scholarly journals The Mitochondrial Genomes of Neuropteridan Insects and Implications for the Phylogeny of Neuroptera

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 108 ◽  
Author(s):  
Nan Song ◽  
Xin-xin Li ◽  
Qing Zhai ◽  
Hakan Bozdoğan ◽  
Xin-ming Yin
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Genomic Data ◽  
Considerable Progress ◽  
Mitochondrial Genomes ◽  
Special Focus ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Taxonomic Sampling ◽  
Inference Methods

The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

A revision of the planthopper genus Chionomus Fennah (Hemiptera: Fulgoroidea: Delphacidae)

Zootaxa ◽  
2020 ◽  
Vol 4811 (1) ◽  
pp. 1-63
Author(s):  
KATHRYN M. WEGLARZ ◽  
CHARLES R BARTLETT
Keyword(s):  
Mixed Model ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Molecular Evidence ◽  
Additional Species ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Original Definition ◽  
Definition Of

The planthopper genus Chionomus Fennah, 1971 (Hemiptera: Fulgoroidea: Delphacidae) currently includes three Neotropical species, removed from the polyphyletic genus Delphacodes Fieber, 1866. Morphological and molecular evidence further redefine Chionomus to include ten additional species (eight species removed from Delphacodes, two described as new, viz. Chionomus dolonus n. sp. and C. herkos n. sp.), with another four species synonymized. Phylogenetic analyses of morphological and molecular sequence data of the mitochondrial gene Cytochrome Oxidase I provide support for the monophyly of Chionomus. We use a mixed model Bayesian optimality criterion to define phylogenetic relationships among Chionomus and support paraphyly of the original definition of Chionomus (with respect to Delphacodes) and monophyly of the revised genus. 

Across Lydekker's Line - first report of mite harvestmen (Opiliones : Cyphophthalmi : Stylocellidae) from New Guinea

2007 ◽  
Vol 21 (3) ◽  
pp. 207 ◽  
Author(s):  
Ronald M. Clouse ◽  
Gonzalo Giribet
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Guinea ◽  
Single Male ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
Biogeographic Region ◽  
Molecular Phylogenetic ◽  
History Of

Opiliones (harvestmen) in the suborder Cyphophthalmi are not known to disperse across oceans and each family in the suborder is restricted to a clear biogeographic region. While undertaking a revisionary study of the South-east Asian family Stylocellidae, two collections of stylocellids from New Guinea were noted. This was a surprising find, since the island appears never to have had a land connection with Eurasia, where the rest of the family members are found. Here, 21 New Guinean specimens collected from the westernmost end of the island (Manokwari Province, Indonesia) are described and their relationships to other cyphophthalmids are analysed using molecular sequence data. The specimens represent three species, Stylocellus lydekkeri, sp. nov., S. novaguinea, sp. nov. and undescribed females of a probable third species, which are described and illustrated using scanning electron microscope and stereomicroscope photographs. Stylocellus novaguinea, sp. nov. is described from a single male and it was collected with a juvenile and the three females of the apparent third species. Molecular phylogenetic analyses indicate that the new species are indeed in the family Stylocellidae and they therefore reached western New Guinea by dispersing through Lydekker’s line – the easternmost limit of poor dispersers from Eurasia. The New Guinean species may indicate at least two episodes of oceanic dispersal by Cyphophthalmi, a phenomenon here described for the first time. Alternatively, the presence in New Guinea of poor dispersers from Eurasia may suggest novel hypotheses about the history of the island.

scholarly journals Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

2014 ◽  
Vol 28 (1) ◽  
pp. 32 ◽  
Author(s):  
Rüdiger Bieler ◽  
Paula M. Mikkelsen ◽  
Timothy M. Collins ◽  
Emily A. Glover ◽  
Vanessa L. González ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Analytical Framework ◽  
Morphological Characters ◽  
Molecular Data ◽  
Probabilistic Methods ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Protein Encoding ◽  
Encoding Genes

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

Molecular phylogeny of rhynchonellide articulate brachiopods (Brachiopoda, Rhynchonellida)

2013 ◽  
Vol 87 (2) ◽  
pp. 211-216 ◽  
Author(s):  
Bernard L. Cohen ◽  
Maria Aleksandra Bitner
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequences ◽  
Relaxed Clock

We present here the first report based on phylogenetic analyses of small subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA) sequences from a wider-than-token sample of rhynchonellide articulate brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging to all four extant superfamilies. Data exploration by network and saturation analyses shows that the molecular sequence data are free from major aberrations and are suitable for phylogenetic reconstruction despite the presence of large deletions in four SSU rDNA sequences. Although molecular sequence analyses cannot directly illuminate the systematics of fossils, the independent, genealogical evidence and phylogenetic inferences about extant forms that they make possible are highly relevant to paleontological systematics because they highlight the limitations of evolutionary inference from morphology. Parsimony, distance, maximum likelihood (no clock) and Bayesian (relaxed-clock) analyses all find a tree topology that disagrees strongly with the existing superfamily classification. All tested phylogenetic reconstructions agree that the taxa analyzed fall into three clades designated A1, A2, and B that reflect two major divergence events. The relaxed-clock analysis indicates that clades A and B diverged in the Paleozoic, while clades A1 and A2 reflect Permo-Triassic (and later) events. Morphological homoplasy and possible gene co-option are suggested as the main sources for the discord between the morpho-classification, the results of cladistic analyses of morphology, and the relationships reconstructed from molecular sequences. The origin, function and evolutionary implications of the deletion-bearing rhynchonellide SSU rDNA sequences are briefly discussed in relation to pseudogenes and concerted evolution in the rDNA genomic region.

scholarly journals PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

2018 ◽  
Author(s):  
Dong Zhang ◽  
Fangluan Gao ◽  
Wen X Li ◽  
Ivan Jakovlić ◽  
Hong Zou ◽  
...  
Keyword(s):  
Data Management ◽  
Sequence Data ◽  
Bioinformatic Analysis ◽  
Mitochondrial Genomes ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Bioinformatic Tools ◽  
User Friendly ◽  
Scientific Questions ◽  
Entire Procedure

Multi-gene and genomic datasets have become commonplace in the field of phylogenetics, but many of the existing tools are not designed for such datasets, which makes the analysis time-consuming and tedious. We therefore present PhyloSuite, a user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It employs a plugin-based system that integrates a number of useful phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation, with the following features: (i) point-and-click and drag-and-drop graphical user interface, (ii) a workspace to manage and organize molecular sequence data and results of analyses, (iii) GenBank entries extraction and comparative statistics, (iv) a phylogenetic workflow with batch processing capability, (v) elaborate bioinformatic analysis for mitochondrial genomes. The aim of PhyloSuite is to enable researchers to spend more time playing with scientific questions, instead of wasting it on conducting standard analyses. The compiled binary of PhyloSuite is available under the GPL license at https://github.com/dongzhang0725/PhyloSuite/releases, implemented in Python and runs on Windows, Mac OSX and Linux.

Two new species of Inocybe from Australia and North America that include novel secotioid forms

Botany ◽  
2014 ◽  
Vol 92 (1) ◽  
pp. 9-22 ◽  
Author(s):  
Christine C. Braaten ◽  
P. Brandon Matheny ◽  
Debra L. Viess ◽  
Michael G. Wood ◽  
Joseph H. Williams ◽  
...  
Keyword(s):  
New Species ◽  
North America ◽  
Sequence Data ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Western North America ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Two New Species ◽  
Phenotypic Variant

The secotioid form of fruit bodies of mushroom-forming fungi may be an intermediate evolutionary modification of epigeous agaricoid or pileate–stipitate forms (i.e., with pileus, spore-bearing tissues, and stipe) and typically hypogeous, gasteroid- or truffle-forming species, in which the fruit bodies have been reduced to enclosed structures containing modified spore-producing tissues. To date, only a single secotioid species (Auritella geoaustralis Matheny & Bougher ex Matheny & Bougher) has been described in the ectomycorrhizal family Inocybaceae, a hyperdiverse clade of ca. 500–700 species with a cosmopolitan distribution. Fieldwork in Australia and western North America, however, has revealed two novel secotioid forms of Inocybe (Fr.) Fr., the first to be formally described in the genus. In this investigation, we analyze their phylogenetic relationships using molecular sequence data from multiple unlinked loci to test whether these are environmental variants of agaricoid forms or represent independent lineages. Results of phylogenetic analyses suggest these fungi have converged to the secotioid form independently. However, the California secotioid taxon (Inocybe multifolia f. cryptophylla f. nov.) is a phenotypic variant of the newly described agaricoid taxon (Inocybe multifolia sp. nov.). Similarly, the Australian secotioid form (Inocybe bicornis f. secotioides f. nov.) is nested within a clade of otherwise agaricoid forms of a second novel species (Inocybe bicornis sp. nov.) described from southwest Western Australia. Overall, four species with sequestrate forms within Inocybaceae can now be recognized, three of which are distributed in Australia and one in western North America, in the genera Auritella and Inocybe.

Gerricola queenslandensis n. g., n. sp., a new monorchiid trematode from the eastern Australian coast and its life cycle partially elucidated

2021 ◽  
Vol 95 ◽  
Author(s):  
N.Q.-X. Wee ◽  
S.C. Cutmore ◽  
T.H. Cribb
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Lack Of Information ◽  
Terminal Organ ◽  
As Species ◽  
Wide Range ◽  
Generic Position

Abstract Of over 250 species of Monorchiidae Odhner, 1911, just four are known from gerreid fishes. Here, we report adult specimens of a new species infecting Gerres oyena (Forsskål) and Gerres subfasciatus Cuvier from off Heron Island and North Stradbroke Island, Queensland, Australia. The species is morphologically most similar to the concept of Lasiotocus Looss, 1907, which currently comprises eight species, in the possession of an unspined genital atrium, bipartite terminal organ, round oral sucker and unlobed ovary. However, phylogenetic analyses of the 28S ribosomal DNA gene region shows the species to be distantly related to the two sequenced species of Lasiotocus – Lasiotocus mulli (Stossich, 1883) Odhner, 1911 and Lasiotocus trachinoti Overstreet & Brown, 1970 – and that it clearly requires a distinct genus; thus, we propose Gerricola queenslandensis n. g., n. sp. Morphologically, G. queenslandensis n. g., n. sp. differs significantly from L. mulli and L. trachinoti only in the possession of distinctly longer caeca, which terminate in the post-testicular region, and in the absence of a distinct gap in the terminal organ spines. The remaining species of Lasiotocus possess caeca that also terminate in the post-testicular region, which might warrant their transfer to Gerricola n. g. However, doubt about their monophyly due to a combination of significant morphological variation, a lack of information on some features and infection of a wide range of hosts, lead us to retain these taxa as species of Lasiotocus until molecular sequence data are available to better inform their phylogenetic and taxonomic positions. Sporocysts and cercariae of G. queenslandensis n. g., n. sp. were found in a lucinid bivalve, Codakia paytenorum (Iredale), from Heron Island. Sexual adult and intramolluscan stages were genetically matched with the ITS2 ribosomal DNA and cox1 mitochondrial DNA regions. This is the second record of the Lucinidae as a first intermediate host for the Monorchiidae. Additionally, we report sporocysts and cercariae of another monorchiid infection in a tellinid bivalve, Jactellina clathrata (Deshayes), from Heron Island. Molecular sequence data for this species do not match any sequenced species and phylogenetic analyses do not suggest any generic position.

Molecular phylogeny of Ceriantharia (Cnidaria: Anthozoa) reveals non-monophyly of traditionally accepted families

2019 ◽  
Vol 190 (2) ◽  
pp. 397-416 ◽  
Author(s):  
Anny C Forero Mejia ◽  
Tina Molodtsova ◽  
Carina Östman ◽  
Giorgio Bavestrello ◽  
Greg W Rouse
Keyword(s):  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Phylogenetic Reconstructions ◽  
Molecular Phylogenetic ◽  
Integrative Study ◽  
Nuclear Loci ◽  
Significant Support

Abstract We present an integrative study with molecular phylogenetic reconstructions and morphological assessment across the three Ceriantharia families: Arachnactidae, Botrucnidiferidae and Cerianthidae. The Arachnactidae specimens (Isarachnanthus spp.) form a well-supported clade, whereas Cerianthidae and Botrucnidiferidae are not recovered as monophyletic. Consequently, the validity of the suborder Spirularia is questioned. Cerianthus was recovered as polyphyletic and Ceriantheomorphe may prove to be a junior synonym of Cerianthus. The taxonomic position of Cerianthus cf. mortenseni is also discussed. All specimens identified on morphology as belonging to Pachycerianthus are recovered as a clade. Further revision of taxa within Ceriantharia is necessary. Molecular phylogenetic analyses based on six mitochondrial or nuclear loci place Ceriantharia as sister to Hexacorallia s.s., but with no significant support relative to an alternative hypothesis that it is the sister taxon to Octocorallia. Further molecular sequence data and taxon sampling will be needed to resolve the position of Ceriantharia.

scholarly journals Inferring the deep past from molecular data

2021 ◽  
Author(s):  
Tom A Williams ◽  
Dominik Schrempf ◽  
Gergely J Szöllősi ◽  
Cymon J Cox ◽  
Peter G Foster ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Sister Group Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Phylogenetic Methods ◽  
Alternative Hypotheses ◽  
Correct Tree

Abstract There is an expectation that analyses of molecular sequences might be able to distinguish between alternative hypotheses for ancient relationships, but the phylogenetic methods used and types of data analyzed are of critical importance in any attempt to recover historical signal. Here we discuss some common issues that can influence the topology of trees obtained when using overly-simple models to analyze molecular data that often display complicated patterns of sequence heterogeneity. To illustrate our discussion, we have used three examples of inferred relationships which have changed radically as models and methods of analysis have improved. In two of these examples, the sister-group relationship between thermophilic Thermus and mesophilic Deinococcus, and the position of long-branch Microsporidia among eukaryotes, we show that recovering what is now generally considered to be the correct tree is critically dependent on the fit between model and data. In the third example, the position of eukaryotes in the tree of life, the hypothesis that is currently supported by the best available methods is fundamentally different from the classical view of relationships between major cellular domains. Since heterogeneity appears to be pervasive and varied among all molecular sequence data, and even the best available models can still struggle to deal with some problems, the issues we discuss are generally relevant to phylogenetic analyses. It remains essential to maintain a critical attitude to all trees as hypotheses of relationship that may change with more data and better methods.

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