| 1. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 3. |
- Chakma, Sanjib, et al.
(författare)
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Preliminary report on freshwater oligochaetes from some districts of Tamil Nadu (India), along with DNA barcode sequence of a commercially important oligochaete in Chennai
- 2020
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Ingår i: Zoosymposia. - : Magnolia Press. - 1178-9905 .- 1178-9913. ; 17, s. 45-52
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Tidskriftsartikel (refereegranskat)abstract
- A survey of aquatic Oligochaeta was conducted at Thiruvallur, Chennai, Kanchipuram, Villupuram and Nilgiris districts of Tamil Nadu from October 2015 to June 2016. Eleven taxa were recorded from a total of 922 specimens examined, eight of them were identified to species level. Five naidids identified during the present study: Branchiodrilus semperi, Dero dorsalis, Dero digitata, Dero indica and Dero zeylanica, and six tubificid taxa Branchiura sowerbyi, Tubificidae sp. 1, Tubificidae sp. 2, Tubificidae sp. 3, Limnodrilus hoffmeisteri and L. udekemianus. Dero dorsalis constitute the first report for Kanchipuram district. A DNA barcode sequence (GenBank accession no. MF125273) of the commercially important Limnodrilus hoffmeisteri, commonly known as ‘Tubifex worms’ in Chennai, was obtained and compared with other published COI sequences from that morphospecies from around the world.
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| 4. |
- Erséus, Christer, 1951, et al.
(författare)
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Case 3826 – Propappus Michaelsen, 1905 and PROPAPPIDAE Coates, 1986 (Annelida, Clitellata): proposed conservation by suppression of Propappus Seeley, 1888 (Vertebrata, Reptilia)
- 2021
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Ingår i: The Bulletin of Zoological Nomenclature. - : The Bulletin of Zoological Nomenclature. - 0007-5167. ; 78:1, s. 17-25
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Tidskriftsartikel (refereegranskat)abstract
- conserve the well-used names Propappus Michaelsen, 1905 and Propapidae Coates, 1986 (Annelida) by suppression of the senior homonym Propappus Seeley, 1888 (Reptilia), a junior subjective synonym of Pareiasaurus Owen, 1876.
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| 5. |
- Erséus, Christer, 1951, et al.
(författare)
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The popular model annelid Enchytraeus albidus is only one species in a complex of seashore White Worms (Clitellata, Enchytraeidae)
- 2019
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Ingår i: Organisms Diversity & Evolution. - : Springer Science and Business Media LLC. - 1439-6092 .- 1618-1077. ; 19:2, s. 105-133
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Tidskriftsartikel (refereegranskat)abstract
- The white worm Enchytraeus albidus Henle, 1837 (Clitellata, Enchytraeidae) is easy to keep in laboratory cultures, and has therefore been employed as a model organism in basic and applied biological research. Its natural habitat includes terrestrial composts and wrack beds on seashores. However, the name E. albidus is currently used for a complex of morphologically similar and closely related species. We here revise the components of the E. albidus species complex based on a sample of 100 Enchytraeus specimens from 56 sites, most of which are across Europe. These samples were DNA-barcoded for the mitochon- drial COI gene. A subset of them was sequenced for the nuclear ITS2 and H3 markers. Six species were delimited with strong support by the COI and ITS2 gene trees, as well as by a multi-locus species delimitation analysis. These species are identified morphologically and described as E. albidus s. str. (with designation of a neotype); Enchytraeus moebii (Michaelsen, 1885); Enchytraeus albellus Klinth, Erséus and Rota, sp. nov., E. cf. krumbachi (Čejka, 1913), E. sp. 1 (unnamed), and Enchytraeus polatdemiri Arslan and Timm, 2018. The last-mentioned species is a soda lake specialist, whereas E. albidus s. str. is both terrestrial and marine littoral; all other species occur only in seashores. The phylogeny of this group was estimated using the multi-species coalescent model. Monophyly of the E. albidus complex was recovered. Within this complex, three groups were recovered as monophyletic, but the relationship between them is unclear. One group comprises E. albidus s. str., E. albellus, and E. moebii; the second group E. cf. krumbachi and the unnamed E. sp. 1, and the third consists of only E. polatdemiri. This study serves as a framework for genetic identification of white worms used for experimental purposes.
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| 6. |
- Klinth, Mårten, 1990, et al.
(författare)
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New insights into the systematics of Lumbricillus and Marionina (Clitellata: Enchytraeidae) inferred from Southern Hemisphere samples, including three new species
- 2022
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 194:4, s. 1103-1133
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Tidskriftsartikel (refereegranskat)abstract
- Enchytraeid worms collected in South Africa and on the Marion, South Orkney, South Georgia and South Shetland Islands during 2008-2015 were studied using morphology and seven genetic markers. Nine species were recognized: one terrestrial (Christensenidrilus blocki) and all the others marine littoral (five Lumbricillus and three Marionina s.s.). An estimated phylogeny including other enchytraeids from the Northern Hemisphere, many of which are members of Lumbricillus and some representing Marionina s.l., confirmed a non-monophyletic Lumbricillus, with some of its current species closely related to Grania or Marionina s.s. The phylogeny also corroborated a non-monophyletic Marionina s.l., with Marionina s.s. closely related to Grania and Lumbricillus s.l., but not to the remaining sequenced 'Marionina' or to Ch. blocki. These results provide a long-needed starting point for a revision of both Marionina and Lumbricillus. We provide morphological descriptions of all nine species, three of which are new to science: Lumbricillus finisafricae sp. nov., Lumbricillus nivalis sp. nov., and Marionina fusca sp. nov. Comments on three related species of Marionina s.s. based on re-examined type material are also provided.
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| 7. |
- Klinth, Mårten, 1990, et al.
(författare)
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Phylogeny and species delimitation of North European Lumbricillus (Clitellata, Enchytraeidae)
- 2017
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256. ; 46:1, s. 96-110
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Tidskriftsartikel (refereegranskat)abstract
- The enchytraeid genus Lumbricillus comprises about 80 described species of clitellate worms, which are up to a few centimetres long, and they mostly inhabit the littoral zone of nontropical marine and brackish waters world-wide. The phylogeny of this genus is poorly studied, but previous work has suggested that Lumbricillus is a non-monophyletic group. In this study, species boundaries and the phylogeny of this genus is re-assessed using more than 300 DNA-barcoded specimens (using COI mtDNA), part of which was also sequenced for two additional mitochondrial and four nuclear molecular markers. Statistical and coalescent based applications were used for the delimitation of a total of 24 species, of which 20 were identified as belonging to 17 described morphospecies; one morphospecies was found to be a complex of four delimited species, and another four delimited species could not be matched with any described species. Furthermore, gene trees, concatenation and multispecies coalescent based species trees were estimated using Bayesian inference. The estimated phylogenies confirm a non-monophyletic Lumbricillus as L. semifuscus is clearly excluded from the genus. Furthermore, the placement of a monophyletic clade consisting of L. arenarius, L. dubius, and an unidentified species varies between analyses; they are either found as the sister-group to the genus Grania or as sister-group to the remaining Lumbricillus, where the latter relationship is supported by the multispecies coalescent, which we consider as the most reliable method.
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| 8. |
- Liu, Yingkui, et al.
(författare)
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Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)
- 2017
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Ingår i: Organisms Diversity and Evolution. - : Springer Science and Business Media LLC. - 1439-6092 .- 1618-1077. ; 17:2, s. 477-495
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Tidskriftsartikel (refereegranskat)abstract
- Limnodrilus hoffmeisteri Claparède, 1862 is a common freshwater worm, often regarded as an indicator of organic pollution. The taxonomic status of this species is controversial due to great variation in morphological features. Numerous morphological forms of L. hoffmeisteri are recorded in the literature, especially from Europe and North America. Today, DNA-based species delimitation assumes that species boundaries can be more objectively and effectively estimated using genetic data rather than with morphological data alone. To investigate if L. hoffmeisteri is a single species, 295 worms identified as either L. hoffmeisteri or other similar (congeneric) morphospecies, using currently accepted morphological criteria, were collected from 82 locations in the northern hemisphere. The number of primary species hypotheses (PSHs) was first explored with cytochrome oxidase subunit I (COI), the proposed DNA barcode for animal species, and with data for all specimens. Both automatic barcoding gap discovery (ABGD) and the Bayesian general mixed Yule coalescent (bGMYC) model revealed the existence of ≥25 distinct PSHs (COI lineages) in our dataset. Then, smaller samples of individuals representing major COI lineages were used for exploration of a nuclear locus, the internal transcribed spacer (ITS) region. In the ITS gene tree (81 sequences), generated by BEAST, 16 well-supported terminal groups were found, but not all of these groups were congruent with the PSHs found in the COI tree. As results across these different analyses were inconsistent, we resorted to analyzing reciprocal monophyly between gene trees and used a minimum consensus of all evidence, suggesting that there are 13 separately evolving lineages (=13 species) within our sample. The smallest uncorrected COI p-distance between these species is 12.1%, and the largest intraspecific p-distance is 16.4%, illustrating the problem of species delimitation with a DNA-barcoding gap as the sole criterion. Ten of these species are morphologically identified as “L. hoffmeisteri,” the remaining three can be attributed to morphologically distinct congeneric species. An individual from the type locality in Switzerland was designated as a neotype of L. hoffmeisteri sensu stricto. This worm belongs to one of the ten species, and this lineage is widely distributed in Europe, Asia, and North America. The remaining nine species show a mixed distribution pattern; some appear to be endemic to a restricted area, others are Holarctic. Our results provide clues to the future revalidation of some of the nominal species today placed in synonymy with L. hoffmeisteri. A BEAST analysis, based on previously published and newly generated 16S data, suggested that this complex contains also other species than those studied by us. By integrating additional genetic data, it will be possible to identify these and additional specimens in future studies of Limnodrilus, and the neotype provides a baseline for further revisions of the taxonomy of the L. hoffmeisteri complex.
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| 9. |
- Liu, Yingkui, et al.
(författare)
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Multi-locus phylogenetic analysis of the genus Limnodrilus (Annelida: Clitellata: Naididae)
- 2017
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 112, s. 244-257
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Tidskriftsartikel (refereegranskat)abstract
- Limnodrilus species are annelid worms distributed worldwide in various freshwater sediments. The systematics of Limnodrilus has chiefly been based on morphology, but the genus has not been subject to any closer phylogenetic studies over the past two decades. To reconstruct the evolutionary history of Limnodrilus, and to assess the monophyly of this genus and its systematic position within the subfamily Tubificinae (Annelida: Clitellata: Naididae), 45 Limnodrilus specimens, representing 19 species, and 35 other naidid species (representing 24 genera) were sampled. The data consisted of sequences of three mitochondrial genes (COI, 12S and 16S rDNA) and four nuclear markers (18S and 28S rDNA, Histone 3, and ITS). The phylogeny was estimated, using Maximum Likelihood and Bayesian analyses of concatenated data of seven DNA loci, as well as a multi-locus coalescent-based approach. All analyses strongly suggest that Limnodrilus is monophyletic, but only if the morphospecies L. rubripenis is removed from it. Limnodrilus rubripenis and (at least) Baltidrilus, Lophochaeta and some species attributed to Varichaetadrilus comprise the sister group to the Glade Limnodrilus sensu stricto, and the latter is further divided into three well-supported groups. One of them contains morphospecies characterized by short cuticular penis sheaths and enlarged chaetae in anterior segments (L udekemianus, L. silvani and L. grandisetosus). The second is a small group of species with moderately long penis sheaths, i.e., L. sulphurensis and L profundicola. The third, and largest group, includes not only the multitude of cryptic species in the L hoffmeisteri complex, but also other, morphologically distinct, species nested within this complex. All studied species in this large group have long penis sheaths, which are exceptionally long in L. claparedianus, L. maumeensis, and a form morphologically intermediate between L. claparedianus and L cervix. The identification and classification of these groups provide a framework for directed sampling in further phylogenetic studies, and for revisionary work on the L. hoffmeisteri complex and other unresolved Limnodrilus species. (C) 2017 Elsevier Inc. All rights reserved.
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| 10. |
- Mack, J. M., et al.
(författare)
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Cryptic carnivores: Intercontinental sampling reveals extensive novel diversity in a genus of freshwater annelids
- 2023
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 182
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Tidskriftsartikel (refereegranskat)abstract
- Freshwater annelids are globally widespread in aquatic ecosystems, but their diversity is severely under-estimated. Obvious morphological features to define taxa are sparse, and molecular phylogenetic analyses regularly discover cryptic diversity within taxa. Despite considerable phylogenetic work on certain clades, many groups of freshwater annelids remain poorly understood. Included among these are water nymph worms of the genus Chaetogaster (Clitellata: Tubificida: Naididae: Naidinae). These worms have diverged from the detri-tivorous diet of most oligochaetes to become more predatory and exist as omnivores, generalist predators, parasites, or symbionts on other invertebrates. Despite their unusual trophic ecology, the true diversity of Chaetogaster and the phylogenetic relationships within the genus are uncertain. Only three species are commonly referenced in the literature (Chaetogaster diaphanus, Chaetogaster limnaei, and Chaetogaster diastrophus), but additional species have been described and prior molecular data suggests that there is cryptic diversity within named species. To clarify the phylogenetic diversity of Chaetogaster, we generated the first molecular phylogeny of the genus using mitochondrial and nuclear sequence data from 128 worms collected primarily across North America and Europe. Our phylogenetic analyses suggest that the three commonly referenced species are a complex of 24 mostly cryptic species. In our dataset, Chaetogaster "diaphanus" is represented by two species, C. "limnaei" is represented by three species, and C. "diastrophus" is represented by 19 species. North American and European sequences are largely interspersed across the phylogeny, with four pairs of clades involving distinct North American and European sister groupings. Overall, our study demonstrates that the species di-versity of Chaetogaster has been underestimated and that carnivory has evolved at least twice in the genus. Chaetogaster is being used as a model for symbiotic evolution and the loss of regenerative ability, and our study indicates that researchers must be careful to identify which species of Chaetogaster they are working with in future studies.
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