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1.
  • Nilsson, R. Henrik, 1976-, et al. (författare)
  • Mycobiome diversity: high-throughput sequencing and identification of fungi.
  • 2019
  • Ingår i: Nature reviews. Microbiology. - 1740-1534. ; 17, s. 95-109
  • Forskningsöversikt (refereegranskat)abstract
    • Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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2.
  • Rosenblad, Magnus Alm, et al. (författare)
  • Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
  • 2016
  • Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 13, s. 21-33
  • Tidskriftsartikel (refereegranskat)abstract
    • During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
3.
  • Zhao, Min, et al. (författare)
  • Phylogenetic position of the Wallcreeper Tichodroma muraria
  • 2016
  • Ingår i: Journal Of Ornithology. - 0021-8375. ; 157:3, s. 913-918
  • Tidskriftsartikel (refereegranskat)abstract
    • The Wallcreeper Tichodroma muraria is usually placed in a monotypic family or subfamily within the superfamily Certhioidea, with assumed close relationships to Certhia (treecreepers), Sitta (nuthatches) and Salpornis (spotted creepers). Previous studies have suggested that Tichodroma is most closely related to Sitta, alternatively to Salpornis. We analysed the relationships of Tichodroma using two mitochondrial and five nuclear loci. The tree based on concatenated sequences strongly supported a sister relationship between Tichodroma and Sitta, as well as between Salpornis and Certhia. However, species tree analysis (MP-EST) was unable to resolve these relationships, and although the concatenation tree remains the best hypothesis, more data are needed to corroborate this.
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4.
  • Airaud, M, et al. (författare)
  • Biologie - Les manuels visuels pour la Licence
  • 2018
  • Bok (övrigt vetenskapligt)abstract
    • En couleurs et très illustré, ce manuel a été conçu pour vous qui débutez un cursus scientifique universitaire. Il vous permettra d’acquérir les connaissances fondamentales en biologie, mais aussi la démarche et la rigueur scientifiques indispensables aux études supérieures. De multiples rubriques vous garantissent un apprentissage progressif et complet : un cours visuel avec de nombreux exemples concrets pour introduire et illustrer les notions et concepts clés ; des encadrés méthodologiques pour vous guider vers les bonnes pratiques et vous faire découvrir les grandes méthodes expérimentales ; des focus sur des applications, sujets de recherche ou thèmes d’actualité ; des repères historiques ; de nombreux QCM et exercices (tous corrigés) pour tester vos acquis et vous entraîner.
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5.
  • Alström, Per, et al. (författare)
  • A review of the recent advances in the systematics of the avian superfamily Sylvioidea
  • 2013
  • Ingår i: Chinese Birds. - 1674-7674. ; 4:2, s. 99-131
  • Tidskriftsartikel (refereegranskat)abstract
    • The systematics of the avian superfamily Sylvioidea are reviewed, focusing on studies of relationships among families and within genera, more superficially on taxonomic studies at the species level. For the families Bernieridae and Phylloscopidae, new analyses based on already published sequence data are presented. Our understanding of relationships has been vastly improved in recent years due to a large number of molecular studies. However, the relationships among the different families remain largely obscured, probably mainly as a result of rapid divergence of the different primary lineages (families). Also, species level taxonomy has been much improved in recent years due to a large number of studies applying molecular markers and/or vocalizations and other life-history data. It seems likely that the number of species will continue to increase, as new groups are being studied with modern integrative methods.
6.
  • Alström, Per, et al. (författare)
  • Dramatic niche shifts and morphological change in two insular bird species
  • 2015
  • Ingår i: Royal Society Open Science. - 2054-5703. ; 2:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.
7.
  • Alström, Per, et al. (författare)
  • Integrative taxonomy of the Plain-backed Thrush (Zoothera mollissima) complex (Aves, Turdidae) reveals cryptic species, including a new species.
  • 2016
  • Ingår i: Avian research. - 2053-7166. ; 7:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric.Methods: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic (two mitochondrial and two nuclear markers), ecological and distributional datasets.Results: In earlier field observations, we noted two very different song types of “Plain-backed” Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China (“Alpine Thrush”); a forest breeder in the eastern Himalayas and northwest Yunnan (at least), China (“Himalayan Forest Thrush”); and a forest breeder in central Sichuan (“Sichuan Forest Thrush”). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists (“Yunnan Thrush”). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative “Yunnan Thrush” as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato (s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto (s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush.Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises at least three species: Alpine Thrush Z. mollissima s.s., with a widespread alpine breeding distribution; Sichuan Forest Thrush Z. griseiceps, breeding in central Sichuan forests; and Himalayan Forest Thrush, breeding in the eastern Himalayas and northwest Yunnan (at least), which is described herein as a new species. “Yunnan Thrush” requires further study.
8.
  • Halwachs, Bettina, et al. (författare)
  • Critical Issues in mycobiota analysis
  • 2017
  • Ingår i: Frontiers in Microbiology. - 1664-302X. ; 8
  • Tidskriftsartikel (refereegranskat)abstract
    • Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data. Specific points are discussed at each step and special emphasis is placed on the bioinformatics challenges emerging during operational taxonomic unit (OTU) picking, a critical step in mycobiota analysis. By using an in silico ITS1 mock community we demonstrate that standard analysis pipelines fall short if used with default settings showing erroneous fungal community representations. We highlight that switching OTU picking to a closed reference approach greatly enhances performance. Finally, recommendations are given on how to perform ITS based mycobiota analysis with the currently available measures.
9.
  • Olsson, Urban, et al. (författare)
  • Assessment of species limits in African "brown buntings' (Emberiza, Passeriformes) based on mitochondrial and nuclear sequence data
  • 2013
  • Ingår i: Ibis. - 0019-1019. ; 155:3, s. 534-543
  • Tidskriftsartikel (refereegranskat)abstract
    • We estimated a phylogeny for 10 taxa currently placed in four polytypic species that collectively encompass the African brown buntings': Cape Bunting Emberiza capensis, Cinnamon-breasted Bunting Emberiza tahapisi, Lark-like Bunting Emberiza impetuani and House Bunting Emberiza striolata. We made use of the mitochondrial cytochrome b gene and the nuclear introns 6-7 of ornithine decarboxylase (ODC), and intron 2 of myoglobin. There was substantial cytochrome b sequence divergence between taxa currently treated as conspecific: sahari vs. striolata (2.6-3.1% (uncorrected-p); 3.0-3.6% (HKY+I)), and goslingi vs. tahapisi (4.4-4.7% (uncorrected-p); 5.4-5.9% (HKY+I)). The degree of divergence of the nuclear loci among taxa was limited, and these loci lacked reciprocal monophyly, most likely as a consequence of incomplete lineage sorting. A single representative of the taxon septemstriata, generally treated as a member of the dark-throated tahapisi group, here appears to be genetically consistent with the grey-throated goslingi, and may be of hybrid origin. All other taxa allocated to E.striolata and E.tahapisi make up four reciprocally monophyletic groups consistent with sahari, striolata, tahapisi and goslingi, respectively. The extent of genetic evidence suggests that these taxa have been evolving as separate evolutionary lineages for a long time. This is further manifested in several morphological and vocal characteristics described previously, and we propose that these divergent taxa be treated as separate species: Cinnamon-breasted Bunting Emberiza tahapisi, Gosling's Bunting Emberiza goslingi, Striolated Bunting Emberiza striolata and House Bunting Emberiza sahari. We do not propose any taxonomic changes regarding Emberiza impetuani or Emberiza capensis.
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10.
  • Olsson, Urban, et al. (författare)
  • The Lanius excubitor (Aves, Passeriformes) conundrum – Taxonomic dilemma when molecular and non-molecular data tell different stories.
  • 2010
  • Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903. ; 55:2, s. 347-357
  • Tidskriftsartikel (refereegranskat)abstract
    • The phylogeny of 18 taxa in the Lanius excubitor complex, and the related species L sphenocercus, L. ludovicianus and L somalicus, was estimated based on the mitochondrial cytochrome b gene and the non-coding D-loop (in total similar to 1.3 kb). According to the mitochondrial gene tree, Lanius excubitor s.l. is non-monophyletic, with some of its subspecies being more closely related to L sphenocercus, L ludovicianus, and L somalicus. Also the division of the L. excubitor complex into a northern (L. excubitor) and a southern (L. meridionalis) species, as has been proposed based on morphological and ecological similarity and geographical distributions, is not compatible with the mitochondrial tree. Overall, genetic divergences among the ingroup taxa are small, indicating a recent radiation. A tree based on the nuclear ornithine decarboxylase (ODC) introns 6-7 is unresolved with respect to the ingroup, but provides strong support for a clade containing the Lanius excubitor complex, L. sphenocercus, L. ludovicianus and L. somalicus. We discuss the incongruence between the current taxonomy and the mitochondrial gene tree, and conclude that based on the latter the Lanius excubitor complex may be treated as at least six species, L. borealis, L. elegans, L. excubitor, L. lahtora, L. meridionalis, and L uncinatus, but that other taxonomic treatments are also possible. However, uncertainty regarding to which extent the mitochondrial gene tree reflects the species phylogeny prevents us from recommending taxonomic change without further investigation. This study highlights the possible danger of relying on a single molecular marker, such as mitochondrial DNA, in taxonomic revisions and phylogenetic inference.
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