Molecular evidence for the cladistic classification of euptyctimous moss mites (Acari, Oribatida, Euptyctima)

2021 ◽  
Author(s):  
Wojciech Niedbała ◽  
Jerzy Błoszyk ◽  
Katarzyna Buczkowska
Keyword(s):  
Phylogenetic Trees ◽  
Maximum Likelihood Method ◽  
Morphological Characters ◽  
Likelihood Method ◽  
Molecular Evidence ◽  
Separate Species ◽  
Sister Relationship ◽  
Mitochondrial Coi ◽  
Cladistic Classification

The cladistic classification of Phthiracaroidea (Niedbała 1986) and Euphthiracaroidea (Mahunka 1990) (Acari, Oribatida), based on morphological symplesio- and synapomorphic characters has been subjected to verification by molecular analysis of mitochondrial COI and nuclear ITS2, 18S and 28S DNA regions. Twenty-one selected species from representative genera of both superfamilies were analyzed. The phylogenetic trees generated by maximum likelihood method confirm the classification of ptyctimous mites resulting from the analysis of morphological characters. Mesoplophoridae, representing the supercohorts Enarthronota, were placed separately to the clade Mixonomata containing Phthiracaroidea and Euphthiracaroidea that are in a sister relationship. The percentage of genetic divergence between the main clades is high in three markers (COI, ITS2 and 28S), it ranges from 36.8% to 38.7% in the barcode marker COI from 26.0% to 35.4% in ITS2 and from 16.2% to 30.0% in 28S, while in 18S it is very low (1.1% - 3.3%). In the Phthiracaroidea, two sister clades Steganacaridae and Phthiracaridae are distinguished. Steganacaridae include three clades Atropacarus, Hoplophthiracarus and Steganacarus with Steganacarus and Tropacarus as the sister clades. Closely related S. (T.) carinatus and S. (T.) pulcherrimus are separate species. Within the Euphthiracaroidea, the four clades: Mesotritia, Microtritia, Acrotritia and Euphthiracarus are resolved. Mesotritia is the most distant, and Microtritia and Acrotritia show the closest relationship.

New insights on the taxonomy and phylogenetic relationships of the Neotropical genus Phoebis (Pieridae: Coliadinae) revealed by molecular and morphological data

Zootaxa ◽  
2018 ◽  
Vol 4457 (1) ◽  
pp. 179 ◽  
Author(s):  
LEIDYS MURILLO-RAMOS ◽  
RENZO HERNÁNDEZ TORRES ◽  
RAYNER NÚÑEZ ÁGUILA ◽  
ROGER AYAZO
Keyword(s):  
Morphological Characters ◽  
Point Of View ◽  
Morphological Data ◽  
Caribbean Region ◽  
Greater Antilles ◽  
Data Set ◽  
Mitochondrial Coi ◽  
The Matrix ◽  
Taxonomic Point

Phoebis Hübner (1819) is a genus of the Neotropical subfamily Coliadinae (Lepidoptera: Pieridae). The highest diversity is found in the Greater Antilles islands in the Caribbean region. Although from the taxonomic point of view, Phoebis seems to be a stable genus, there is no phylogenetic hypothesis corroborating the monophyly of the genus. In this study, we used both morphological characters and a genetic dataset consisting of one mitochondrial (COI) and three nuclear markers (RpS5, MDH, Wingless). The matrix was concatenated and analysed with parsimony under implied weights (IW). Also, the concatenated data set was analysed using maximum likelihood and Bayesian inference evolutionary methods, and ancestral states reconstruction with characters traditionally used for classification of Phoebis was carried out. The same topology was recovered by Parsimony, ML and BI analysis, and suggest that Phoebis is not a monophyletic genus, with Aphrissa and Rhabdodryas nested within it. Our findings allow us to consider the genera Rhabdodryas syn.rev. and Aphrissa syn.rev. to be synonyms of Phoebis. These results have implications for the systematics of Phoebis and the genera that should be accepted in Coliadinae.

Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)

2015 ◽  
Vol 29 (6) ◽  
pp. 591 ◽  
Author(s):  
Marco Gebiola ◽  
Antonio P. Garonna ◽  
Umberto Bernardo ◽  
Sergey A. Belokobylskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A Posteriori ◽  
Morphological Examination ◽  
Ongoing Effort ◽  
The Status ◽  
Molecular Phylogenetic

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.

scholarly journals Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

2020 ◽  
Vol 70 (11) ◽  
pp. 5753-5798 ◽  
Author(s):  
Radhey S. Gupta ◽  
Sudip Patel ◽  
Navneet Saini ◽  
Shu Chen
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Bacillus Species ◽  
Comparative Genomic ◽  
Molecular Evidence ◽  
Content Type ◽  
Link Type ◽  
Conserved Signature Indels ◽  
Genomic Scale

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium . The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer ‘ Bacillus kyonggiensi s’ to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis ) or the Cereus clade (containing B. anthracis and B. cereus ). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

scholarly journals Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6013 ◽  
Author(s):  
Sanja Maria Hakala ◽  
Perttu Seppä ◽  
Maria Heikkilä ◽  
Pekka Punttila ◽  
Jouni Sorvari ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Morphological Characters ◽  
Coi Gene ◽  
Species Status ◽  
Separate Species ◽  
Mitochondrial Coi ◽  
Recent Addition ◽  
Morphological Differences ◽  
Dna Microsatellite ◽  
Dna Microsatellite Markers

Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.

Spectrum Classification of Easily Confused Ground Objects in ALI Remote Sensing Image Based on Texture Features

2012 ◽  
Vol 610-613 ◽  
pp. 3606-3611
Author(s):  
Ling Ling Zhang ◽  
Ge Ying Lai ◽  
Xiang Gui Zeng ◽  
Fa Zhao Yi
Keyword(s):  
Maximum Likelihood Method ◽  
Research Result ◽  
Principal Component ◽  
Window Size ◽  
Texture Features ◽  
Likelihood Method ◽  
Forest Land ◽  
Classification Result ◽  
Occurrence Matrix

According to the problem that the classification result of shrub and forest land was easy to confuse when used spectrum of Advanced Land Image (ALI) to classify. This paper used the Meijiang River watershed as the study area. Used the Principal Component Analysis (PCA) to reduce dimension, taken the Contrast, Second moment, Mean and Dissimilarity as the texture values, and extracted the texture by Gray level co-occurrence matrix (GLCM). The texture features extracted from different window sizes were used the Maximum likelihood method to classify, and chosen the texture features extracted by the most suitable window size to join the classification. The research result shows that the texture features extracted by window size of 11×11 can distinguish well the two easily ground objects; moreover, the overall accuracy of classification used texture and spectrum features reached to 87.55%, which is 4.4% higher than the classification with spectrum.

Description and phylogenetic classification of Stackelberginia cerberus sp. nov. (Diptera: Asilidae), comprising the first record of this genus from the Nearctic

Zootaxa ◽  
2017 ◽  
Vol 4306 (4) ◽  
pp. 567 ◽  
Author(s):  
TRISTAN A. MCKNIGHT ◽  
ROBERT A. CANNINGS
Keyword(s):  
Central Asia ◽  
Nuclear Protein ◽  
First Record ◽  
Morphological Characters ◽  
Western Hemisphere ◽  
Protein Coding ◽  
Mitochondrial Coi ◽  
Late Autumn ◽  
Phylogenetic Classification

Stackelberginia cerberus sp. nov. (Diptera: Asilidae) is described from the Amargosa desert (USA: Nevada) and compared to related taxa. This is the first record of the genus in the Western Hemisphere; other species live in the deserts of central Asia. Stackelberginia Lehr is proposed as the sister taxon to Lasiopogon Loew in the subfamily Stichopogoninae based on morphological characters and a Bayesian species tree estimated from one mitochondrial (COI) and three nuclear protein-coding loci (AATS, PEPCK, wingless). Stackelberginia has the medially divided epandrium and rotated hypopygium of Lasiopogon, but the facial gibbosity is flat, macrosetae of thorax, head, and legs are unusually long, and phenology peaks in late autumn. 

scholarly journals Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

2021 ◽  
Author(s):  
Takehiro K Katoh ◽  
Ji-Min Chen ◽  
Jin-Hua Yang ◽  
Guang Zhang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Morphological Data ◽  
Sister Relationship ◽  
Mitochondrial Coi ◽  
Adaptive Diversification ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Cladistic Analyses ◽  
Species Groups

The genus Dichaetophora Duda is of 69 formally described, Old World species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. Most of these species were delimitated morphologically, with the within-genus relationship established largely via cladistic analyses of morphological characters. In the present study, we first conducted species-delimitation with aids of morphological data as well DNA barcodes (nucleotide sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I, gene), for a huge sample of Dichaetophora and allied taxa (genus Mulgravea and subgenus Dudaica of Drosophila) collected from a wide geographical range. Then, multiple-locus phylogenetic reconstruction was conducted based on elaborate taxon sampling from the known and newly recognized species in the above taxa, with the maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, 189 species (186 of Dichaetophora, 2 of Mulgravea, and 1 for Dudaica) were newly recognized. In our ML and BI trees, several well-supported species clusters equivalent to the species groups agbo (excluding of neocirricauda), tenuicauda, sinensis (inclusive of neocirricauda) and trilobita of Dichaetophora, were recovered, with the sister-relationship between the third and fourth proved. Other well-supported clusters include 1) a clade comprising of Di. acutissima group and Dudaica, with the former proved to be paraphyletic to the latter; 2) genus Mulgravea; 3) a clade comprising exclusively of newly recognized Dichaetophora species, and was placed as sister to Mulgravea. Three of the remaining five representatives of Dichaetophora species form a solid cluster, leaving the positions of the last two unresolved. The present study greatly renewed out knowledge about the species diversity in a pan-Dichaetophora clade, providing us with an unprecedented historical framework for further taxonomy revision of this clade, and valuable baseline knowledge for future reconstruction of the history of its adaptive diversification in the particular microhabitats.

Phylogeny, major clades and infrageneric classification of Corymbia (Myrtaceae), based on nuclear ribosomal DNA and morphology

2009 ◽  
Vol 22 (5) ◽  
pp. 384 ◽  
Author(s):  
Carlos Parra-O. ◽  
Michael J. Bayly ◽  
Andrew Drinnan ◽  
Frank Udovicic ◽  
Pauline Ladiges
Keyword(s):  
Ribosomal Dna ◽  
Convergent Evolution ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
Nuclear Rdna ◽  
Infrageneric Classification ◽  
Taxonomic Categories

Phylogenetic relationships of sections and species within Corymbia (Myrtaceae), the bloodwood eucalypts, were evaluated by using combined analyses of nuclear rDNA (ETS + ITS) and morphological characters. Combining morphological characters with molecular data provided resolution of relationships within Corymbia. The analyses supported the monophyly of the genus and recognition of the following two major clades, treated here as new subgenera: subgenus Corymbia, including informal sections recognised by Hill and Johnson (1995), namely Rufaria (red bloodwoods), Apteria and Fundoria; and subgenus Blakella, including sections Politaria (spotted gums), Cadagaria, Blakearia (paper-fruited bloodwoods or ghost gums) and Ochraria (yellow bloodwoods). Hill and Johnson’s section Rufaria is monophyletic if Apteria and Fundoria are included. It is evident that, among the red bloodwoods, series are not monophyletic and several morphological characters result from convergent evolution. There was strong morphological and molecular evidence that the three species of red bloodwoods that occur in south-western Western Australia (series Gummiferae: C. calophylla and C. haematoxylon, and series Ficifoliae: C. ficifolia) form a monophyletic group, separate from the eastern C. gummifera (series Gummiferae), which is probably sister to the clade of all other red bloodwoods. Phylogenetic results supported recognition of new taxonomic categories within Corymbia, and these are formalised here.

A phylogenetic approach to the Philippines endemic centipedes of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae), with the description of a new species

Zootaxa ◽  
2018 ◽  
Vol 4483 (3) ◽  
pp. 401
Author(s):  
CARLES DOMÉNECH ◽  
VICTOR M. BARBERA ◽  
EDUARDO LARRIBA
Keyword(s):  
Dna Sequences ◽  
Endemic Species ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Genetic Distances ◽  
The Philippines ◽  
Neighbor Joining ◽  
Separate Species ◽  
Additional Species ◽  
A New Species

The genus Scolopendra Linnaeus, 1758 is represented in the Philippines’ fauna by five species, two of which are endemic. Mitochondrial DNA sequences of gene cytochrome c oxidase subunit I (COI) were obtained from six Scolopendra specimens belonging to two endemic species and a new one, described here as Scolopendra paradoxa Doménech sp. nov. These sequences were analyzed together with another forty-one sequences from GenBank, including additional species of Scolopendra and a few representatives of other Scolopendridae genera. Phylogenetic trees inferred from the COI analysis using maximum likelihood and neighbor joining showed the three Philippines Scolopendra endemic species as a polyphyletic group coherent with their respective morphologies, although the position of S. spinosissima Kraepelin, 1903 varied within the obtained trees. Species delimitation based on standard external morphological characters was also concordant with the observed genetic distances, monophyly and node support, confirming S. subcrustalis Kronmüller, 2009 and S. paradoxa sp. nov. as separate species also at the molecular level, while only the position of S. spinosissima could not be properly established with any of the statistical methods used. In addition, the male genitalia of the three studied species were found to lack gonopods and a penis. Remarks on the ultimate legs prefemoral spinous formula of S. spinosissima plus a key to the species of the genus Scolopendra in the Philippines are provided. 

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