scholarly journals Systematic implications from a robust phylogenetic reconstruction of the genus Helianthemum (Cistaceae) based on genotyping-by-sequencing (GBS) data

2021 ◽  
Vol 78 (2) ◽  
pp. e113
Author(s):  
Sara Martín-Hernanz ◽  
Mauricio Velayos ◽  
Rafael G. Albaladejo ◽  
Abelardo Aparicio
Keyword(s):  
Maximum Likelihood ◽  
Molecular Systematics ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Genotyping By Sequencing ◽  
New Combinations ◽  
Bayesian Analyses ◽  
Taxonomic Sampling ◽  
New Subgenus ◽  
Phylogenetic Framework

Molecular systematics requires the establishment of a robust phylogenetic framework including extensive geographical and taxonomic sampling. In this work, we proposed systematic changes in the genus Helianthemum based on phylogenetic trees obtained by both maximum likelihood and Bayesian analyses of GBS data. The implications of these phylogenetic results for the systematics of Helianthemum entail the establishment of a new subgenus and novel re-ascriptions of sections and species along with some nomenclatural novelties. The following new combinations are proposed: Helianthemum subg. Eriocarpum (Dunal) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. oelandicum subsp. conquense (Borja & Rivas Goday ex G.López) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. cantabricum (M.Laínz) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. tinetense (M.Mayor & Fern.Benito) Martín-Hernanz, Velayos, Albaladejo & Aparicio.

Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA

Zootaxa ◽  
2010 ◽  
Vol 2603 (1) ◽  
pp. 53 ◽  
Author(s):  
R. TERRY CHESSER ◽  
CAROL K. L. YEUNG ◽  
CHENG-TE YAO ◽  
XIU-HUA TIAN ◽  
SHOU-HSIEN LI
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Bayesian Analyses ◽  
Limited Sampling

Spoonbills (genus Platalea) are a small group of wading birds, generally considered to constitute the subfamily Plataleinae (Aves: Threskiornithidae). We reconstructed phylogenetic relationships among the six species of spoonbills using variation in sequences of the mitochondrial genes ND2 and cytochrome b (total 1796 bp). Topologies of phylogenetic trees reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses were virtually identical and supported monophyly of the spoonbills. Most relationships within Platalea received strong support: P. minor and P. regia were closely related sister species, P. leucorodia was sister to the minor-regia clade, and P. alba was sister to the minor-regia-leucorodia clade. Relationships of P. flavipes and P. ajaja were less well resolved: these species either formed a clade that was sister to the four-species clade, or were successive sisters to this clade. This phylogeny is consistent with ideas of relatedness derived from spoonbill morphology. Our limited sampling of the Threskiornithinae (ibises), the putative sister group to the spoonbills, indicated that this group is paraphyletic, in agreement with previous molecular data; this suggests that separation of the Threskiornithidae into subfamilies Plataleinae and Threskiornithinae may not be warranted.

A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: I. Atraphaxis kamelinii spec. nov. from Mongolia

Phytotaxa ◽  
2016 ◽  
Vol 268 (1) ◽  
pp. 1
Author(s):  
OLGA V. YURTSEVA ◽  
OXANA I. KUZNETSOVA ◽  
EVGENY V. MAVRODIEV
Keyword(s):  
Maximum Likelihood ◽  
New Taxa ◽  
Endemic Species ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
The Novel ◽  
Bayesian Analyses

Maximum Likelihood (ML) and Bayesian analyses (BI) applied for 3-plastid loci (cpDNA trnL(UAA) intron, trnL–trnF IGS, and rpl32–trnL(UAG) IGS regions) / 65 tips matrix resulted in preliminary phylogenetic reconstruction of the genus Atraphaxis. In combination with the morphological data the obtained phylogeny appears sufficient for recognition of challenging taxonomic entities. We found that a collection of Atraphaxis from the Dzungarian Gobi, which appears to be phylogenetically related to A. pungens, is morphologically different from the latter by the predominantly dimerous perianth and gynoecium, shorter outer perianth segments, and the absence of the spiny shoots. It also differs from all other species of Atraphaxis that occur in Mongolia and neighboring countries. As a result, we described the novel endemic species Atraphaxis kamelinii O.V.Yurtseva sp. nov. More investigations are necessary to fully understand the origin of the newly described species.

scholarly journals Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l.

2021 ◽  
Author(s):  
Tijana Cvetković ◽  
Fabiola Areces-Berazain ◽  
Damien D Hinsinger ◽  
Daniel C Thomas ◽  
Jan J Wieringa ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Economic Importance ◽  
Plant Family ◽  
Bayesian Analyses ◽  
Plastid Genomes ◽  
Great Economic Importance ◽  
The Family ◽  
Evolutionary Studies ◽  
Phylogenetic Framework

Abstract Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Despite numerous phylogenetic analyses employing multiple markers, relationships between several of its nine subfamilies, particularly within the largest lineage/Malvadendrina, remain unclear. In this study, we attempted to resolve the relationships within the major clades of Malvaceae s.l. using plastid genomes of 48 accessions representing all subfamilies. Maximum likelihood and Bayesian analyses recovered a fully resolved and well-supported topology confirming the split of the family into/Byttneriina (/Grewioideae +/Byttnerioideae) and/Malvadendrina. Within/Malvadendrina,/Helicteroideae occupied the earliest branching position, followed by/Sterculioideae./Brownlowioideae,/Tiliodeae, and/Dombeyoideae formed a clade sister to/Malvatheca (/Malvoideae +/Bombacoideae), a grouping morphologically supported by the lack of androgynophore. Results from dating analyses suggest that all subfamilies originated during hot or warm phases in the Late Cretaceous to Paleocene. This study presents a well-supported phylogenetic framework for Malvaceae s.l. that will aid downstream revisions and evolutionary studies of this economically important plant family.

Species of Agaricus section Agaricus from China

Phytotaxa ◽  
2020 ◽  
Vol 452 (1) ◽  
pp. 1-18
Author(s):  
AN-QI LIU ◽  
RONG-CHUN DAI ◽  
MING-ZHE ZHANG ◽  
BIN CAO ◽  
YA-LI XI ◽  
...  
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Its Sequences ◽  
Monophyletic Group ◽  
Morphological Examination ◽  
Bayesian Analyses ◽  
Two New Species

Agaricus section Agaricus is generally recognized as a monophyletic group. In this study, 28 specimens of this section were collected from five provinces of China. Phylogenetic trees were produced based on the ITS sequences using Maximum Likelihood and Bayesian analyses. Based on this phylogenetic approach combined with their morphological examination, five species are identified including two new species named as A. jilinensis and A. zhangyensis, and three new recorded species from China, A. aristocratus, A. griseicephalus and A. argenteus. All species were described and illustrated in detail.

scholarly journals The holomorph of Parasarcopodium (Stachybotryaceae), introducing P. pandanicola sp. nov. on Pandanus sp.

Phytotaxa ◽  
2016 ◽  
Vol 266 (4) ◽  
pp. 250 ◽  
Author(s):  
SAOWALUCK TIBPROMMA ◽  
SARANYAPHAT BOONMEE ◽  
NALIN N. WIJAYAWARDENE ◽  
SAJEEWA S.N. MAHARACHCHIKUMBURA ◽  
ERIC H. C. MCKENZIE ◽  
...  
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Bayesian Analyses ◽  
Sexual Morph ◽  
Distinct Morphology ◽  
Asexual Morphs ◽  
A New Species

Collections of microfungi on Pandanus species (Pandanaceae) in Krabi, Thailand resulted in the discovery of a new species in the genus Parasarcopodium, producing both its sexual and asexual morphs. In this paper, we introduce P. pandanicola sp. nov., with an illustrated account. Evidence for the new species is provided by distinct morphology and phylogenetic analyses. This is also the first report of the sexual morph of Parasarcopodium. The phylogenetic trees used Maximum Likelihood and Bayesian analyses of combined LSU, SSU, TEF1 and RPB2 sequence data to show the placement of the new species in Stachybotryaceae.

The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Second Generation ◽  
Emergency Situation ◽  
The World ◽  
Break Points ◽  
Sex With Men ◽  
Full Length Genome ◽  
Virus Strains ◽  
Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

scholarly journals Evolutionary relationships of completely sequenced Clostridia species and close relatives

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4276-4283 ◽  
Author(s):  
Takashi Kunisawa
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Gene Arrangement ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Sequence Information ◽  
Bayesian Tree ◽  
Maximum Likelihood Methods ◽  
Genome Sequence Information ◽  
Close Relatives

The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.

scholarly journals GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

2019 ◽  
Author(s):  
Benoit Morel ◽  
Alexey M. Kozlov ◽  
Alexandros Stamatakis ◽  
Gergely J. Szöllősi
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Simulated Data ◽  
Gene Families ◽  
Species Tree ◽  
Homologous Gene ◽  
Sequence Alignments ◽  
Full Likelihood ◽  
True Tree

AbstractInferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges species tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data pre-processing (e.g., computing bootstrap trees), and rely on approximations and heuristics that limit the degree of tree space exploration. Here we present GeneRax, the first maximum likelihood species tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared to competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson-Foulds distance. On empirical datasets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1099 Cyanobacteria families in eight minutes on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax.

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