scholarly journals Phylogenetic inference identifies two eumetazoan TRPM clades and an 8th family of TRP channel, TRP soromelastatin (TRPS)

2019 ◽  
Author(s):  
Nathaniel J. Himmel ◽  
Thomas R. Gray ◽  
Daniel N. Cox
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Ion Homeostasis ◽  
Evolutionary Relationship ◽  
Phylogenetic Inference ◽  
Trp Channel ◽  
Trpm Channels

AbstractTRP melastatins (TRPMs) are most well-known as cold and menthol sensors, but are in fact broadly critical for life, from ion homeostasis to reproduction. Yet the evolutionary relationship between TRPM channels remains largely unresolved, particularly with respect to the placement of several highly divergent members. To characterize the evolution of TRPM and like channels, we performed a large-scale phylogenetic analysis of >1,300 TRPM-like sequences from 14 phyla (Annelida, Arthropoda, Brachiopoda, Chordata, Cnidaria, Echinodermata, Hemichordata, Mollusca, Nematoda, Nemertea, Phoronida, Priapulida, Tardigrada, and Xenacoelomorpha), including sequences from a variety of recently sequenced genomes that fill what would otherwise be substantial taxonomic gaps. These findings suggest: (1) The previously recognized TRPM family is in fact two distinct families, including canonical TRPM channels, and an 8th major, previously undescribed family of animal TRP channel, TRP soromelastatin (TRPS); (2) two TRPM clades predate the last bilaterian-cnidarian ancestor; and (3) the vertebrate-centric trend of categorizing TRPM channels as 1-8 is inappropriate for most phyla, including other chordates.

scholarly journals Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS)

2020 ◽  
Vol 37 (7) ◽  
pp. 2034-2044 ◽  
Author(s):  
Nathaniel J Himmel ◽  
Thomas R Gray ◽  
Daniel N Cox
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Transient Receptor Potential ◽  
Ion Homeostasis ◽  
Evolutionary Relationship ◽  
Receptor Potential ◽  
Trp Channel ◽  
Transient Receptor ◽  
Trpm Channels

Abstract Transient receptor potential melastatins (TRPMs) are most well known as cold and menthol sensors, but are in fact broadly critical for life, from ion homeostasis to reproduction. Yet, the evolutionary relationship between TRPM channels remains largely unresolved, particularly with respect to the placement of several highly divergent members. To characterize the evolution of TRPM and like channels, we performed a large-scale phylogenetic analysis of >1,300 TRPM-like sequences from 14 phyla (Annelida, Arthropoda, Brachiopoda, Chordata, Cnidaria, Echinodermata, Hemichordata, Mollusca, Nematoda, Nemertea, Phoronida, Priapulida, Tardigrada, and Xenacoelomorpha), including sequences from a variety of recently sequenced genomes that fill what would otherwise be substantial taxonomic gaps. These findings suggest: 1) the previously recognized TRPM family is in fact two distinct families, including canonical TRPM channels and an eighth major previously undescribed family of animal TRP channel, TRP soromelastatin; 2) two TRPM clades predate the last bilaterian–cnidarian ancestor; and 3) the vertebrate–centric trend of categorizing TRPM channels as 1–8 is inappropriate for most phyla, including other chordates.

Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin & Cochran, 1963 (Anura: Brachycephaloidea)

Zootaxa ◽  
2018 ◽  
Vol 4514 (4) ◽  
pp. 487
Author(s):  
ANDRÉS R. ACOSTA-GALVIS ◽  
JEFFREY W. STREICHER ◽  
LUIGI MANUELLI ◽  
TRAVIS CUDDY ◽  
RAFAEL O. DE SÁ
Keyword(s):  
Phylogenetic Analysis ◽  
New World ◽  
Taxonomic Revision ◽  
Phylogenetic Inference ◽  
Genetic Distances ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Placement ◽  
Molecular Phylogenetic ◽  
First Time

Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus Niceforonia Goin & Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species Niceforonia nana were collected and for the first time the genus is included in a molecular phylogenetic analysis of mitochondrial (mtDNA; 12S and 16S) and nuclear (nucDNA; TYR and RAG1) markers. Molecular phylogenetic inference based on concatenated and separate mtDNA and nucDNA analyses recovered Niceforonia nana nested within Hypodactylus Hedges et al. 2008, rendering the latter genus paraphyletic. Consequently, herein we place the genus Hypodactylus in the synonymy of Niceforonia to resolve the paraphyly and place Niceforonia in the subfamily Hypodactylinae. Based on our revised concept of the genus Niceforonia we conducted preliminary morphological comparisons using specimens and literature descriptions. Finally, Nicefornia nana is quite divergent from other species of Niceforonia (uncorrected genetic distances of ca. 10% 16S and 7% TYR) suggesting that further taxonomic revision may be warranted. 

scholarly journals The putative lissamphibian stem-group: phylogeny and evolution of the dissorophoid temnospondyls

2018 ◽  
Vol 93 (1) ◽  
pp. 137-156 ◽  
Author(s):  
Rainer R. Schoch
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Sensu Stricto ◽  
New Taxon ◽  
Stem Group ◽  
Phylogeny And Evolution

AbstractDissorophoid temnospondyls are widely considered to have given rise to some or all modern amphibians (Lissamphibia), but their ingroup relationships still bear major unresolved questions. An inclusive phylogenetic analysis of dissorophoids gives new insights into the large-scale topology of relationships. Based on a TNT 1.5 analysis (33 taxa, 108 characters), the enigmatic taxonPerryellais found to nest just outside Dissorophoidea (phylogenetic defintion), but shares a range of synapomorphies with this clade. The dissorophoids proper are found to encompass a first dichotomy between the largely paedomorphic Micromelerpetidae and all other taxa (Xerodromes). Within the latter, there is a basal dichotomy between the large, heavily ossified Olsoniformes (Dissorophidae + Trematopidae) and the small salamander-like Amphibamiformes (new taxon), which include four clades: (1) Micropholidae (Tersomius,Pasawioops,Micropholis); (2) Amphibamidae sensu stricto (Doleserpeton,Amphibamus); (3) Branchiosauridae (Branchiosaurus,Apateon,Leptorophus,Schoenfelderpeton); and (4) Lissamphibia. The generaPlatyrhinopsandEoscopusare here found to nest at the base of Amphibamiformes. Represented by their basal-most stem-taxa (Triadobatrachus,Karaurus,Eocaecilia), lissamphibians nest withGerobatrachusrather than Amphibamidae, as repeatedly found by former analyses.UUID:http://zoobank.org/dadf36db-e003-4af7-bfa7-44d79bc04450

scholarly journals The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

2018 ◽  
Vol 109 (1-2) ◽  
pp. 301-323 ◽  
Author(s):  
Emanuel TSCHOPP ◽  
Paul UPCHURCH
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Parsimony ◽  
Large Scale ◽  
Intraspecific Variability ◽  
Species Level ◽  
A Posteriori ◽  
Operational Taxonomic Units ◽  
Vertebrate Palaeontology ◽  
Tree Topologies ◽  
Parsimony Criterion

ABSTRACTSpecimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura

Gene ◽  
2019 ◽  
Vol 695 ◽  
pp. 75-83 ◽  
Author(s):  
Li Gong ◽  
Hui Jiang ◽  
Kehua Zhu ◽  
Xinting Lu ◽  
Liqin Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hermit Crab ◽  
Large Scale ◽  
Mitochondrial Gene ◽  
Gene Rearrangements

scholarly journals Phylogenetic analysis of SARS-CoV-2 data is difficult

2020 ◽  
Author(s):  
Benoit Morel ◽  
Pierre Barbera ◽  
Lucas Czech ◽  
Ben Bettisworth ◽  
Lukas Hübner ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Phylogenetic Inference ◽  
Daily Basis ◽  
Extreme Caution ◽  
Data Analyses ◽  
Phylogenetic Methods ◽  
Degree Of Confidence

Abstract Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

scholarly journals Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 446 ◽  
Author(s):  
Karen Ebersohn ◽  
Peter Coetzee ◽  
Louwrens P. Snyman ◽  
Robert Swanepoel ◽  
Estelle H. Venter
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Full Genome Sequence ◽  
African Horse Sickness Virus ◽  
Gene Encoding ◽  
Phylogenetic Characterization ◽  
Next Generation Sequencing Ngs ◽  
High Degree

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

scholarly journals Phylogenetic Analysis of Chlamydia trachomatis Tarp and Correlation with Clinical Phenotype

2010 ◽  
Vol 78 (9) ◽  
pp. 3678-3688 ◽  
Author(s):  
Erika I. Lutter ◽  
Christine Bonner ◽  
Martin J. Holland ◽  
Robert J. Suchland ◽  
Walter E. Stamm ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chlamydia Trachomatis ◽  
Clinical Phenotype ◽  
Evolutionary Relationship ◽  
Actin Binding ◽  
Disease Phenotype ◽  
Sexually Transmitted ◽  
Binding Domains ◽  
High Degree ◽  
Reference Strains

ABSTRACT Chlamydia trachomatis is the leading cause of infectious blindness worldwide and is the most commonly reported pathogen causing sexually transmitted infections. Tarp (translocated actin recruiting phosphoprotein), a type III secreted effector that mediates actin nucleation, is central to C. trachomatis infection. The phylogenetic analysis of tarP from reference strains as well as ocular, genital, and lymphogranuloma venereum (LGV) clinical isolates demonstrated an evolutionary relationship with disease phenotype, with LGV and ocular isolates branched into clades that were separate from the urogenital isolates. The sequence analysis of Tarp indicated a high degree of variability and identified trends within clinical groupings. Tarps from LGV strains contained the highest number of tyrosine-rich repeat regions (up to nine) and the fewest (two) predicted actin binding domains. The converse was noted for Tarp proteins from ocular isolates that contained up to four actin binding domains and as few as one tyrosine-rich repeat region. The results suggest that Tarp is among the few known genes to play a role in C. trachomatis adaptations to specific niches within the host.

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