scholarly journals Molecular phylogeny of common sun skink, Eutropis (Squamata: Scincidae), of northwestern part of Bangladesh

2019 ◽  
Vol 47 (1) ◽  
pp. 13-25
Author(s):  
Mosharrof Hossain ◽  
Che Jing
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Molecular Phylogeny ◽  
Posterior Probability ◽  
Common Ancestor ◽  
Northwestern Part ◽  
Congeneric Species ◽  
Relationship Of ◽  
Posterior Probability Support

A study on the phylogenetic relationship of Bangladeshi Skink confirmed species as Eutropis multifasciata by Bayesian inference (BI) (100%) and 98% node support to maximum likelihood (ML) tree topology, respectively. The sequence divergences between Eutropis multifasciata and other congeneric species were significant, ranging from 0.1 to 13.6% for 16S rRNA. Intraspecific genetic divergence within E. multifasciata was estimated 10.3%. E. multifasciata formed a distinct clade with high posterior probability support. This maiden study on Bangladeshi Skink results support that one monophyletic subgroup containing all specimens of E. multifasciata and all recently recognized E. multifasciata populations have evolved from one common ancestor. Bangladesh J. Zool. 47(1): 13-25, 2019

Systematic relationships of the Taeniapterini (Diptera: Micropezidae, Taeniapterinae)

Zootaxa ◽  
2021 ◽  
Vol 5004 (2) ◽  
pp. 370-384
Author(s):  
GUSTAVO BORGES FERRO ◽  
JEFFREY H. SKEVINGTON ◽  
STEPHEN A. MARSHALL ◽  
SCOTT KELSO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Cytochrome C ◽  
16S Rrna ◽  
Molecular Phylogeny ◽  
Cytochrome C Oxidase ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Oxidase Subunit ◽  
Systematic Relationships

A molecular phylogeny for the Taeniapterinae is presented based on mitochondrial (cytochrome c oxidase subunit I, COI), ribosomal (16S rRNA and 28S rRNA) and nuclear (EF-1α and CAD) genes of 48 specimens including 40 species. Maximum likelihood and Bayesian inference were used to analyze the total concatenated dataset of 8769 bp. The results confirm that tribal classifications in Taeniapterinae are artificial and support the separation of Paragrallomyia Hendel and Taeniaptera sensu Ferro & Marshall (2020).

scholarly journals Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and the cockroach Cryptocercus

2008 ◽  
Vol 276 (1655) ◽  
pp. 239-245 ◽  
Author(s):  
Moriya Ohkuma ◽  
Satoko Noda ◽  
Yuichi Hongoh ◽  
Christine A Nalepa ◽  
Tetsushi Inoue
Keyword(s):  
Molecular Phylogeny ◽  
Common Ancestor ◽  
Sister Group ◽  
Small Subunit ◽  
Sister Group Relationship ◽  
Small Subunit Rrna ◽  
Family Level ◽  
Cryptocercus Punctulatus ◽  
Relationship Of ◽  
Comprehensive Study

Cryptocercus cockroaches and lower termites harbour obligate, diverse and unique symbiotic cellulolytic flagellates in their hindgut that are considered critical in the development of social behaviour in their hosts. However, there has been controversy concerning the origin of these symbiotic flagellates. Here, molecular sequences encoding small subunit rRNA and glyceraldehyde-3-phosphate dehydrogenase were identified in the symbiotic flagellates of the order Trichonymphida (phylum Parabasalia) in the gut of Cryptocercus punctulatus and compared phylogenetically to the corresponding species in termites. In each of the monophyletic lineages that represent family-level groups in Trichonymphida, the symbionts of Cryptocercus were robustly sister to those of termites. Together with the recent evidence for the sister-group relationship of the host insects, this first comprehensive study comparing symbiont molecular phylogeny strongly suggests that a set of symbiotic flagellates representative of extant diversity was already established in an ancestor common to Cryptocercus and termites, was vertically transmitted to their offspring, and subsequently became diversified to distinct levels, depending on both the host and the symbiont lineages.

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 New insights into the molecular phylogeny and taxonomy of the family Issidae (Hemiptera: Auchenorrhyncha: Fulgoroidea)

2020 ◽  
Vol 324 (1) ◽  
pp. 146-161 ◽  
Author(s):  
V.M. Gnezdilov ◽  
F.V. Konstantinov ◽  
S.Y. Bodrov
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
New World ◽  
Common Ancestor ◽  
The Family ◽  
Molecular Dataset ◽  
Western Palaearctic ◽  
High Support

The phylogenetic relationships among major lineages of the planthopper family Issidae were explored by analyzing a molecular dataset of nine fragments (COI, CytB, 12S, H3, 16S, 18SII, 18SIII, 28S D3–D5, 28S D6–D7) and 48 terminal taxa. Bayesian and Maximum likelihood analyses yielded similar and mostly well-resolved trees with moderate to high support for most branches. The obtained results suggest subdivision of the family Issidae Spinola into two subfamilies, Issinae Spinola, 1839 (= Thioniinae Melichar, 1906, = Hemisphaeriinae Melichar, 1906) and Hysteropterinae Melichar, 1906. The Issinae was clustered into the tribes Issini Spinola, 1839, with the subtribes Issina Spinola, 1839 and Thioniina Melichar, 1906, Sarimini Wang, Zhang et Bourgoin, 2016, Parahiraciini Cheng et Yang, 1991, Hemisphaeriini Melichar, 1906, and Kodaianellini Wang, Zhang et Bourgoin, 2016. The Hysteropterinae incorporates the rest of Western Palaearctic taxa except Issina. Chimetopini Gnezdilov, 2017, stat. nov. is elevated to tribe from the subtribal level. Most well-supported clades showed clear geographical pattering. Newly obtained data contradicts the scenario of an early split of American Thioniinae from other Issidae and possible origin of the family in the New World, while the combination of Palaearctic Issus Fabricius and Latissus Dlabola with Oriental and American taxa in one well supported clade may serve as an evidence for a common ancestor for extant Oriental, American, and Palaearctic issids.

A molecular phylogeny of the Palaearctic and Oriental members of the tribe Boarmiini (Lepidoptera : Geometridae : Ennominae)

2017 ◽  
Vol 31 (4) ◽  
pp. 427 ◽  
Author(s):  
Nan Jiang ◽  
Xinxin Li ◽  
Axel Hausmann ◽  
Rui Cheng ◽  
Dayong Xue ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Species Diversity ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
New Combinations ◽  
Mitochondrial Coi ◽  
Morphological Studies ◽  
High Species Diversity

Owing to the high species diversity and the lack of a modern revision, the phylogenetic relationships within the tribe Boarmiini remain largely unexplored. In this study, we reconstruct the first molecular phylogeny of the Palaearctic and Oriental members of Boarmiini, and infer the relationships among tribes within the ‘boarmiine’ lineage. One mitochondrial (COI) and four nuclear (EF-1α, CAD, RpS5, GAPDH) genes for 56 genera and 96 species of Boarmiini mostly from the Palaearctic and Oriental regions were included in the study. Analyses of Bayesian inference and maximum likelihood recovered largely congruent results. The monophyly of Boarmiini is supported by our results. Seven clades and seven subclades within Boarmiini were found. The molecular results coupled with morphological studies suggested the synonymisation of Zanclopera Warren, 1894, syn. nov. with Krananda Moore, 1868. The following new combinations are proposed: Krananda straminearia (Leech, 1897) (comb. nov.), Krananda falcata (Warren, 1894) (comb. nov.), and Krananda fulva (Yazaki, 1994) (comb. nov.). Our results also supported the monophyly of the ‘boarmiine’ lineage. Boarmiini were recovered as sister to the remaining taxa within the ‘boarmiine’ lineage, and Macariini were recovered as sister to Abraxini, Eutoeini and Cassymini.

Molecular phylogeny of sea-skaters (Halobates Eschscholtz, 1822), relationship between Halobatini and Metrocorini, and a catalogue of the subfamily Halobatinae (Hemiptera: Heteroptera: Gerridae)

2020 ◽  
Vol 51 (2) ◽  
pp. 139-240 ◽  
Author(s):  
Cristian Román-Palacios ◽  
Jakob Damgaard ◽  
Lanna Cheng ◽  
Felipe Ferraz Figueiredo Moreira ◽  
Terumi Ikawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Open Ocean ◽  
Rrna Genes ◽  
28S Rrna ◽  
The Common ◽  
Geographic Distributions

We investigated the phylogenetic relationships among seven of the ten Halobatinae genera (Heteroptera: Gerridae) based on COI+II, 16S rRNA, and 28S rRNA genes. Our analyses recovered monophyly of Halobatinae, and suggested paraphyly of Metrocorini caused by the position of Ventidius and Esakia. Since our phylogenies did not infer monophyly of the subgenus Halobates (s.str.) within Halobatini, we synonymized Austrobates and Halobates (Hilliella) with Halobates. We confirmed that (1) the limnic lifestyle of Metrocorini was ancestral in Halobatinae, (2) the marine lifestyle evolved only once in the common ancestor of Asclepios + Halobates, (3) the limnic lifestyle of some members of Halobates was independently derived from marine ancestors, and that (4) the open ocean was colonized at least three times in Halobates. A catalogue of Halobatinae organized according to an updated classification is presented, including all known geographic distributions, bibliographical references, and additional notes to all species of the subfamily.

scholarly journals Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10618
Author(s):  
Shuran Liao ◽  
Yishu Wang ◽  
Duting Jin ◽  
Rong Chen ◽  
Zongqing Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Close Relationship ◽  
Relationship Of ◽  
The Relationship ◽  
Six Genes

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

scholarly journals Enabling inference for context-dependent models of mutation by bounding the propagation of dependency

2021 ◽  
Author(s):  
Erick Matsen ◽  
Peter L. Ralph
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Common Ancestor ◽  
Phylogenetic Inference ◽  
R Package ◽  
Flanking Sequence ◽  
Model Refinement ◽  
Iterative Model ◽  
The Common ◽  
Context Dependent

Although the rates at which positions in the genome mutate are known to depend not only on the nucleotide to be mutated, but also on neighboring nucleotides, it remains challenging to do phylogenetic inference using models of context-dependent mutation. In these models, the effects of one mutation may in principle propagate to faraway locations, making it difficult to compute exact likelihoods. This paper shows how to use bounds on the propagation of dependency to compute likelihoods of mutation of a given segment of genome by marginalizing over sufficiently long flanking sequence. This can be used for maximum likelihood or Bayesian inference. Protocols examining residuals and iterative model refinement are also discussed. Tools for efficiently working with these models are provided in an R package, that could be used in other applications. The method is used to examine context dependence of mutations since the common ancestor of humans and chimpanzee.

scholarly journals Revisiting the phylogeny of phylum Ctenophora: a molecular perspective

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2881
Author(s):  
Luis A. Arteaga-Figueroa ◽  
Valentina Sánchez-Bermúdez ◽  
Nicolás D. Franco-Sierra
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Ribosomal Rna ◽  
Single Gene ◽  
Probabilistic Methods ◽  
Data Set ◽  
Protein Coding ◽  
Rrna Sequences ◽  
Made In

The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora, are not totally understood. Previous studies have been developed on this subject, mostly based on morphology and single gene analyses (rRNA sequences). Several loci (protein coding and ribosomal RNA) from taxa belonging to this phylum are currently available on public databases (e.g. GenBank). Here we revisit Ctenophora molecular phylogeny using public sequences and probabilistic methods (Bayesian inference and maximum likelihood). To get more reliable results multi-locus analyses were performed using 5.8S, 28S, ITS1, ITS2 and 18S, and IPNS and GFP-like proteins. Best topologies, consistent with both methods for each data set, are shown and analysed. Comparing the results of the pylogenetic reconstruction with previous research, most clades showed the same relationships as the ones found with morphology and single gene analyses, consistent with hypotheses made in previous research. There were also some unexpected relationships clustering species from different orders.

Taxonomic status and phylogenetic position of Oxymycterus juliacae Allen 1900 (Rodentia: Cricetidae)

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Dennisse Ruelas ◽  
Víctor Pacheco
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Cytochrome B ◽  
Morphological Traits ◽  
Genetic Material ◽  
Taxonomic Status ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Congeneric Species ◽  
Morphological Distinction

Abstract The phylogenetic position of the “Upper yungas inca hocicudo” Oxymycterus juliacae, one of the lesser-known species of the genus Oxymycterus, is still unresolved. Several authors considered it a subspecies or synonym of Oxymycterus inca, but more recently, it was recognized as a valid species based on morphometric analysis and morphological traits. The objectives of this study were then to substantiate the morphological distinction of O. juliacae and evaluate its phylogenetic position using cytochrome b sequences. We evaluated the morphology of O. juliacae and compared it with congeneric species. In addition, a Cytochrome b gene matrix was subjected to analyses of maximum likelihood and Bayesian inference. Our results support the morphometric and morphological distinction of O. juliacae and found that this species is more closely related to Oxymycterus willkaurco than to O. inca. Therefore, the recognition of O. juliacae as a full species is supported and a rediagnosis is provided. In addition, we found O. inca is more related to other lowland species from Argentina, Brazil, and Uruguay, than to central Andean species. More efforts are needed to secure genetic material of Oxymycterus species, mainly the Andean species, for a better understanding of their phylogenetic relationship.

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