Polygonum schischkinii is a member of Atraphaxis (Polygonaceae, Polygoneae): evidences from morphological and molecular analyses

Phytotaxa ◽  
2021 ◽  
Vol 491 (3) ◽  
pp. 193-216
Author(s):  
OLGA V. YURTSEVA ◽  
ELENA E. SEVEROVA ◽  
ANDREY G. DEVIATOV ◽  
MARINA V. OLONOVA ◽  
TAHIR H. SAMIGULLIN
Keyword(s):  
Maximum Likelihood ◽  
New Combination ◽  
Nuclear Rdna ◽  
Bayesian Analyses ◽  
Molecular Analyses ◽  
Points Of View ◽  
Combined Data

The Chinese endemic Polygonum schischkinii was studied from both morphological and molecular points of view. On the basis of the structure of ocreas and ocreolas, P. schischkinii appears to be a member of the genus Atraphaxis. The results of Maximum Likelihood and Bayesian analyses of combined data of the plastid [rpl32-trnL(UAG) IGS, trnL(UAA) intron, trnL-trnF IGS] and nuclear rDNA ITS1–2 regions, carried out on 61 members of tribe Polygoneae, confirmed position of P. schischkinii in the Atraphaxis clade. A new combination—Atraphaxis glareosa—based on P. glareosum, which has nomenclatural priority over P. schischkinii, is proposed. Ecological notes and a detailed distributional map of the species are also provided.

Camarosporium sensu stricto in Pleosporinae, Pleosporales with two new species

Phytotaxa ◽  
2014 ◽  
Vol 183 (1) ◽  
pp. 16 ◽  
Author(s):  
NALIN N. WIJAYAWARDENE ◽  
D. JAYARAMA BHAT ◽  
KEVIN D. HYDE ◽  
E. CAMPORESI ◽  
K. W.T. CHETHANA ◽  
...  
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Type Species ◽  
Sensu Stricto ◽  
The Other ◽  
Bayesian Analyses ◽  
Molecular Analyses ◽  
Two New Species ◽  
High Bootstrap

Three coelomycete species with muriform conidia were collected in Italy and subjected to morpho-molecular analyses. In morphology, all species are similar to Camarosporium sensu stricto. Based on morphology, one was identified as C. spartii and the other two taxa are introduced as new species, viz. C. clematidis and C. robiniicola. Maximum likelihood, maximum parsimony and Bayesian analyses of the combined LSU, SSU and ITS dataset show that the three taxa cluster with C. quaternatum, the type species of Camarosporium, with high bootstrap and PP values. All four species can be considered as Camarosporium sensu stricto. Cucurbitaria elongata groups in the Camarosporium clade near to Camarosporium robiniicola and is considered that it is not congeneric with Cucurbitaria sensu stricto (Cucurbitariaceae).

A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

Phytotaxa ◽  
2021 ◽  
Vol 484 (1) ◽  
pp. 44-74
Author(s):  
OLGA V. YURTSEVA ◽  
N.K. BADMAEVA ◽  
EVGENY V. MAVRODIEV
Keyword(s):  
Maximum Likelihood ◽  
Nucleotide Substitution ◽  
Single Nucleotide Substitution ◽  
Sem Images ◽  
Single Nucleotide ◽  
Bayesian Analyses ◽  
Dune Sands ◽  
F Region ◽  
Specific Morphology ◽  
Length Width

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) / 55 tips of Atraphaxis revealed a subclade of two endemics from Transbaikalia (Dahuria) which are often mistaken for A. pungens and A. frutescens but phylogenetically distant from both. Atraphaxis selengensis is a species new to science which inhabits dune sands along the Selenga and Chikoy rivers and has specific morphology of perianth, fruits, ochreas, leaf blades, and pollen. Atraphaxis davurica inhabits stony mountain steppe in Buryatia and Chita region and differs from A. pungens and A. frutescens by longer ochreas, fruits, styles and stigmas extended to ends. Two varieties recognized by Ledebour in plants from Russian Transbaikalia have no clear morphological and molecular distinctions, but the plants from Khentei-Chikoy Highlands subtly differ in leaf ratio (length/width), bark colour, and a single-nucleotide substitution in trnL–F region. These plants are described as A. davurica var. chikoensis var. nov. Morphological descriptions of A. selengensis and A. davurica are supplied with LM and SEM images and a distributional map. Atraphaxis frutescens and A. pungens are absent from Russian Transbaikalia but distributed in Altai, Tuva, Khakassia, Mongolia and China.

A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes

Zootaxa ◽  
2011 ◽  
Vol 2966 (1) ◽  
pp. 37 ◽  
Author(s):  
MILLICENT D. SANCIANGCO ◽  
LUIZ A. ROCHA ◽  
KENT E. CARPENTER
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Strong Support ◽  
Morphological Characters ◽  
Cyt B ◽  
Bayesian Analyses ◽  
Mitochondrial Coi ◽  
Outgroup Species ◽  
Molecular Studies ◽  
Upper Jaw

We infer a phylogeny of haemulid genera using mitochondrial COI and Cyt b genes and nuclear RAG1, SH3PX3, and Plagl2 genes from 56 haemulid species representing 18 genera of the expanded haemulids (including the former inermiids) and ten outgroup species. Results from maximum parsimony, maximum likelihood, and Bayesian analyses show strong support for a monophyletic Haemulidae with the inclusion of Emmelichthyops atlanticus. The former inermiids did not form a clade indicating that the highly protrusible upper jaw specialization to planktivory evolved more than once within Haemulidae. The subfamilies Haemulinae and Plectorhinchinae, currently diagnosed by eight morphological characters, most notably the number of chin pores and the origin of the retractor dorsalis, are also recovered from these analyses with the Haemulinae sister to the Plectorhinchinae. Plectorhinchus is monophyletic only with the inclusion of Diagramma. Within the Haemulinae, Pomadasys and Conodon are polyphyletic. In addition, Anisotremus is monophyletic only with the inclusion of Genyatremus and Conodon nobilis, and Haemulon is monophyletic only with the inclusion of Xenistius. These results suggest that further morphological and molecular studies are needed to revise the limits of several haemulid genera.

Taxonomic delimitation of the genera Bryoria and Sulcaria, with a new combination Sulcaria spiralifera introduced

2014 ◽  
Vol 46 (6) ◽  
pp. 737-752 ◽  
Author(s):  
Leena MYLLYS ◽  
Saara VELMALA ◽  
Hanna LINDGREN ◽  
Doug GLAVICH ◽  
Tom CARLBERG ◽  
...  
Keyword(s):  
Sequence Data ◽  
New Combination ◽  
Phylogenetic Position ◽  
Bayesian Analyses ◽  
Generic Delimitation

AbstractBryoria pseudocapillaris and B. spiralifera are currently treated as members of Bryoria section Implexae although conspicuous, long and depressed pseudocyphellae characterizing both species resemble those found in the genus Sulcaria. Both genera belong in Parmeliaceae and form an alectorioid group together with Alectoria, Gowardia and Pseudephebe. Parsimony and Bayesian analyses of ITS, partial GAPDH and partial Mcm7 sequence data were used to examine the phylogenetic position of B. pseudocapillaris and B. spiralifera, and in light of these results evaluate the generic delimitation of Bryoria and Sulcaria. A total of 110 specimens of 53 species containing representatives from alectorioid and closely related genera were included in the analyses. The results clearly show first, that both B. pseudocapillaris and B. spiralifera belong in Sulcaria rather than in Bryoria, and second, that they should be considered conspecific. Bryoria pseudocapillaris is proposed as a synonym under B. spiralifera and the name Sulcaria spiralifera comb. nov. is introduced.

Recent Methods for the Study of Measurement Invariance With Many Groups

2017 ◽  
Vol 47 (4) ◽  
pp. 637-664 ◽  
Author(s):  
Bengt Muthén ◽  
Tihomir Asparouhov
Keyword(s):  
Monte Carlo ◽  
Maximum Likelihood ◽  
Item Response Theory ◽  
Item Response ◽  
Alignment Method ◽  
Random Loading ◽  
Bayesian Analyses ◽  
Factor Analytic ◽  
Random Intercept ◽  
Level Method

This article reviews and compares recently proposed factor analytic and item response theory approaches to the study of invariance across groups. Two methods are described and contrasted. The alignment method considers the groups as a fixed mode of variation, while the random-intercept, random-loading two-level method considers the groups as a random mode of variation. Both maximum likelihood and Bayesian analyses are applied. A survey of close to 50,000 subjects in 26 countries is used as an illustration. In addition, the two methods are studied by Monte Carlo simulations. A list of considerations for choosing between the two methods is presented.

Iris tibetica, a new combination in I. ser. Lacteae (Iridaceae) from China: evidence from morphological and chloroplast DNA analyses

Phytotaxa ◽  
2018 ◽  
Vol 338 (3) ◽  
pp. 223 ◽  
Author(s):  
EUGENY V. BOLTENKOV ◽  
ELENA V. ARTYUKOVA ◽  
MARINA M. KOZYRENKO ◽  
ANNA TRIAS-BLASI
Keyword(s):  
Species Composition ◽  
Chloroplast Dna ◽  
Morphological Characters ◽  
Distribution Range ◽  
New Combination ◽  
Molecular Analyses ◽  
Qualitative And Quantitative ◽  
Dna Analyses ◽  
Short Beak ◽  
Obtuse Apex

Historically, the species composition of Iris ser. Lacteae has been controversial. Morphological and molecular analyses have been conducted here including specimens covering most of their distribution range. The results suggest I. ser. Lacteae includes three species: the well-known I. lactea and I. oxypetala, plus a newly defined taxon which is endemic to the Gansu and Qinghai provinces, China. We here propose it as a new combination at the species rank, I. tibetica. Morphologically, this species is close to I. lactea but differs by its horizontal, creeping rhizome, scapes with no more than two flowers, its bracts reach the middle of the first flower, its broader inner perianth segments, its obovate with obtuse apex outer perianth segments, and its fruit apex always abruptly narrowed to a very short beak. The most useful qualitative and quantitative morphological characters used to distinguish this species are highlighted. Additionally, all three names are here typified, and a neotype for the name I. lactea and a lectotype for the name I. tibetica are designated. Notes on distribution and habitat are provided for all the accepted species.

Palicella lueckingii (Lecanorales, Ascomycota), a new lichen species inhabiting Araucaria from the extratropical South America

Phytotaxa ◽  
2018 ◽  
Vol 344 (1) ◽  
pp. 24 ◽  
Author(s):  
PAMELA RODRIGUEZ-FLAKUS
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
South America ◽  
Gene Locus ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Bayesian Analyses ◽  
Morphological Studies ◽  
Molecular Phylogenetic ◽  
Araucaria Araucana

Palicella lueckingii is a newly described corticolous lecideoid lichen from the Malalcahuelo National Reserve growing on the bark of Araucaria araucana in Chile. Detailed morphological studies and inference from molecular phylogenetic analyses, based on maximum likelihood and Bayesian analyses of single gene locus (ITS), clearly indicate that the new species is a member of the recently introduced genus Palicella. Palicella lueckingii is most closely related to P. glaucopa, but clearly differs in having smaller ascospores, comparatively thicker thallus, epruinose apothecia, lack of oil droplets inside of exciple and presence of thiophanic acid as a major metabolite.

Taxonomy and phylogeny of Chara (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2017 ◽  
Vol 302 (2) ◽  
pp. 101 ◽  
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Molecular Markers ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
American Studies ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
South American ◽  
Bayesian Analyses ◽  
Sem Analyses

South American studies on the genus Chara are relatively scarce, most consisting of floristic surveys and using only traditional morphological characters. This study is a first approach to the systematics of the genus Chara applying modern techniques (DNA sequences and oospore SEM analyses) in addition to the alpha-taxonomy investigations that have been conducted in Brazil. Twelve populations of Chara were analyzed from the midwest and southeast regions of Brazil. Sequences of three molecular markers were applied to infer phylogenies. The ultrastructure of the oospore wall and currently used morphological characters were analyzed for Chara populations. Maximum likelihood and Bayesian analyses of sequences of rbcL, ITS2, and matK were congruent in that they grouped the species in six clades, each representing one species: Chara braunii C.C. Gmelin, C. foliolosa C.L.Willdenow, C. guairensis R.Bicudo, C. haitensis M.P.J.F. Turpin, C. hydropitys H. Reichenbach and C. rusbyana M. Howe. Morphological characters, including ultrastructure of oospore wall, provided good evidences to characterize each species. Molecular data supported the recent view that some traditional infra-generic taxa (e.g. subgenus Charopsis and subsection Willdenowia) are not supported in phylogenetic analyses, whereas some species (e.g. C. foliolosa, C. haitensis, C. hydropitys and C. rusbyana previously considered as varieties and forms of C. zeylanica) were consistently distinguished in the analyses for the three molecular markers.

scholarly journals Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders

2019 ◽  
Author(s):  
Kirill V. Mikhailov ◽  
Viatcheslav N. Ivanenko
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Statistical Test ◽  
Original Study ◽  
Molecular Phylogenetic Analysis ◽  
Approximately Unbiased ◽  
Bayesian Analyses ◽  
Molecular Phylogenetic ◽  
Key Nodes

AbstractReanalysis of the dataset used by Khodami et al. (2017) reveals low support values for the key nodes of the copepod (Crustacea) phylogeny and fails to reproduce the results obtained in the study. Maximum likelihood (ML) and Bayesian analyses with the dataset produce phylogenies that are inconsistent with the branching of copepod groups proposed by Khodami et al. (2017). The proposed phylogeny is refuted by the approximately unbiased (AU) statistical test, which undermines several conclusions drawn from the original study.

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