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You searched for: Subject "phylogeny" Remove constraint Subject: "phylogeny"
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1. Auxin’s origin: do PILS hold the key?

Author:
Kenny Arthur Bogaert; Jonas Blomme; Tom Beeckman; Olivier De Clerck
Source:
Trends in plant science 2022 v.27 no.3 pp. 227-236
ISSN:
1360-1385
Subject:
phylogeny,   etc   ; algae; auxins;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.tplants.2021.09.008

2. Morpho-molecular characterization of Brunneofissuraceae fam. nov., Cirsosia mangiferae sp. nov., and Asterina neomangiferae nom. nov

Author:
Diana S. Marasinghe; Sinang Hongsanan; Dhanushka N. Wanasinghe; Saranyaphat Boonmee; Saisamorn Lumyong; Kevin D. Hyde; Xie Ning
Source:
Mycological progress 2022 v.21 no.1 pp. 279-295
ISSN:
1617-416X
Subject:
phylogeny,   etc   ; fungi; Thailand;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1007/s11557-021-01767-9

3. SHOOT: phylogenetic gene search and ortholog inference

Author:
David Mark Emms; Steven Kelly
Source:
Genome biology 2022 v.23 no.1 pp. 85
ISSN:
1474-760X
Subject:
phylogeny,   etc   ; databases; genes;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1186/s13059-022-02652-8

4. Inherent conflicts between reaction norm slope and plasticity indices when comparing plasticity: a conceptual framework and empirical test

Author:
Shuo Wang; Wei-Wei Feng; Ming-Chao Liu; Kai Huang; Pieter A. Arnold; Adrienne B. Nicotra; Yu-Long Feng
Source:
Oecologia 2022 v.198 no.3 pp. 593-603
ISSN:
0029-8549
Subject:
phylogeny,   etc   ; cultivars; phenotypic plasticity;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1007/s00442-022-05122-x

5. Phylogenetic definitions for 25 higher-level clade names of birds

Author:
George Sangster; Edward L. Braun; Ulf S. Johansson; Rebecca T. Kimball; Gerald Mayr; Alexander Suh
Source:
Avian research 2022 v.13 pp. 100027
ISSN:
2053-7166
Subject:
phylogeny,   etc   ; birds; genomics; research;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1016/j.avrs.2022.100027

6. Revisiting Phyllactinia species on Broussonetia spp. in China

Author:
Shu‐Rong Tang; Shu‐Yan Liu; Jing Feng; Guan‐Xiu Guan; Xin‐Qiang Liu; Ren‐Jing Jiang; Li Liu; Dan‐Ni Jin; Zhao‐Yang Zhang; Xi‐Yu Wang
Source:
Forest pathology 2022 v.52 no.1 pp. e12727
ISSN:
1437-4781
Subject:
phylogeny,   etc   ; Phyllactinia; forests; China;     Show all 4 Subjects
Abstract:
... 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 ...
DOI:
10.1111/efp.12727

7. An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis

Author:
Denis Jacob Machado; Fernando Portella de Luna Marques; Larry Jiménez‐Ferbans; Taran Grant
Source:
Cladistics 2022 v.38 no.3 pp. 392-401
ISSN:
0748-3007
Subject:
phylogeny,   etc   ; data collection; statistical analysis;     Show all 3 Subjects
Abstract:
... 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 ...
DOI:
10.1111/cla.12496

8. FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Author:
Carl R. Hutter; Kerry A. Cobb; Daniel M. Portik; Scott L. Travers; Perry L. Wood Jr.; Rafe M. Brown
Source:
Molecular ecology resources 2022 v.22 no.3 pp. 1100-1119
ISSN:
1755-098X
Subject:
phylogeny,   etc   ; ecology; exons; genomics; introns;     Show all 5 Subjects
Abstract:
... 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, ...
DOI:
10.1111/1755-0998.13517

9. Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida)

Author:
Ekin Tilic; Josefin Stiller; Ernesto Campos; Fredrik Pleijel; Greg W. Rouse
Source:
Molecular phylogenetics and evolution 2022 v.166 pp. 107339
ISSN:
1055-7903
Subject:
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 ...
DOI:
10.1016/j.ympev.2021.107339

10. RiboGrove: a database of full-length prokaryotic 16S rRNA genes derived from completely assembled genomes

Author:
Maxim A. Sikolenko; Leonid N. Valentovich
Source:
Research in microbiology 2022 v.173 no.4-5 pp. 103936
ISSN:
0923-2508
Subject:
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 ...
DOI:
10.1016/j.resmic.2022.103936

11. Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach

Author:
Chunqi Jiang; Mami Tanaka; Sayo Nishikawa; Sayaka Mino; Jesús L. Romalde; Fabiano L. Thompson; Bruno Gomez-Gil; Tomoo Sawabe
Source:
Current microbiology 2022 v.79 no.1 pp. 10
ISSN:
0343-8651
Subject:
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 ...
DOI:
10.1007/s00284-021-02725-0

12. A new monoraphid diatom species from the genus Karayevia sensu lato (Bacillariophyceae: Stauroneidaceae) with remarks on taxonomy and phylogeny of the genus

Author:
Natalia Tseplik; Anton Glushchenko; Yevhen Maltsev; Irina Kuznetsova; Sergei Genkal; John Patrick Kociolek; Maxim Kulikovskiy
Source:
Diatom research 2022 v.37 no.1 pp. 39-50
ISSN:
2159-8347
Subject:
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 ...
DOI:
10.1080/0269249X.2022.2039780

13. Exceptional evolutionary lability of flower‐like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae

Author:
Jakub Baczyński; Hervé Sauquet; Krzysztof Spalik
Source:
American journal of botany 2022 v.109 no.3 pp. 437-455
ISSN:
0002-9122
Subject:
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 ...
DOI:
10.1002/ajb2.1819

14. Exclusion of fast evolving genes or fast evolving sites produces different archaean phylogenies

Author:
A.A. Superson; F.U. Battistuzzi
Source:
Molecular phylogenetics and evolution 2022 v.170 pp. 107438
ISSN:
1055-7903
Subject:
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 ...
DOI:
10.1016/j.ympev.2022.107438

15. Maturyoshka: A maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes

Author:
Kacper Maciszewski; Nadja Dabbagh; Angelika Preisfeld; Anna Karnkowska
Source:
Molecular phylogenetics and evolution 2022 v.170 pp. 107441
ISSN:
1055-7903
Subject:
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 ...
DOI:
10.1016/j.ympev.2022.107441

16. Micropearls and other intracellular inclusions of amorphous calcium carbonate: an unsuspected biomineralization capacity shared by diverse microorganisms

Author:
Inés Segovia‐Campos; Agathe Martignier; Montserrat Filella; Jean‐Michel Jaquet; Daniel Ariztegui
Source:
Environmental microbiology 2022 v.24 no.2 pp. 537-550
ISSN:
1462-2912
Subject:
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 ...
DOI:
10.1111/1462-2920.15498

17. New CTX-M Group Conferring β-Lactam Resistance: A Compendium of Phylogenetic Insights from Biochemical, Molecular, and Structural Biology

Author:
Jacinta Mendonça; Carla Guedes; Carina Silva; Sara Sá; Marco Oliveira; Gustavo Accioly; Pilar Baylina; Pedro Barata; Cláudia Pereira; Ruben Fernandes
Source:
Biology 2022 v.11 no.2 pp. -
ISSN:
2079-7737
Subject:
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 ...
DOI:
10.3390/biology11020256

18. Phylogenetic position of Trichomycterus astromycterus (Siluriformes: Trichomycteridae), an enigmatic trichomycterid from eastern Brazil, inferred from molecular data

Author:
Paulo J. Vilardo; Axel M. Katz; Wilson J. E. M. Costa
Source:
Journal of fish biology 2022 v.100 no.4 pp. 1093-1096
ISSN:
0022-1112
Subject:
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 ...
DOI:
10.1111/jfb.15015

19. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution

Author:
Sara Getachew Amenu; Neng Wei; Lei Wu; Oyetola Oyebanji; Guangwan Hu; Yadong Zhou; Qingfeng Wang
Source:
BMC plant biology 2022 v.22 no.1 pp. 88
ISSN:
1471-2229
Subject:
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 ...
DOI:
10.1186/s12870-022-03480-5

20. Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae

Author:
Ebrahim Osdaghi; Geraldine Taghouti; Cecile Dutrieux; S. Mohsen Taghavi; Amal Fazliarab; Martial Briand; Marion Fischer Le Saux; Perrine Portier; Marie-Agnes Jacques
Source:
Molecular plant-microbe interactions 2022 v.35 no.4 pp. 352-356
ISSN:
1943-7706
Subject:
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 ...
DOI:
10.1094/MPMI-11-21-0282-A