Molecular Phylogenetic Analysis of the Orthoptera (Arthropoda, Insecta) based on Hexamerin Sequences

Zootaxa ◽  
2017 ◽  
Vol 4232 (4) ◽  
pp. 523 ◽  
Author(s):  
XIAOHONG ZHANG ◽  
JINFENG HAO ◽  
YU XIA ◽  
YAGE CHANG ◽  
DAOCHUAN ZHANG ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Study ◽  
Neighbor Joining ◽  
Morphological Classification ◽  
Good Marker ◽  
Insect Order ◽  
Higher Taxa ◽  
Molecular Phylogenetic

The higher taxa classification and phylogeny of the insect order Orthoptera have long been controversial. Hexamerin, as a member of the highly conserved arthropod hemocyanin superfamily, has been shown to be a good marker for the phylogenetic study of insects. However, few studies have used hexamerins on the phylogeny of Orthoptera. In this study, we determined twenty-seven different hexamerin subunit type sequences in seventeen speices of Orthoptera. In order to infer the phylogenetic relationships among the superfamilies within Orthoptera and test the monophyly of Orthoptera, phylogenic trees were reconstructed using Neighbor-Joining (NJ) and Bayesian inference (BI) methods with two dipluran and three hymenopteran hexamerin sequences as outgroups. The result supported the monophyly of Orthoptera, which includes two monophyletic suborders Caelifera and Ensifera. The Caelifera includes Acridoidea, Eumastacoidea, Tetrigoidea and Tridactyloidea, and the Ensifera includes Tettigonioidea, Grylloidea and Gryllotalpoidea. Our study is basically consistent with the study of morphological classification. In addition, our study indicates that a relatively comprehensive taxa sampling is essential to solve some problems in phylogenetic reconstruction. 

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

2008 ◽  
Vol 98 (5) ◽  
pp. 499-507 ◽  
Author(s):  
H.C. Zhang ◽  
G.X. Qiao
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Host Specificity ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Primary Host ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

Phylogenetic analysis of DNA sequence data.

2021 ◽  
pp. 265-282
Author(s):  
Sergei A. Subbotin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Phylogenetic Study ◽  
Public Database ◽  
Sample Collection ◽  
Minimum Evolution ◽  
Molecular Phylogenetic ◽  
Pcr Products ◽  
Selection Of

Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.

scholarly journals A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e58568 ◽  
Author(s):  
Jerome C. Regier ◽  
Charles Mitter ◽  
Andreas Zwick ◽  
Adam L. Bazinet ◽  
Michael P. Cummings ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Study ◽  
Insect Order ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

­Molecular identification of Audouinella-like species (Rhodophyta) from China based on three short DNA fragments

Phytotaxa ◽  
2016 ◽  
Vol 246 (2) ◽  
pp. 107 ◽  
Author(s):  
Fangru Nan ◽  
Jia Feng ◽  
Xiaojing Han ◽  
Junping Lv ◽  
Qi Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Strong Support ◽  
Sequence Divergence ◽  
Phylogenetic Position ◽  
Dna Fragments ◽  
Neighbor Joining ◽  
Molecular Phylogenetic ◽  
Assisted Analysis ◽  
Thallus Color ◽  
Molecular Trees

Four algal specimens with morphological resemblance to Audouinella were collected in China, both bluish and reddish thalli included. Because of the taxonomic obscurity of the acrochaetioid lineage, a molecular phylogenetic analysis was performed to verify the phylogenetic position of these specimens based on three short DNA fragments including psbA, UPA and COI-5P. Molecular sequences were analyzed by neighbor-joining, maximum likelihood, Bayesian, and NeighborNet methods. Phylogenetic relationships based on three DNA fragments were consistent in that the four Audouinella-like thalli clustered together with Thorea hispida (Thore) Desvaux with strong support. The four specimens morphologically similar to Audouinella were concluded to represent the chantransia stage of Thoreales based on molecular trees. The reddish specimen shared no sequence divergence with the bluish ones. For identification of freshwater Audouinellla, criteria of thallus color must be used with caution and molecular tool-assisted analysis are essential. The formerly established new species Audouinella heterospora S.L.Xie & Y.J.Ling was inferred to be synonymous with the chantransia stage of T. hispida. The three DNA molecular markers demonstrated to be effective to ascertain the phylogenetic position of acrochaetioid algae specimens, and to delineate other freshwater Rhodophyta.

scholarly journals Phylogeny of the Genus Dichotrachelus (Coleoptera: Curculionidae: Cyclominae)

Diversity ◽  
2018 ◽  
Vol 10 (3) ◽  
pp. 66 ◽  
Author(s):  
Massimo Meregalli ◽  
Christoph Germann ◽  
Marco V. Bernasconi ◽  
Piero Cervella
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Mediterranean Region ◽  
Phylogenetic Reconstruction ◽  
South American ◽  
Mitochondrial Cytochrome ◽  
Southern France ◽  
The Alps ◽  
Mitochondrial Cytochrome Oxidase ◽  
Male Genital

A phylogenetic analysis of the genus Dichotrachelus (Curculionidae: Cyclominae) was carried out, based on a morphological matrix and, for some species, on mitochondrial cytochrome oxidase I sequences. Bayesian Inference, Maximum Likelihood and Maximum Parsimony were implemented and the results were compared. The genus is found to be isolated in the subfamily, not related to the only other Palaearctic tribe (Hipporhinini) and possibly nearer to the south-American genera of Cyclominae of the tribe Listroderini. Among these, Macrostyphlus is also equally associated to mosses as the host plant. In Dichotrachelus, two main clades were recognized, one distributed in the western part of the Mediterranean region (Iberian Peninsula, northern Africa and southern France) and the second distributed in the Alps and Apennines. Within each clade, some differentiated monophyletic subgroups could be identified. An evaluation of the most important characters that led to the phylogenetic reconstruction indicated the male genital sclerite as the most useful structure to characterize the different clades.

scholarly journals Molecular phylogeny of Lytorhynchus diadema (Reptilia, Colubridae) populations in Saudi Arabia

Herpetozoa ◽  
2021 ◽  
Vol 34 ◽  
pp. 271-276
Author(s):  
Ahmed Alshammari ◽  
Ahmed Badry ◽  
Salem Basuis ◽  
Adel A. Ibrahim ◽  
Eman El-Abd
Keyword(s):  
Phylogenetic Analysis ◽  
Saudi Arabia ◽  
Molecular Phylogeny ◽  
Bayesian Methods ◽  
12S Rrna ◽  
Rrna Gene ◽  
Neighbor Joining ◽  
12S Rrna Gene ◽  
African Populations ◽  
Molecular Phylogenetic

This study presents the molecular phylogenetic relationships among Lytorhynchus diadema (Duméril, Bibron & Duméril, 1854) populations in Saudi Arabia relative to populations from Africa and Asia. This phylogenetic analysis was based on mitochondrial 16S and 12S rRNA partial gene fragments using Neighbor-joining, Maximum Parsimony, and Bayesian methods. The results strongly support the monophyly of Lytorhynchus based on two concatenated genes and the 12S rRNA gene separately. Also, a significant separation is observed between the Arabian samples from Saudi Arabia, Yemen, and Oman, and the African populations from Egypt, Tunisia, and Morocco.

­Phylogenetic Analysis of the Genus Pohlia (Bryophyta, Bryaceae) Using Chloroplast and Nuclear Ribosomal DNA

Phytotaxa ◽  
2018 ◽  
Vol 351 (2) ◽  
pp. 141 ◽  
Author(s):  
JING-YUAN NIU ◽  
☆LIN LI Li ◽  
SHUO SHI ◽  
HUI LI ◽  
XIAO-RUI WANG ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Future Study ◽  
Nuclear Ribosomal Dna ◽  
Molecular Phylogenetic Analysis ◽  
Monophyletic Clade ◽  
Molecular Phylogenetic ◽  
High Support

The genus Pohlia Hedwig is a large moss genus that has been placed in the Bryaceae family as traditionally determined. However, a molecular phylogenetic analysis has indicated that the Pohlia genus is more closely related to genera that are traditionally classified into the Mniaceae or Mielichhoferiaceae families. In this study, we performed a molecular phylogenetic analysis using evidence from four chloroplast regions (atpB-rbcL, rps4, trnG, and trnL-trnF) and one nuclear ribosomal intragenic spacer region (ITS) using different methods (maximum parsimony, maximum likelihood, and Bayesian inference). The phylogenetic relationships between Pohlia and its related genera are discussed.         Two large clades among our samples were well supported in all of the datasets. The traditionally defined Bryaceae species, including Brachymenium pendulum, Bryum caespiticium, Bryum capillare, Anomobryum gemmigerum, and Rhodobryum ontariense, formed a monophyletic clade with high support. The second clade corresponding to the Mielichhoferiaceae-Mniaceae complex also had high support. All of the Pohlia, Mielichhoferia and Mniaceae samples were included in this latter clade.         The clearest result from the phylogenetic analysis is that the Pohlia genus is non-monophyletic. The analysis is identical when using three methods and concludes that Pohlia is closer to the genera in Mielichhoferiaceae and Mniaceae. A formal taxonomic treatment of this clade was not performed because we lacked sufficient specimens of the species, although this work will be included in a future study.

Proposal of a new subfamily of Sciaridae (Diptera: Sciaridae), with description of one new species from South Korea

Zootaxa ◽  
2019 ◽  
Vol 4543 (1) ◽  
pp. 127 ◽  
Author(s):  
SEUNGGWAN SHIN ◽  
HEUNGSIK LEE ◽  
SEUNGHWAN LEE
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Study ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Unidentified Species ◽  
Definition Of ◽  
One New Species ◽  
Key Characters

Here we propose a new monophyletic subfamily, the Chaetosciarinae, based on previous morphological cladistic and molecular phylogenetic studies. This new subfamily includes the genera Chaetosciara Frey, Mouffetina Frey, Schwenckfeldina Frey, and Scythropochroa Enderlein. We also provide a definition of the new subfamily Chaetosciarinae and describe common morphological key characters. Three Korean Chaetosciarinae species in three genera are reported, all of which are new to Korea and one (Scythropochroa pseudoquercicola sp. nov.) of which is new to science. A previous molecular phylogenetic study designated Scy. pseudoquercicola as an unidentified species. Our study provides examined species information for members of this new subfamily to accompany the GenBank accession numbers published by a previous molecular phylogenetic study. Furthermore, we present a multigene molecular phylogenetic analysis for the Chaetosciarinae. 

scholarly journals Phylogenetic relationships of 'Polyalthia' in Fiji

PhytoKeys ◽  
2020 ◽  
Vol 165 ◽  
pp. 99-113
Author(s):  
Bine Xue ◽  
Yanwen Chen ◽  
Richard M. K. Saunders
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
The Other ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Herbarium Specimens ◽  
Molecular Phylogenetic ◽  
Taxonomic Changes

The genus Polyalthia (Annonaceae) has undergone dramatic taxonomic changes in recent years. Nine Polyalthia species have historically been recognized in Fiji, all of which have subsequently been transferred to three different genera, viz. Goniothalamus, Huberantha and Meiogyne. The transfer of six of these species has received strong molecular phylogenetic support, although the other three species, Polyalthia amoena, P. capillata and P. loriformis [all transferred to Huberantha], have never previously been sampled in a phylogenetic study. We address this shortfall by sampling available herbarium specimens of all three species and integrating the data in a molecular phylogenetic analysis. The resultant phylogeny provides strong support for the transfer of these species to Huberantha. The taxonomic realignment of all nine Fijian species formerly classified in Polyalthia is also clearly demonstrated and supported by the resultant phylogeny. The updated taxonomic treatments of the nine species, a key to the three genera and a key to the Fijian Huberantha species are provided.

scholarly journals A new species of the genus Euxaldar Fennah, 1978 (Hemiptera, Fulgoromorpha, Issidae) from China and revision on the molecular phylogeny of the family

ZooKeys ◽  
2021 ◽  
Vol 1021 ◽  
pp. 19-35
Author(s):  
Liang-Jing Yang ◽  
Zhi-Min Chang ◽  
Lin Yang ◽  
Xiang-Sheng Chen
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Molecular Phylogenetic Analysis ◽  
The Family ◽  
Molecular Phylogenetic ◽  
First Time ◽  
A New Species

A new species Euxaldar daweishanensis Yang, Chang & Chen, sp. nov. is described and illustrated from southwestern China. The female genitalia of the genus Euxaldar is described and presented for the first time. A checklist and key to the known species of the genus are provided. A revised molecular phylogenetic analysis of the family Issidae based on combined partial sequences of 18S, 28S, COI, and Cytb is provided using both Maximum likelihood and Bayesian inference analyses.

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