| 1. |
- Burks, Roger A., et al.
(författare)
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Combined molecular and morphological phylogeny of Eulophidae (Hymenoptera: Chalcidoidea), with focus on the subfamily Entedoninae
- 2011
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Ingår i: Cladistics. - : Wiley. - 1096-0031 .- 0748-3007. ; 27:6, s. 581-605
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Tidskriftsartikel (refereegranskat)abstract
- A new combined molecular and morphological phylogeny of the Eulophidae is presented with special reference to the subfamily Entedoninae. We examined 28S D2D5 and CO1 gene regions with parsimony and partitioned Bayesian analyses, and examined the impact of a small set of historically recognized morphological characters on combined analyses. Eulophidae was strongly supported as monophyletic only after exclusion of the enigmatic genus Trisecodes. The subfamilies Eulophinae, Entiinae (=Euderinae) and Tetrastichinae were consistently supported as monophyletic, but Entedoninae was monophyletic only in combined analyses. Six contiguous bases in the 3e' subregion of the 28S D2 rDNA contributed to placement of nominal subgenus of Closterocerus outside Entedoninae. In all cases, Euderomphalini was excluded from Entiinae, and we suggest that it be retained in Entedoninae. Opheliminae n. stat. is raised from tribe to subfamily status. Trisecodes is removed from Entedoninae but retained as incertae sedis in Eulophidae until its family placement can be determined new placement. The genera Neochrysocharisstat. rev. and Asecodesstat. rev. are removed from synonymy with Closterocerus because strong molecular differences corroborate their morphological differences. Closterocerus (Achrysocharis) germanicus is transferred to the genus Chrysonotomyian. comb. based on molecular and morphological characters.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Rethinking taxon sampling in the light of environmental sequencing
- 2011
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Ingår i: Cladistics. - : Wiley. - 1096-0031 .- 0748-3007. ; 27:2, s. 197-203
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Tidskriftsartikel (refereegranskat)abstract
- Environmental DNA sequencing efforts of substrates such as soil, wood, and seawater have been found to present very different views of the underlying biological communities compared with efforts based on morphological examination and culture studies. The taxonomic affiliation of many of these environmental sequences cannot be settled with certainty due to the lack of proximate reference sequences in the corpus of public sequence data, and they are typically submitted to the international sequence databases without much indication of their relatedness. The scientific community has proved reluctant to include such unnamed sequences in phylogenetic analyses and taxonomic studies, but the present study shows such a position to be not only largely unwarranted but also potentially unsound. The sequences of 48 published fungal alignments of the nuclear ribosomal internal transcribed spacer region were subjected to similarity searches in the sequence databases to recover environmental sequences with a clear bearing on the respective ingroup. An average of 20 environmental sequences were added to each alignment, and upon rerunning the phylogenetic analyses of each study we found that topological rearrangements involving the original ingroup sequences were observed for no less than 29 (60%) of the studies. In nearly 20% of these cases, the rearrangements were large enough to question or even overthrow at least one conclusion presented in the original studies. The basal branching order was similarly subject to changes in 16% of the applicable studies. Environmental sequences are thus not only relevant in ecological research but form a requisite source of information also in systematics and taxonomy.
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| 3. |
- Conrad, Jack L., et al.
(författare)
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A combined evidence phylogenetic analysis of Anguimorpha (Reptilia : Squamata)
- 2011
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Ingår i: Cladistics. - : Wiley. - 0748-3007 .- 1096-0031. ; 27:3, s. 230-277
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Forskningsöversikt (refereegranskat)abstract
- Anguimorpha is a clade of limbed and limbless squamates with ca. 196 extant species and a known fossil record spanning the past 130 million years. Morphology-based and molecule-based phylogenetic analyses disagree on several key points. The analyses differ consistently in the placements of monstersaurs (e.g. Gila Monsters), shinisaurs (Crocodile Lizards), the anguid Anniella (American Legless Lizards), carusioids (Knobby Lizards), and the major clades within Varanus (Monitor Lizards). Given different data sources with such different phylogenetic hypotheses, Anguimorpha is an excellent candidate for a combined phylogenetic analysis. We constructed a data matrix consisting of 175 fossil and extant anguimorphs, and 2281 parsimony-informative characters (315 morphological characters and 1969 molecular characters). We analysed these data using the computer program TNT using the "new technology search" with the ratchet. Our result is novel and shows similarities with both morphological and molecular trees, but is identical to neither. We find that a global combined evidence analysis (GCA) does not recover a holophyletic Varanoidea, but omission of fossil taxa reveals cryptic molecular support for that group. We describe these results and others from global morphological analysis, extant-only morphological analysis, molecular data-only analyses, combined evidence analysis of extant taxa, and GCA.
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| 4. |
- Johanson, Kjell Arne, et al.
(författare)
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Phylogeny of the Ecnomidae (Insecta: Trichoptera)
- 2010
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Ingår i: Cladistics. - : Wiley. - 0748-3007 .- 1096-0031. ; 26:1, s. 36-48
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Tidskriftsartikel (refereegranskat)abstract
- Ecnomidae are a family of seven previously accepted extant genera having a typical Gondwanan distribution, except one genus (Ecnomus) being widely distributed also in the Oriental and Palearctic regions. We analysed a molecular data set of 3379 characters representing the sum of four different protein-coding genes (COI, CAD, EF-1a and POL-II). Six equally most parsimonious trees were generated from the combined data set, distributed into two distinct islands. In all maximum parsimony (MP) trees the Ecnomidae is monophyletic when the genus Zelandoptila (Psychomyiidae) is included. The sister group to Ecnomidae including Zelandoptila is Pseudoneureclipsis, previously classified in the other families. This sister-group relationship contradicts earlier findings that the Polycentropodidae are the sister group to Ecnomidae. A Bayesian analysis resulted in a monophyletic Ecnomidae when accepting inclusion of Pseudoneureclipsis, which contradicts the results from the MP analysis by leaving Zelandoptila as the sister group to Ecnomidae including Pseudoneureclipsis. In the majority rule tree from this analysis Polycentropodidae form the sister group to Ecnomidae. We were not able to obtain a monophyletic Ecnomus due to the inclusion of Psychomyillodes. We conclude that the genus Zelandoptila or Pseudoneureclipsis probably belongs to the Ecnomidae, and that Psychomyiellodes and Ecnomus are synonyms. Three additional, as yet undescribed monotypic genera from Australia and New Caledonia remain to be erected in Ecnomidae.
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| 5. |
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| 6. |
- Miettinen, Otto, et al.
(författare)
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Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota)
- 2012
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Ingår i: Cladistics. - : Wiley. - 1096-0031 .- 0748-3007. ; 28:3, s. 251-270
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of the poroid and hydnoid genera Antrodia, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2 and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer that 15 genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinaceae in shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within Steccherinaceae.
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| 7. |
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| 8. |
- Liljeblad, Johan
(författare)
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A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera)
- 2013
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Ingår i: Cladistics. - : Wiley. - 0748-3007 .- 1096-0031. ; 29, s. 466-542
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Tidskriftsartikel (refereegranskat)abstract
- Chalcidoidea (Hymenoptera) is extremely diverse with an estimated 500000 species. We present the first phylogenetic analysis of the superfamily based on both morphological and molecular data. A web-based, systematics workbench mx was used to score 945 character states illustrated by 648 figures for 233 morphological characters for a total of 66645 observations for 300 taxa. The matrix covers 22 chalcidoid families recognized herein and includes 268 genera within 78 of 83 subfamilies. Morphological data were analysed alone and in combination with molecular data from ribosomal 18S (2105bp) and 28S D2-D5 expansion regions (1812bp). Analyses were analysed alone and in combined datasets using implied-weights parsimony and likelihood. Proposed changes in higher classification resulting from the analyses include: (i) recognition of Eriaporidae, revised status; (ii) recognition of Cynipencyrtidae, revised status; (iii) recognition of Azotidae, revised status; (iv) inclusion of Sycophaginae in Agaonidae, revised status; (v) reclassification of Aphelinidae to include Aphelininae, Calesinae, Coccophaginae, Eretmocerinae and Eriaphytinae; (vi) inclusion of Cratominae and Panstenoninae within Pteromalinae (Pteromalidae), new synonymy; (vii) inclusion of Epichrysomallinae in Pteromalidae, revised status. At a higher level, Chalcidoidea was monophyletic, with Mymaridae the sister group of Rotoitidae plus the remaining Chalcidoidea. A eulophid lineage was recovered that included Aphelinidae, Azotidae, Eulophidae, Signiphoridae, Tetracampidae and Trichogrammatidae. Eucharitidae and Perilampidae were monophyletic if Eutrichosomatinae (Pteromalidae) was included, and Eupelmidae was monophyletic if Oodera (Pteromalidae: Cleonyminae) was included. Likelihood recovered a clade of Eupelmidae+(Tanaostigmatidae+(Cynipencyrtus+Encyrtidae). Support for other lineages and their impact on the classification of Chalcidoidea is discussed. Several life-history traits are mapped onto the new phylogeny.
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| 9. |
- Aguado, M. T., et al.
(författare)
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Two apparently unrelated groups of symbiotic annelids, Nautiliniellidae and Calamyzidae (Phyllodocida, Annelida), are a clade of derived chrysopetalid polychaetes
- 2013
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Ingår i: Cladistics. - : Wiley. - 0748-3007. ; 29:6, s. 610-628
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Tidskriftsartikel (refereegranskat)abstract
- Nautiliniellidae Miura and Laubier, 1989 is a small family of marine polychaetes with 20 currently described species in 11 genera, most of which are known to live symbiotically in the mantle cavity of bivalves, mainly from cold seeps and hydrothermal vents, while Calamyzidae (Hartmann-Schroder, 1971) including only one described species, Calamyzas amphictenicola Arwidsson 1932 lives as an ectoparasite on ampharetid polychaetes in Swedish waters. Nautiliniellidae and Calamyzidae have both been considered to belong to Phyllodocida, but the few phylogenetic studies including these taxa have found their positions unstable. The internal relationships within Nautiliniellidae are also poorly understood. Using molecular information from both nuclear and mitochondrial genes and morphological data we assessed the systematic placement of Nautiliniellidae (seven species; collected from Pacific hydrothermal vents and cold seeps and one from Atlantic waters) and Calamyzas amphictenicola. Our results show that C. amphictenicola and Nautiliniellidae formed a well-supported clade that is nested within Chrysopetalidae, a free-living group of polychaetes. The chrysopetalid genus Vigtorniella Kiseleva 1992; a bacterial mat grazer found at methane seeps, anoxic basins and whalefalls, formed a paraphyletic grade with respect to the Nautiliniellidae-Calamyzas clade. The internal relationships within the Nautiliniellidae-Calamyzas clade as well as the relationships with their hosts are also examined. As a result we synonymize Calamyzidae and Nautiliniellidae with Chrysopetalidae, with the last as the oldest available family-group name. Within Chrysopetalidae we refer to the subfamilies Chrysopetalinae Ehlers 1864; Dysponetinae Aguado, Nygren & Rouse, herein; and Calamyzinae Hartmann-Schroder, 1971. Calamyzinae contains C. amphictenicola, all taxa formerly in Nautiliniellidae, and the chrysopetalid genus Vigtorniella. (C) The Willi Hennig Society 2013
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| 10. |
- Andrade, S. C. S., et al.
(författare)
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Disentangling ribbon worm relationships: multi-locus analysis supports traditional classification of the phylum Nemertea
- 2012
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Ingår i: Cladistics. - : Wiley. - 0748-3007. ; 28:2, s. 141-159
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships of selected members of the phylum Nemertea are explored by means of six markers amplified from the genomic DNA of freshly collected specimens (the nuclear 18S rRNA and 28S rRNA genes, histones H3 and H4, and the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I). These include all previous markers and regions used in earlier phylogenetic analyses of nemerteans, therefore acting as a scaffold to which one could pinpoint any previously published study. Our results, based on analyses of static and dynamic homology concepts under probabilistic and parsimony frameworks, agree in the non-monophyly of Palaeonemertea and in the monophyly of Heteronemerta and Hoplonemertea. The position of Hubrechtella and the Pilidiophora hypothesis are, however, sensitive to analytical method, as is the monophyly of the non-hubrechtiid palaeonemerteans. Our results are, however, consistent with the main division of Hoplonemertea into Polystilifera and Monostilifera, the last named being divided into Cratenemertea and Distromatonemertea, as well as into the main division of Heteronemertea into Baseodiscus and the remaining species. The study also continues to highlight the deficient taxonomy at the family and generic level within Nemertea and sheds light on the areas of the tree that require further refinement.
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