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... Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxin transport, together with reports of auxin functi ...
... Asterinales is an important epifoliar order which generally lacks of DNA-based sequence data. There are many genera in Asterinales lacking molecular data and the exact taxonomic placement of those genera is undetermined. In this study, we introduce Brunneofissuraceae fam. nov. and Cirsosia mangiferae sp. nov. and Asterina neomangiferae nom. nov. based on morpho-molecular evidences. All fungal spec ...
... Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this analysis with comparable speed to a BLAST search. We demonstrate that SHOOT phylogenet ...
... Phenotypic plasticity index (PI), the slope of reaction norm (K) and relative distances plasticity index (RDPI), the most commonly used estimators, have occasionally been found to generate different plasticity rankings between groups (species, populations, cultivars or genotypes). However, no effort has been made to determine how frequent this incongruence is, and the factors that influence the oc ...
... Knowledge of the higher-level phylogenetic relationships of birds has grown substantially during the past two decades due to the application of genomic data. However, the nomenclature of higher-level taxa has not become more stable, due to the lack of regulation of taxon names above the level of superfamily by the ICZN, and the usage of rank-based nomenclature, which is not tied to clades in a phy ...
... Broussonetia comprises four species in China, of which three species are known to be infected by Phyllactinia spp. Between 2018 and 2021, five new Phyllactinia samples on B. papyrifera were collected, and two already existing specimens on B. kaempferi and B. kazinoki were re‐examined. Morphological characteristics and phylogenetic analyses showed that two species, Ph. broussonetiae‐kaempferi and P ...
... In maximum likelihood (ML), the support for a clade can be calculated directly as the likelihood ratio (LR) or log‐likelihood difference (S, LLD) of the best trees with and without the clade of interest. However, bootstrap (BS) clade frequencies are more pervasive in ML phylogenetics and are almost universally interpreted as measuring support. In addition to theoretical arguments against that inte ...
... Despite the prevalence of high‐throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, ...
phylogeny, etc ; Eunicida; Phyllodocidae; genes; transcriptome; Show all 5 Subjects
Abstract:
... Aciculata (Eunicida + Phyllodocida) is among the largest clades of annelids, comprising almost half of the known diversity of all marine annelids. Despite the group’s large size and biological importance, most phylogenomic studies on Annelida to date have had a limited sampling of this clade. The phylogenetic placement of many clades within Phyllodocida in particular has remained poorly understood ...
phylogeny, etc ; databases; genes; microbiology; research; Show all 5 Subjects
Abstract:
... 16S rRNA gene is frequently used for the identification of prokaryotic organisms and for phylogeny inference. Several specialized public databases exist that contain complete and partial sequences of 16S rRNA genes. In this paper, we present RiboGrove: the first publicly available database that comprises only full-length sequences of 16S rRNA genes originating from completely assembled prokaryotic ...
phylogeny, etc ; Vibrio; microbiology; ribosomal proteins; Show all 4 Subjects
Abstract:
... Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, “Vibrio Clade 3.0,” the second update of the molecular phylogenetic analysis was performed based on nucleo ...
phylogeny, etc ; Bacillariophyceae; littoral zone; research; Vietnam; Show all 5 Subjects
Abstract:
... A new monoraphid diatom, Karayevia chelonica sp. nov., is described from Nha Trang, Vietnam, isolated from marine littoral habitats. Phylogenetic analysis based on partial 18S rDNA and rbcL sequences places this species within the family Stauroneidaceae, and related to other monoraphid species. Karayevia chelonica sp. nov. differs from other species in the genus in stria density and a broad axial ...
phylogeny, etc ; Apiaceae; color; principal component analysis; Show all 4 Subjects
Abstract:
... PREMISE: Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower‐like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseu ...
phylogeny, etc ; Archaea; case studies; data collection; Show all 4 Subjects
Abstract:
... The large size of modern datasets has inspired a variety of strategies to alter genes, sites and/or species compositions to improve the accuracy of phylogenetic reconstructions. Each of these data-filtering approaches leads to the exclusion of different types of data, which is known to affect phylogenetic outcome. However, the choice of a filtering strategy is often subjective and the robustness o ...
phylogeny, etc ; Eutreptiella; algae; chloroplast genome; introns; Show all 5 Subjects
Abstract:
... Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plastid genomes. To examine the evolutionary diversity ...
phylogeny, etc ; biomineralization; calcium carbonate; eukaryotic cells; Show all 4 Subjects
Abstract:
... An unsuspected biomineralization process, which produces intracellular inclusions of amorphous calcium carbonate (ACC), was recently discovered in unicellular eukaryotes. These mineral inclusions, called micropearls, can be highly enriched with other alkaline‐earth metals (AEM) such as Sr and Ba. Similar intracellular inclusions of ACC have also been observed in prokaryotic organisms. These compar ...
phylogeny, etc ; amino acids; plasticity; structural biology; Show all 4 Subjects
Abstract:
... The production of extended-spectrum β-lactamases (ESBLs) is the main defense mechanism found in Gram negative bacteria. Among all the ESBLs, the CTX-M enzymes appear as the most efficient in terms of dissemination in different epidemiological contexts. CTX-M enzymes exhibit a striking plasticity, with a large number of allelic variants distributed in several sublineages, which can be associated wi ...
phylogeny, etc ; Trichomycterus; data collection; fish; Brazil; Show all 5 Subjects
Abstract:
... Recently in this journal, a new trichomycterine from eastern Brazil, Trichomycterus astromycterus, was described and considered possibly related to the Chilean Bullockia maldonadoi due to morphological similarities. Subsequently, osteological data supported T. astromycterus in the subgenus Psammocambeva of Trichomycterus, from eastern Brazil. Phylogenetic analyses, performed here, using a multigen ...
phylogeny, etc ; Rubiaceae; plant biology; population genetics; Show all 4 Subjects
Abstract:
... BACKGROUND: The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes ...
Ebrahim Osdaghi; Geraldine Taghouti; Cecile Dutrieux; S. Mohsen Taghavi; Amal Fazliarab; Martial Briand; Marion Fischer Le Saux; Perrine Portier; Marie-Agnes Jacques
phylogeny, etc ; genome; genomics; pathotypes; taxonomy; virulence; Show all 6 Subjects
Abstract:
... Curtobacterium flaccumfaciens complex species in the family Microbacteriaceae encompasses a group of plant-pathogenic actinobacterial strains affecting annual crops and ornamental plants. The species includes five pathovars, namely C. flaccumfaciens pv. betae, C. flaccumfaciens pv. flaccumfaciens, C. flaccumfaciens pv. ilicis, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. De ...