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

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.

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Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

Australian Journal of Botany ◽

10.1071/bt14159 ◽

2014 ◽

Vol 62 (8) ◽

pp. 638 ◽

Cited By ~ 2

Author(s):

Farrokh Ghahremaninejad ◽

Mehrshid Riahi ◽

Melina Babaei ◽

Faride Attar ◽

Lütfi Behçet ◽

...

Keyword(s):

Molecular Markers ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Nrdna Its ◽

Starting Point ◽

High Species Diversity ◽

Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

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The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

Insect Systematics & Evolution ◽

10.1163/1876312x-45032119 ◽

2015 ◽

Vol 46 (3) ◽

pp. 269-290 ◽

Cited By ~ 6

Author(s):

Ian J. Kitching ◽

C. Lorna Culverwell ◽

Ralph E. Harbach

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Data Set ◽

Generic Status ◽

Strong Signal ◽

Phylogenetic Studies ◽

Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

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

Phytotaxa ◽

10.11646/phytotaxa.356.3.1 ◽

2018 ◽

Vol 356 (3) ◽

pp. 181

Author(s):

FABIO RENATO BORGES ◽

ORLANDO NECCHI JR

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Molecular Evidence ◽

Type Specimens ◽

Brazilian Studies ◽

Two Populations ◽

Section Level

The genus Nitella is the most species-rich within the Charales. Brazilian studies on the genus are relatively scarce and consist of floristic surveys, lacking modern and more precise information. This investigation applied scanning electron microscopy to analyze the oospore wall and molecular data associated with traditional morphological characters to analyze forty-two populations of Nitella from the midwest and southeast regions of Brazil. Forty-two new sequences of rbcL, twelve of ITS1 and twenty-three of ITS2 were generated for the five species recognized in this study: Nitella acuminata A. Braun ex Wallman, Nitella axillaris A. Braun, Nitella elegans B. P. Pal, Nitella flagellifera J. Groves & G. O. Allen and Nitella microcarpa A. Braun.. Phylogenetic analyses of sequences of these three markers were congruent in that they grouped our species with others from different countries to form five clades. Our results on ultrastrucure of the oospore wall were consistent with previous studies for the same species from other regions of the world. The data reinforced the conclusion that the use of ornamentation of oospore wall may be extremely useful for the construction of a natural system for Characeae at section level. Molecular evidence, reinforced by morphological data, for the Brazilian material analyzed suggests that Nitella subglomerata A. Braun and Nitella gollmeriana A. Braun could be synonymys of Nitella acuminata; and Nitella axilliformis K. Imahori appears to be the same as Nitella axillaris. However, no formal proposition was made considering that type specimens were not analyzed and these observations were based on a relatively small number of samples strictly from Brazil. We showed that even among geographically distant populations, such as from other continents, of some Nitella species, the degree of identity among DNA sequences was high.

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Nectria-related fungi causing dieback and canker diseases in China, with Neothyronectria citri sp. nov. described

MycoKeys ◽

10.3897/mycokeys.56.36079 ◽

2019 ◽

Vol 56 ◽

pp. 49-66

Author(s):

Qin Yang ◽

Wen-Yan Chen ◽

Ning Jiang ◽

Cheng-Ming Tian

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Bright Yellow

To clarify phylogenetic relationships amongst Nectria, Neothyronectria and Thyronectria in Nectriaceae, we examined detailed morphological characters and performed phylogenetic analyses of a concatenated dataset, based on the ITS, LSU, tef1 and tub2 DNA sequences of fungal specimens in China. Four species of nectria-related fungi were identified, i.e. Nectriadematiosa, N.pseudotrichia, Neothyronectriacitri and Thyronectriapinicola. The newly described species, Neothyronectriacitri, is characterised by its ascomatal wall with bright yellow scurf, unitunicate asci, each with 4-spored and ascospores allantoid to short-cylindrical, uniseriate, muriform, hyaline to slightly yellowish-brown. This species has affinities with other one known species of Neothyronectria and can be distinguished by molecular data.

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Morphological and phylogenetic evidence for two new species of Russula subg. Heterophyllidia from Guangdong Province of China

MycoKeys ◽

10.3897/mycokeys.82.64913 ◽

2021 ◽

Vol 82 ◽

pp. 139-157

Author(s):

Bin Chen ◽

Jie Song ◽

Yanliu Chen ◽

Jinhua Zhang ◽

Junfeng Liang

Keyword(s):

New Species ◽

Maximum Likelihood ◽

Molecular Phylogeny ◽

Phylogenetic Analyses ◽

Guangdong Province ◽

Morphological Characters ◽

Molecular Data ◽

Terminal Cell ◽

Two New Species ◽

Long Chains

Two new species of Russula subg. Heterophyllidia from Guangdong Province of China were described and illustrated based on morphological characters, and their identity supported by molecular phylogeny. R. luofuensis is morphologically characterized by a grayish yellow to brownish orange pileus center with a purplish gray to grayish magenta margin, a surface that is cracked and broken into small golden-brown patches, subglobose to broadly ellipsoid basidiospores with warts fused in short or long chains and a suprapellis composed of hyphal extremities with inflated, ellipsoid or globose cells and attenuated terminal cell. R. subbubalina is distinguished by the blanched almond to dark salmon pileus that is cracked with age, subglobose to broadly ellipsoid basidiospores with wart fused in short or long chains and frequently connected by line connections, a suprapellis with hyphal ends composed of inflated or ellipsoid cells and attenuated terminal cell, and pileocystidia that are mainly clavate and sometimes with round or ellipsoid appendage. The phylogenetic analyses based on ITS-nrLSU-mtSSU-TEF1 dataset were performed using maximum likelihood and Bayesian analysis. In terms of morphological features and molecular data, the former species belongs to subsect. Virescentinae, whereas the latter comes under subsect. Heterophyllinae.

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Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological characters

Antarctic Science ◽

10.1017/s0954102010000477 ◽

2010 ◽

Vol 22 (6) ◽

pp. 727-741 ◽

Cited By ~ 29

Author(s):

Ulrike Ruprecht ◽

H. Thorsten Lumbsch ◽

Georg Brunauer ◽

T.G. Allan Green ◽

Roman Türk

Keyword(s):

Ross Sea ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Secondary Chemistry ◽

Bayesian Analyses ◽

Test Species ◽

Rdna Sequences ◽

Continental Antarctica ◽

Nuclear Its

AbstractThe diversity of lichens, especially crustose species, in continental Antarctica is still poorly known. To overcome difficulties with the morphology based species delimitations in these groups, we employed molecular data (nuclear ITS and mitochondrial SSU rDNA sequences) to test species boundaries within the genus Lecidea. Sampling was done along a north–south transect at five different areas in the Ross Sea region (Cape Hallett, Botany Bay to Mount Suess, Taylor Valley, Darwin Area and Mount Kyffin). A total of 153 specimens were collected from 13 localities. Phylogenetic analyses also include specimens from other regions in Antarctica and non-Antarctic areas. Maximum parsimony, maximum likelihood and Bayesian analyses agreed in placing the samples from continental Antarctica into four major groups. Based on this phylogenetic estimate, we restudied the micromorphology and secondary chemistry of these four clades to evaluate the use of these characters as phylogenetic discriminators. These clades are identified as the following species Lecidea cancriformis, L. andersonii as well as the new species L. polypycnidophora Ruprecht & Türk sp. nov. and another previously unnamed clade of uncertain status, referred to as Lecidea sp. (L. UCR1).

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Phylogenetic studies in the South American tribe Dichroplini (Orthoptera: Acrididae: Melanoplinae): is the Paranaense-Pampeano informal genus group a natural clade?

Zootaxa ◽

10.11646/zootaxa.2174.1.6 ◽

2009 ◽

Vol 2174 (1) ◽

pp. 51-62 ◽

Cited By ~ 4

Author(s):

P. A. DINGHI ◽

V. CONFALONIERI ◽

M. M. CIGLIANO

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Morphological Characters ◽

Molecular Data ◽

South American ◽

Male And Female ◽

Weak Support ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Group A

The Dichroplini genera Scotussa, Leiotettix, Ronderosia, Atrachelacris, Chlorus, Eurotettix and Dichromatos have been grouped into the “Paranaense-Pampeano” informal genus group, based on characters of the male genitalia. However, recent molecular phylogenetic analyses showed weak support values or no support at all for this group. In this study, we used molecular and morphological characters to test the monophyly of this informal genus group. Morphological characters included aspects of the general morphology, and male and female genitalia as well. Whereas the molecular data was based on one mitochondrial gene: cytochrome oxidase I. Independent and combined phylogenetic analyses of the data were performed under both unweighted and implied weighting parsimony. Our results showed that, when only molecular data is considered, the “Paranaense-Pampeano” informal genus group is not recovered. However, the group is monophyletic according to morphological and combined analyses. The “Paranaense-Pampeano” informal genus group is considered to be a natural clade; therefore, we propose the genus group name Scotussae. As a final remark, the molecular data provided in most cases the same evidence of relationships as morphology.

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Phylogeny of the Erysiphales (powdery mildews) inferred from internal transcribed spacer ribosomal DNA sequences

Canadian Journal of Botany ◽

10.1139/b98-235 ◽

1999 ◽

Vol 77 (1) ◽

pp. 150-168 ◽

Cited By ~ 30

Author(s):

Gregory S Saenz ◽

John W Taylor

Keyword(s):

Dna Sequences ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Powdery Mildews ◽

Outgroup Species ◽

Morphological And Molecular Data ◽

Clade 1

Phylogenetic relationships were inferred for 45 powdery mildews plus two outgroup species from internal transcribed spacer sequence data. Phylogenetic analyses revealed that the powdery mildews formed six evolutionary lineages, which corresponded well to recently revised mitosporic taxa. Clade 1 consisted of Erysiphe, Microsphaera, and Uncinula, all of which have an Oidium subgenus Pseudoidium mitosporic state. Clade 2 consisted of Erysiphe galeopsidis and Erysiphe cumminsiana, which have an Oidium subgenus Striatoidium mitosporic state. Clade 3 consisted of Erysiphe species with an Oidium subgenus Reticuloidium mitosporic state. Clade 4 consisted of Leveillula and Phyllactinia, which have Oidiopsis and Ovulariopsis mitosporic states, respectively. Clade 5 consisted of Sphaerotheca, Podosphaera, and Cystotheca, which have Oidium subgenera Fibroidium and Setoidium mitosporic states. Clade 6 consisted of Blumeria graminis, which has an Oidium subgenus Oidium mitosporic state. Seventeen morphological characters were analysed and found not to conflict with the molecular data, so the morphological and molecular data were combined. The combined data increased the overall support for the six clades.Key words: Ascomycete, Blumeria, Erysiphe, fungi, molecular evolution, plant pathogen.

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Respiratory syncytial virus B sequence analysis reveals a novel early genotype

Scientific Reports ◽

10.1038/s41598-021-83079-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juan C. Muñoz-Escalante ◽

Andreu Comas-García ◽

Sofía Bernal-Silva ◽

Daniel E. Noyola

Keyword(s):

Molecular Markers ◽

Respiratory Syncytial Virus ◽

Maximum Likelihood ◽

Respiratory Infections ◽

Phylogenetic Analyses ◽

Detection Methods ◽

Sequence Alignments ◽

Multiple Sequence ◽

Individual Gene ◽

Syncytial Virus

AbstractRespiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

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Loose Ends in the Cortinarius Phylogeny: Five New Myxotelamonoid Species Indicate a High Diversity of These Ectomycorrhizal Fungi with South American Nothofagaceae

Life ◽

10.3390/life11050420 ◽

2021 ◽

Vol 11 (5) ◽

pp. 420

Author(s):

María Eugenia Salgado Salomón ◽

Carolina Barroetaveña ◽

Tuula Niskanen ◽

Kare Liimatainen ◽

Matthew E. Smith ◽

...

Keyword(s):

New Species ◽

Current Knowledge ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Global Scale ◽

South American ◽

Edible Fungi ◽

Rdna Its ◽

Morphological And Molecular Data ◽

High Diversity

This paper is a contribution to the current knowledge of taxonomy, ecology and distribution of South American Cortinarius (Pers.) Gray. Cortinarius is among the most widely distributed and species-rich basidiomycete genera occurring with South American Nothofagaceae and species are found in many distinct habitats, including shrublands and forests. Due to their ectomycorrhizal role, Cortinarius species are critical for nutrient cycling in forests, especially at higher latitudes. Some species have also been reported as edible fungi with high nutritional quality. Our aim is to unravel the taxonomy of selected Cortinarius belonging to phlegmacioid and myxotelamonioid species based on morphological and molecular data. After widely sampling Cortinarius specimens in Patagonian Nothofagaceae forests and comparing them to reference collections (including holotypes), we propose five new species of Cortinarius in this work. Phylogenetic analyses of concatenated rDNA ITS-LSU and RPB1 sequences failed to place these new species into known Cortinarius sections or lineages. These findings highlight our knowledge gaps regarding the fungal diversity of South American Nothofagaceae forests. Due to the high diversity of endemic Patagonian taxa, it is clear that the South American Cortinarius diversity needs to be discovered and described in order to understand the evolutionary history of Cortinarius on a global scale.

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