SIMS data, in turn, display a frequency peak at 5.8‰, which allows us to estimate the δ18O value of the primary mafic magma at Merapi to ~ 6.1‰ when assuming closed system differentiation.
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| 40. |
- Dehasque, Marianne, et al.
(författare)
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Inference of natural selection from ancient DNA
- 2020
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Ingår i: Evolution Letters. - : JOHN WILEY & SONS LTD. - 2056-3744. ; 4:2, s. 94-108
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
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