The genus Karoowia (Parmeliaceae, Ascomycota) includes unrelated clades nested within Xanthoparmelia

2010 ◽  
Vol 23 (3) ◽  
pp. 173 ◽  
Author(s):  
Guillermo Amo de Paz ◽  
H. Thorsten Lumbsch ◽  
Paloma Cubas ◽  
John A. Elix ◽  
Ana Crespo
Keyword(s):  
Maximum Likelihood ◽  
Bayesian Approach ◽  
Cell Walls ◽  
Growth Form ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
New Combinations ◽  
Hyphal Cell ◽  
Rdna Sequences

Thallus morphology has traditionally played a major role in the classification of lichenised fungi. We have used a combined dataset of nuITS, nuLSU and mtSSU rDNA sequences to evaluate the phylogenetic relationships between the subcrustose genus Karoowia and the mostly foliose genus Xanthoparmelia. Our phylogenetic analyses using maximum parsimony, maximum likelihood and a Bayesian approach show that Karoowia species do not form a monophyletic group but cluster in different clades nested within Xanthoparmelia. The monophyly of Karoowia either as a separate clade from Xanthoparmelia, or nested within Xanthoparmelia is significantly rejected using alternative hypothesis testing. These results suggest that the usefulness of the phenotypic features used to define Karoowia has been overestimated because the subcrustose growth form has evolved independently in several clades within Xanthoparmelia. Other characters used to circumscribe Karoowia, such as the presence of cylindrical conidia, also occur in Xanthoparmelia, and the differences in rhizine morphology are minimal. Consequently, we propose to reduce Karoowia to synonymy with Xanthoparmelia. The enlarged genus is characterised by the presence of Xanthoparmelia-type lichenan in the hyphal cell walls and the presence of an arachiform vacuolar body in the ascospores. Fifteen new combinations in Xanthoparmelia and the new name Xanthoparmelia mucinae for Karoowia squamatica are made.

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae)

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 180-202 ◽  
Author(s):  
Bernard R. Baum ◽  
Tara Edwards ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
Comprehensive Picture ◽  
Host Parasite

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host–parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.

scholarly journals A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)

Phytotaxa ◽  
2014 ◽  
Vol 159 (4) ◽  
pp. 241 ◽  
Author(s):  
Yu-lan Peng ◽  
Yu Zhang ◽  
Xin-fen Gao ◽  
Lin-jing Tong ◽  
Liang Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Chloroplast Dna ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Likelihood Inference ◽  
Nuclear Its ◽  
Chloroplast Dna Regions

The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.

Towards a monophyletic classification of Lejeuneaceae V: the systematic position of Pictolejeunea

Phytotaxa ◽  
2016 ◽  
Vol 280 (3) ◽  
pp. 259 ◽  
Author(s):  
JULIA BECHTELER ◽  
GAIK EE LEE ◽  
ALFONS SCHÄFER-VERWIMP ◽  
MATT A. M. RENNER ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Sister Relationship ◽  
Bayesian Analyses ◽  
Outgroup Species ◽  
Made In

With more than 1,000 species in some 70 genera, Lejeuneaceae represent the largest family of liverworts. Although much progress has been made in recent years, the supraspecific classification of Lejeuneaceae has not yet been satisfactorily solved. Maximum likelihood and Bayesian analyses of a three marker dataset (nrITS, cp DNA rbcL and trnL-trnF) derived from 85 accessions of Lejeuneeae and 13 outgroup species revealed Pictolejeunea picta in a sister relationship to the remainder of Lejeuneeae, the most speciose tribe of Lejeuneaceae. Based on the outcome of the phylogenetic analyses, we establish subtribe Pictolejeuneinae subtr. nov.

Neoalbatrellus odorus sp. nov. (Albatrellaceae, Russulales) from Southwest China

Phytotaxa ◽  
2017 ◽  
Vol 309 (3) ◽  
pp. 217 ◽  
Author(s):  
YUAN-YUAN CHEN ◽  
MIN WANG ◽  
BO ZHANG ◽  
BAO-KAI CUI
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Southwest China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Pore Surface ◽  
Rdna Sequences ◽  
Dark Violet ◽  
28S Rdna Sequences

We describe herein the Neoalbatrellus odorus sp. nov. accounting on its peculiar morphological features and molecular data. It is characterized by fleshy basidiomata with a deep violet to dark violet pileal surface, which turns blackish blue and glossy after drying. It also has a white pore surface, light violet to bluish violet stipe, simple septate generative hyphae, and thick-walled, non-amyloid basidiospores. The phylogenetic analyses, based on ITS and 28S rDNA sequences of Neoalbatrellus and its related genera, were performed using Maximum Parsimony, Maximum Likelihood and Bayesian Inference, confirming the affiliation of the new species to Neoalbatrellus.

Plectania lutea (Sarcosomataceae), a new species from southwestern karst areas of China

Phytotaxa ◽  
2021 ◽  
Vol 509 (3) ◽  
Author(s):  
GUANG-FU MOU ◽  
TOLGOR BAU
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Internal Transcribed Spacer ◽  
External Surface ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
New Taxon ◽  
Rdna Sequences ◽  
Karst Areas ◽  
A New Species

Plectania lutea, is described as a new species from subtropical karst areas of China. The main distinguishing characteristics of P. lutea are the yellow hymenium, the external surface with ridges, the gelatinous but not semifluid medullary excipulum, and the large finely warted ascospores. The phylogenetic analyses based on internal transcribed spacer (ITS) and the large subunit (LSU) regions of rDNA sequences using Bayesian (BA) and Maximum Likelihood (ML) methods showed that the new taxon can be distinguished from phenotypically similar and phylogenetically related species.

A new species, two new combinations and notes on Fomitopsidaceae (Agaricomycetes, Polyporales)

Phytotaxa ◽  
2017 ◽  
Vol 331 (1) ◽  
pp. 75 ◽  
Author(s):  
ADRIENE MAYRA SOARES ◽  
GEORGEA NOGUEIRA-MELO ◽  
HELIO LONGONI PLAUTZ JR ◽  
TATIANA BAPTISTA GIBERTONI
Keyword(s):  
New Species ◽  
Atlantic Forest ◽  
Phylogenetic Analyses ◽  
Tropical Species ◽  
Brazilian Atlantic Forest ◽  
New Combinations ◽  
Molecular Analyses ◽  
Rdna Sequences ◽  
A New Species

Rhodofomitopsis roseomagna sp. nov. is described as a new species from the Brazilian Atlantic forest based on morphological and molecular analyses. The species is characterized by the brownish to lilac, pileate basidiomata, round pores (5–6 per mm), and cylindrical to subcylindrical basidiospores (4–5 × 2.0–2.5 μm). Phylogenetic analyses based on combined ITS and nLSU rDNA sequences show that the new species belongs to the recently described genus Rhodofomitopsis. We also propose Rhodofomitopsis flabellata and Fomitopsis bondartsevae as new combinations. Notes on some tropical species of Fomitopsidaceae, description and illustration of the new species, and a key to the species of Rhodofomitopsis reported from the Neotropics are provided.

Phylogenetic Classification of Subtribe Castillejinae (Orobanchaceae)

2009 ◽  
Vol 34 (1) ◽  
pp. 182-197 ◽  
Author(s):  
David C. Tank ◽  
J. Mark Egger ◽  
Richard G. Olmstead
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Systematic Research ◽  
New Combinations ◽  
Phylogenetic Hypothesis ◽  
Molecular Systematic ◽  
Genus Level ◽  
Formal Classification ◽  
Molecular Phylogenetic

Recent molecular systematic research has indicated the need for a revised circumscription of generic boundaries in subtribe Castillejinae (tribe Pedicularideae, Orobanchaceae). Based on a well-resolved and well-supported phylogenetic hypothesis, we present a formal reclassification of the major lineages comprising the Castillejinae. Prior to this treatment, subtribe Castillejinae included Castilleja (ca. 190 spp.), Cordylanthus (18 spp.), Orthocarpus (9 spp.), Triphysaria (5 spp.), and the monotypic genera Clevelandia and Ophiocephalus. In the classification presented here, Orthocarpus and Triphysaria retain their current circumscriptions, Castilleja is expanded to include Clevelandia and Ophiocephalus, and Cordylanthus is split into three genera; a key to the genera as they are recognized here is provided. Two new combinations, Castilleja beldingii and Castilleja ophiocephala, are proposed within the expanded Castilleja. The concept of Cordylanthus is restricted to the 13 species formerly recognized as subg. Cordylanthus, while subg. Dicranostegia and subg. Hemistegia are elevated to genus level (Dicranostegia and Chloropyron, respectively). We resurrect the generic name Chloropyron for the halophytes previously recognized as subg. Hemistegia. Five new combinations are proposed for Chloropyron (Chloropyron maritimum subsp. canescens, Chloropyron maritimum subsp. palustre, Chloropyron molle subsp. hispidum, Chloropyron palmatum, and Chloropyron tecopense). In addition to the formal classification, we provide phylogenetic clade definitions for Castillejinae, each of the genera, and two additional clades that are not assigned formal ranks. Morphological characteristics used to recognize traditional groups are evaluated, and synapomorphies are discussed. Finally, the current infrageneric classifications for Castilleja and Cordylanthus are evaluated in light of the recent molecular phylogenetic analyses.

Homortomyces tamaricis sp. nov. and convergent evolution of Homortomyces and Stilbospora

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 156 ◽  
Author(s):  
NALIN N. WIJAYAWARDENE ◽  
KEVIN D. HYDE ◽  
ERIO CAMPORESI ◽  
D. JAYARAMA BHAT ◽  
YU SONG ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Convergent Evolution ◽  
Phylogenetic Analyses ◽  
Bootstrap Support ◽  
Lsu Rdna ◽  
Maximum Likelihood Analysis ◽  
Data Set ◽  
Incertae Sedis ◽  
Rdna Sequences ◽  
Likelihood Analysis

A new species Homortomyces tamaricis is introduced from Cervia, Italy. It is distinct from H. combreti, the type species of this monotypic genus, in having smaller conidia, smaller paraphyses and shorter supporting cells. Morphologically Homortomyces is similar to Stilbospora, which groups in Diaporthales incertae sedis in maximum-likelihood analysis of LSU rDNA sequences. Maximum-likelihood analysis of the combined data set of LSU and ITS rDNA sequences indicates that Homortomyces species cluster with Tubeufiaceae with 77% bootstrap support, but group as a distinct clade with high bootstrap value (100%). These two genera show convergent evolution since both share very similar morphological characters, but have distinct phylogenetic lineages. Further phylogenetic analyses are needed, when more strains of Homortomyces and related genera are available, to resolve the genus familial placement. We maintain the genus in Dothideomycetes incertae sedis. No sexual state has yet been reported for this genus.

scholarly journals Phylogenetic Analyses of New Aquatic Hyphomycetes Provide Molecular Evidence for Microthyriaceae (Dothideomycetes, Ascomycota) Anamorph

2021 ◽  
Author(s):  
Min Qiao ◽  
Hua Zheng ◽  
Jishu Guo ◽  
Rafael F. Castañeda-Ruiz ◽  
Jianping Xu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Aquatic Hyphomycetes ◽  
Ecological Niches ◽  
Molecular Evidence ◽  
New Combinations ◽  
Phylogenetic Placement ◽  
The Family

The fungal family Microthyriaceae is represented by relatively few mycelial cultures and DNA sequences. As a result, the taxonomy and classification of this group of organisms remain poorly understood. Here, based on DNA sequences at four gene fragments (nuLSU rDNA, nuSSU rDNA, TEF1 and RPB2) in our analyses of aquatic hyphomycetes from southern China, we identify and report four new genera (Antidactylaria, Isthmomyces, Keqinzhangia, Pseudocoronospora) and thirteen new species (Antidactylaria minifimbriata, Pseudocoronospora hainanensis, Isthmomyces oxysporus, I. dissimilis, I. macrosporus, I. relanceatus, Keqinzhangia aquatica, Triscelophorus anakonajensis, T. anisopterioides, T. guizhouensis, T. mugecuoensis, T. multibrachiatus, T. neoseptatus; new combinations Isthmomyces asymmetrica, I. basitruncata, I. geniculata, I. lanceata, I. minima, I. rotundata) belonging to Microthyriaceae. Our results provided the first molecular evidence of asexual morph of this family and strengthened the phylogenetic placement of the family in class Dothideomycetes. The addition of these new taxa made Microthyriaceae the largest family comprising freshwater asexual genera in Pleosporomycetidae. In addition, we confirmed the monophyly of the genus Triscelophorus, the paraphyly of the genus Isthmolongispora, and revised 6 new combinations in Isthmolongispora. ITS barcoding of 13 species were also provided to help identify aquatic hyphomycetes in the future. Our results suggest that the asexual genera and sexual genera identified so far within this family have completely different ecological niches.

scholarly journals A molecular perspective on generic concepts in the Hypotrachyna clade (Parmeliaceae, Ascomycota)

Phytotaxa ◽  
2013 ◽  
Vol 132 (1) ◽  
pp. 21 ◽  
Author(s):  
PRADEEP K. DIVAKAR ◽  
ANA CRESPO ◽  
JANO NÚÑEZ-ZAPATA ◽  
ADAM FLAKUS ◽  
HARRIE J.M. SIPMAN ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
New Combinations ◽  
Generic Delimitation ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Alternative Hypotheses ◽  
Nuclear Its

Recently, molecular phylogenetic studies have revolutionized the generic concepts in Parmeliaceae and in lichen forming fungi in general. In the present study, the generic delimitation in the Hypotrachyna clade is revised using a molecular phylogeny of nuclear ITS, LSU and mitochondrial SSU rDNA sequences of 88 hypotrachynoid taxa. Morphological and chemical features are also revised in each group. 118 sequences are newly generated for this study. Our phylogenetic analyses show the polyphyly of Hypotrachyna as currently circumscribed which falls into four well-supported and one unsupported clade. Cetrariastrum, Everniastrum and Parmelinopsis are nested within Hypotrachyna s. lat., Parmelinopsis being also polyphyletic and nested in one of the Hypotrachyna clades. Cetrariastrum is monophyletic but clustered within Everniastrum. Two alternative hypotheses tests significantly rejected the monophyly of these three genera. As a consequence, the genera Cetrariastrum, Everniastrum, and Parmelinopsis are reduced to synonymy with Hypotrachyna. Furthermore, we here propose an alternative classification to recognize the well-supported clades at subgeneric level and leave the remaining species unclassified within the genus. Five new subgenera are proposed: Hypotrachyna subgen. Cetrariastrum, Hypotrachyna subgen. Everniastrum, Hypotrachyna subgen. Longilobae, Hypotrachyna subgen. Parmelinopsis, and Hypotrachyna subgen. Sinuosae. Forty-nine new combinations are proposed.

Sign in / Sign up

Export Citation Format

Share Document