scholarly journals Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders

2019 ◽  
Author(s):  
Kirill V. Mikhailov ◽  
Viatcheslav N. Ivanenko
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Statistical Test ◽  
Original Study ◽  
Molecular Phylogenetic Analysis ◽  
Approximately Unbiased ◽  
Bayesian Analyses ◽  
Molecular Phylogenetic ◽  
Key Nodes

AbstractReanalysis of the dataset used by Khodami et al. (2017) reveals low support values for the key nodes of the copepod (Crustacea) phylogeny and fails to reproduce the results obtained in the study. Maximum likelihood (ML) and Bayesian analyses with the dataset produce phylogenies that are inconsistent with the branching of copepod groups proposed by Khodami et al. (2017). The proposed phylogeny is refuted by the approximately unbiased (AU) statistical test, which undermines several conclusions drawn from the original study.

Revision of Hygrochilus (Orchidaceae: Epidendroideae: Aeridinae) and a molecular phylogenetic analysis

Phytotaxa ◽  
2014 ◽  
Vol 159 (4) ◽  
pp. 256 ◽  
Author(s):  
MING-HE LI ◽  
GUO-QIANG ZHANG ◽  
ZHONG-JIAN LIU ◽  
SI-REN LAN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Bayesian Methods ◽  
New Combination ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
A New Species

Hygrochilus and Sedirea are genera of orchids with only three species endemic to Asia. An analysis of ITS and five plastid regions using parsimony, maximum likelihood, and Bayesian methods obtain clear evidence that Sedirea is nested within and should be considered synonymous with Hygrochilus. We adopt a broadly defined Hygrochilus characterized by possession of four pollinia. A new combination, namely, Hygrochilus japonica, and a new species, namely, Hygrochilus tsii (Orchidaceae: Epidedroideae: Aeridinae), are proposed.

­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.

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.

scholarly journals Molecular data support the placement of the enigmatic Cheguevaria as a subfamily of Lampyridae (Insecta: Coleoptera)

2019 ◽  
Vol 187 (4) ◽  
pp. 1253-1258 ◽  
Author(s):  
Vinicius S Ferreira ◽  
Oliver Keller ◽  
Marc A Branham ◽  
Michael A Ivie
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
18S Rrna ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Incertae Sedis ◽  
Maximum Likelihood Approach ◽  
Molecular Phylogenetic ◽  
Likelihood Approach

Abstract Since the description of the genus Cheguevaria as incertae sedis (Lampyridae), the placement of these beetles has been uncertain. This study is the first to address the placement of this genus based on a molecular phylogenetic analysis. We used three genes (18S rRNA, rrnl mitochondrial DNA and cox1 mitochondrial DNA) and a maximum likelihood approach with W-IQ-TREE to support Cheguevaria as a member of the Lampyridae and recognize it as the sole genus in the new subfamily Cheguevariinae stat. nov.

A description of eleven new species of Agaricus sections Xanthodermatei and Hondenses collected from Tibet and the surrounding areas

Phytotaxa ◽  
2016 ◽  
Vol 257 (2) ◽  
pp. 99 ◽  
Author(s):  
Jun-Liang Zhou ◽  
Sheng-Yu Su ◽  
Hong-Yan Su ◽  
Bo Wang ◽  
Philippe Callac ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Molecular Phylogenetic Analysis ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods ◽  
Molecular Phylogenetic ◽  
Surrounding Areas ◽  
First Time

Specimens of Agaricus sections Xanthodermatei and Hondenses were collected in Tibet and the surrounding areas. All specimens were morphologically described and subjected to molecular phylogenetic analysis of the ITS and combined ITS, LSU and tef-1α sequence data using Bayesian and Maximum Likelihood methods. Twelve species were identified in this study, eleven of which were new species and one of which was identified in China for the first time. All of the identified species are described and illustrated with photo plates.

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

Molecular phylogenetic analysis of dinoflagellate Scrippsiella trochoidea isolated from the East Asian waters

2010 ◽  
Vol 28 (2) ◽  
pp. 323-328 ◽  
Author(s):  
Xianghai Tang ◽  
Rencheng Yu ◽  
Qingchun Zhang ◽  
Yunfeng Wang ◽  
Tian Yan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
East Asian ◽  
Molecular Phylogenetic Analysis ◽  
Scrippsiella Trochoidea ◽  
Molecular Phylogenetic

scholarly journals Molecular phylogenetic analysis of the Amiota taurusata species group within the Chinese species, with descriptions of two new species

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Zhen-fang Shao ◽  
Tong Li ◽  
Jian-jun Jiang ◽  
Jin-ming Lu ◽  
Hong-wei Chen
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Group ◽  
Molecular Phylogenetic Analysis ◽  
Two New Species ◽  
Molecular Phylogenetic
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