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| 2. |
- 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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| 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. |
- 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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| 5. |
- Charette, M, et al.
(författare)
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The Transpolar Drift as a Source of Riverine and Shelf‐Derived Trace Elements to the Central Arctic Ocean
- 2020
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Ingår i: Journal of Geophysical Research - Oceans. - 2169-9275 .- 2169-9291. ; 125, s. 1-34
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Tidskriftsartikel (refereegranskat)abstract
- A major surface circulation feature of the Arctic Ocean is the Transpolar Drift (TPD), a current that transports river‐influenced shelf water from the Laptev and East Siberian Seas toward the center of the basin and Fram Strait. In 2015, the international GEOTRACES program included a high‐resolution pan‐Arctic survey of carbon, nutrients, and a suite of trace elements and isotopes (TEIs). The cruises bisected the TPD at two locations in the central basin, which were defined by maxima in meteoric water and dissolved organic carbon concentrations that spanned 600 km horizontally and ~25–50 m vertically. Dissolved TEIs such as Fe, Co, Ni, Cu, Hg, Nd, and Th, which are generally particle‐reactive but can be complexed by organic matter, were observed at concentrations much higher than expected for the openocean setting. Other trace element concentrations such as Al, V, Ga, and Pb were lower than expected due to scavenging over the productive East Siberian and Laptev shelf seas. Using a combination of radionuclide tracers and ice drift modeling, the transport rate for the core of the TPD was estimated at 0.9 ± 0.4 Sv(106m3 s−1). This rate was used to derive the mass flux for TEIs that were enriched in the TPD, revealing the importance of lateral transport in supplying materials beneath the ice to the central Arctic Ocean and potentially to the North Atlantic Ocean via Fram Strait. Continued intensification of the Arctic hydrologicc ycle and permafrost degradation will likely lead to an increase in the flux of TEIs into the Arctic Ocean.
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| 6. |
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| 7. |
- Li, Xinlei, et al.
(författare)
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Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of White Wagtail Motacilla alba (Aves: Passeriformes).
- 2016
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Ingår i: Journal of Avian Biology. - : Wiley. - 0908-8857 .- 1600-048X. ; 47, s. 263-274
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Tidskriftsartikel (refereegranskat)abstract
- We studied the phylogeography and population history of the white wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of white wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in central and south Europe; and clade SE was distributed in central and east Asia. e deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of east Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. e recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.
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| 8. |
- Qu, Yanhua, 1974-, et al.
(författare)
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Genetic responses to seasonalvariation in altitudinal stress: whole-genome resequencing ofgreat tit in eastern Himalayas
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Species that undertake altitudinal migrations are exposed to a considerable seasonal variationin oxygen levels and temperature. How they cope with this was studied in a population of greattit (Parus major) that breeds at high elevations and winters at lower elevations in the easternHimalayas. Comparison of population genomics of high altitudinal great tits and those living inlowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (aminosugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt,mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR andMAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thusindirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategiesobserved in high altitudinal great tits differ from those described in a closely related species onthe Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selectionin lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparativepopulation genomics also revealed selection for larger body size in high altitudinal great tits.
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| 9. |
- Qu, Yanhua, 1974-, et al.
(författare)
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Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
- 2013
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2071-
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Tidskriftsartikel (refereegranskat)abstract
- The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and 'tit-to-jay' change for coping with the life in an extreme environment.
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| 10. |
- Qu, Yanhua, 1974-, et al.
(författare)
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Postglacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis.
- 2005
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 14:6, s. 1767-81
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Tidskriftsartikel (refereegranskat)abstract
- Most phylogeographical studies of postglacial colonization focus on high latitude locations in the Northern Hemisphere. Here, we studied the phylogeographical structure of the red-necked snow finch Pyrgilauda ruficollis, an endemic species of the Tibetan plateau. We analysed 879 base pairs (bp) of the mitochondrial cytochrome b gene and 529 bp of the control region in 41 birds from four regional groups separated by mountain ranges. We detected 34 haplotypes, 31 of which occurred in a single individual and only three of which were shared among sampling sites within regional groups or among regional groups. Haplotype diversity was high (h = 0.94); nucleotide diversity was low (eth = 0.00415) and genetic differentiation was virtually non-existent. Analyses of mismatch distributions and geographically nested clades yielded results consistent with contiguous range expansion, and the expansion times were estimated as 0.07-0.19 million years ago (Ma). Our results suggest that P. ruficollis colonized the Tibetan plateau after the extensive glacial period (0.5-0.175 Ma), expanding from the eastern margin towards the inner plateau. Thus, in contrast to many of the post-glacial phylogeographical structures known at high latitudes, this colonization occurred without matrilineal population structuring. This might be due to the short glacial cycles typical of the Tibetan plateau, adaptation of P. ruficollis to cold conditions, or refugia and colonized habitat being semicontinuous and thus promoting population mixing.
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