Phylogenetic relationships in Hypomyces and allied genera, with emphasis on species growing on wood-decaying homobasidiomycetes

2000 ◽  
Vol 77 (12) ◽  
pp. 1756-1768 ◽  
Author(s):  
Kadri Põldmaa ◽  
Ellen Larsson ◽  
Urmas Kõljalg
Keyword(s):  
Maximum Likelihood ◽  
Sexual Reproduction ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
28S Rdna ◽  
The Other ◽  
Molecular Evidence

To infer phylogenetic relationships among species of Hypomyces (Fr.) Tul and allied genera, partial sequences of the 28S rDNA were obtained for 21 strains representing 19 species. On the basis of these data and 38 sequences obtained from GenBank, phylogenetic analyses were performed using the programs PAUP and Pee-Wee. Hypomyces appears to be paraphyletic, with species having wet-conidial phialidic anamorphs more closely related to other genera. Hypomyces chrysostomus Berk & Broome is a sister group to the clade that includes species of Aphysiostroma Barrasa et al., Arachnocrea Moravec, and Hypocrea Fr. Based on morphological and molecular evidence, a new genus, Sporophagomyces, is described for Hypomyces chrysostomus and two allied species. Hypomyces broomeanus Tul. forms one clade with species of Sphaerostilbella Sacc. and is transferred to this genus. The recognition of Arachnocrea is justified. The integration of Cladobotryum Nees species that are not known to undergo sexual reproduction with Hypomyces species that possess Cladobotryum anamorphs receives strong support, but the whole complex of these species appears to be paraphyletic. However, constraint trees, which require monophyly of all these ana- and pleo-morphic species, do not appear significantly less likely than the other trees obtained under maximum likelihood or parsimony criteria. For the remaining species of Hypomyces, four distinct lineages are distinguished.

Phylogenetic relationships of three families of the suborder Mononchina Kirjanova & Krall, 1969 inferred from 18S rDNA

Nematology ◽  
2015 ◽  
Vol 17 (9) ◽  
pp. 1113-1125 ◽  
Author(s):  
Mina Koohkan ◽  
Ebrahim Shokoohi ◽  
Peter Mullin
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
18S Rdna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Genome ◽  
Sister Group ◽  
Ssu Rdna ◽  
Rdna Analysis

Mononchida is an order of predatory nematodes and includes the suborders Bathyodontina and Mononchina. In this survey, sequences of the 18S rDNA were amplified and used to reconstruct the phylogeny of the Mononchina. Phylogenetic analyses using Neighbour Joining (NJ) and Maximum Likelihood (ML) were employed with five outgroup taxa and 65 mononch sequences including 14 new sequences from Iran. Both analyses indicated that the Anatonchus is monophyletic. Actus was placed as the sister group of Mylonchulus with weak and strong support, respectively, from the ML and NJ analyses. In both phylogenetic analyses, trees obtained from SSU rDNA alignments were subdivided into five highly- or moderately-supported clades, designated Clade I: Mylonchulus spp., Clade II: Actus salvadoricus, Clade III: Anatonchus spp., a group comprising the genera Clarkus, Coomansus, Miconchus and Prionchulus, Clade IV: Mononchus spp., and Clade V: Granonchulus sp. The 18S rDNA analysis demonstrated that this region of the nuclear genome can be used to resolve the relationships of members of this suborder.

Revisiting the phylogeny and taxonomy of Osmanthus (Oleaceae) including description of the new genus Chengiodendron

Phytotaxa ◽  
2020 ◽  
Vol 436 (3) ◽  
pp. 283-292 ◽  
Author(s):  
YONG-FU LI ◽  
MIN ZHANG ◽  
XIAN-RONG WANG ◽  
STEVEN PAUL SYLVESTER ◽  
QI-BAI XIANG ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
New Genus ◽  
Morphological Character ◽  
Strong Support ◽  
Its Region ◽  
Phylogenetic Placement ◽  
Morphological Patterns

Osmanthus (Oleaceae) is considered one of the most confusing genera with regards to circumscription and phylogenetic placement of taxa within the subtribe Oleinae of Oleaceae, with controversies mainly focused on the attribution of section Leiolea. In the present study, we analyzed 71 samples that represent the broad taxonomic, biogeographic, and morphological patterns in the subtribe Oleinae. Based on concatenation of four plastid genes (trnL-F, trnT-L, trnS-G, and matK) and comparison with the ITS region, Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenies were inferred. Morphological character traits and geographical distributions of taxa were also studied. These results provide strong support for the segregation of the Leiolea clade (Osmanthus marginatus, O. matsumuranus and O. minor) of sect. Leiolea from Osmanthus. Therefore, the Leiolea clade is instated as the new genus Chengiodendron, with a taxonomic treatment provided. This study provides a clearer understanding of the phylogenetic relationships of genera in the subtribe Oleinae.

Phlebia nigrodontea sp. nov. in Meruliaceae (Polyporales) with a black hymenial surface

Phytotaxa ◽  
2020 ◽  
Vol 458 (3) ◽  
pp. 195-206
Author(s):  
RUO-XIA HUANG ◽  
KAI-YUE LUO ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
Phlebioid Clade ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungus, Phlebia nigrodontea, is proposed based on a combination of morphological features and molecular evidence. The species is characterized by a grandinioid hymenophore with vinaceous brown to black colour, a monomitic hyphal system with clamped generative hyphae and ellipsoid, colourless, thin-walled, smooth basidiospores (3.9–4.9 × 2.3–3.1 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses carried out using maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on the molecular data of ITS+nLSU sequences showed that P. nigrodontea nested within the phlebioid clade. A further investigation of more representative taxa from Phlebia, based on ITS+nLSU sequences, demonstrated that the species P. nigrodontea formed a monophyletic lineage with strong support (100% BS, 100% BT, 1.00 BPP) and closely grouped with P. chrysocreas.

Delving deeper into the phylogenetics of the herbaceous bamboos (Poaceae, Bambusoideae, Olyreae): evaluation of generic boundaries within the Parodiolyra/Raddiella clade uncovers a new genus

2019 ◽  
Vol 192 (1) ◽  
pp. 61-81 ◽  
Author(s):  
Iasmin L C Oliveira ◽  
Andreza O Matos ◽  
Christian Silva ◽  
Maria Luiza S Carvalho ◽  
Christopher D Tyrrell ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Plastid Genomes ◽  
Herbaceous Bamboos

Abstract The present study aims to expand the knowledge of phylogenetic relationships in Olyrinae, a subtribe of herbaceous bamboos (Poaceae: Bambusoideae: Olyreae). Our focus is on Parodiolyra and Raddiella, two historically related genera that, with their sister Diandrolyra, form one of the four main lineages in the subtribe. Previous phylogenetic analyses suggested that Parodiolyra is not monophyletic, but its taxonomic boundaries and its relationship with Raddiella remain uncertain due to low sampling. We increased the taxon sampling and sequenced five regions of the nuclear and plastid genomes for this lineage and other representatives of Olyreae. We used maximum parsimony, maximum likelihood, Bayesian inference and coalescence analysis. Our results corroborate the paraphyly of Parodiolyra, with P. micrantha sister to a clade including the remaining Parodiolyra and Raddiella. All remaining Parodiolyra form a well-supported clade, but Raddiella had conflicting resolutions, being either monophyletic or not. Thus, based on phylogenetic and morphological evidence, we here recircumscribe Parodiolyra, transferring P. micrantha and P. colombiensis to the new genus Taquara (described here). Regarding Raddiella, sampling is still not comprehensive and does not allow a decision on to its taxonomic status to be made at this time. Inclusion of other phreatophytic species may be crucial to resolve the problem of conflicting topologies.

Phylogenetic relationships of the lower Cyclorrhapha (Diptera: Brachycera) based on 28S rDNA sequences

2002 ◽  
Vol 33 (4) ◽  
pp. 445-456 ◽  
Author(s):  
Brian M. Wiegmann ◽  
Kenneth P. Collins
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
28S Rdna ◽  
Morphological Data ◽  
Monophyletic Clade ◽  
Rdna Sequences ◽  
28S Rdna Sequences

AbstractCyclorrhaphan Diptera are an extremely successful clade of ecologically and phylogenenetically important flies. Despite their significance the relationships among lower cyclorrhaphans ('Aschiza') remain controversial in spite of several morphologically based phylogenetic analyses. We sequenced a 2.7-kb fragment of 28S rDNA for taxa representing all lower cyclorrhaphan families (except Ironomyiidae), four schizophoran families, and seven empidoid out-group taxa. Phylogenetic analysis of these data strongly supports a monophyletic Cyclorrhapha (including the enigmatic taxon Opetia nigra) that is divided into two clades - a well-supported Eumuscomorpha (Syrphidae + Pipunculidae + Schizophora), and a weakly-supported Platypezoidea (all non-Eumuscomorpha). Consequently, the former grouping known as Aschiza, which included syrphids and pipunculids, is not a valid monophyletic clade. Within Platypezoidea, most of our analyses place Lonchopteridae as sister group to Opetiidae, and strongly support the monophyly of Sciadoceridae + Phoridae. Among the Eumuscomorpha we do not recover the monophyly of Syrphoidea (Syrphidae + Pipunculidae). Instead, all analyses place Pipunculidae as the sister group to Schizophora. This novel finding has never been proposed based on morphological data and will require more data (both molecular and morphological) and taxa to confirm.

scholarly journals Complete mitogenomes of Anopheles peditaeniatus and Anopheles nitidus and phylogenetic relationships within the genus Anopheles inferred from mitogenomes

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jing Guo ◽  
Zhen-Tian Yan ◽  
Wen-Bo Fu ◽  
Huan Yuan ◽  
Xu-Dong Li ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Repeat Unit ◽  
Taxonomic Revision ◽  
Sister Group ◽  
The Other ◽  
Genome Variations ◽  
Medical Importance ◽  
First Time

Abstract Background Despite the medical importance of mosquitoes of the genus Anopheles in the transmission of malaria and other human diseases, its phylogenetic relationships are not settled, and the characteristics of mitochondrial genome (mitogenome) are not thoroughly understood. Methods The present study sequenced and analyzed the complete mitogenomes of An. peditaeniatus and An. nitidus, investigated genome characteristics, and inferred the phylogenetic relationships of 76 Anopheles spp. Results The complete mitogenomes of An. peditaeniatus and An. nitidus are 15,416 and 15,418 bp long, respectively, and both include 13 PCGs, 22 tRNAs, two tRNAs and one control region (CR). Mitogenomes of Anopheles spp. are similar to those of other insects in general characteristics; however, the trnR and trnA have been reversed to “trnR-trnA,” as has been reported in other mosquito genera. Genome variations mainly occur in CR length (493–886 bp) with six repeat unit types identified for the first time that demonstrate an evolutionary signal. The subgenera Lophopodomyia, Stethomyia, Kerteszia, Nyssorhynchus, Anopheles and Cellia are inferred to be monophyletic, and the phylogenetic analyses support a new phylogenetic relationship among the six subgenera investigated, in that subgenus Lophopodomyia is the sister to all other five subgenera, and the remaining five subgenera are divided into two clades, one of which is a sister-taxon subgenera Stethomyia + Kerteszia, and the other consists of subgenus Nyssorhynchus as the sister to a sister-group subgenera Anopheles + Cellia. Four series (Neomyzomyia, Pyretophorus, Neocellia and Myzomyia) of the subgenus Cellia, and two series (Arribalzagia and Myzorhynchus) of the subgenus Anopheles were found to be monophyletic, whereas three sections (Myzorhynchella, Argyritarsis and Albimanus) and their subdivisions of the subgenus Nyssorhynchus were polyphyletic or paraphyletic. Conclusions The study comprehensively uncovered the characteristics of mitogenome and the phylogenetics based on mitogenomes in the genus Anopheles, and provided information for further study on the mitogenomes, phylogenetics and taxonomic revision of the genus. Graphical abstract

scholarly journals The Morphological Characteristics and Phylogenetic Analyses Revealed an Additional Taxon in Heteroradulum (Auriculariales)

Diversity ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 40
Author(s):  
Jia-Jin Li ◽  
Chang-Lin Zhao ◽  
Chao-Mao Liu
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Fungal Species ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Monophyletic Lineage ◽  
Thin Walled

Auriculariales is diverse, embracing a number of corticioid, poroid, and hydnoid genera. The present study covers a new wood-inhabiting fungal species of Heteroradulum niveum sp. nov that is proposed on the basis of a combination of morphological features and molecular evidence. The species is characterized by the resupinate basidiomata, a monomitic hyphal system with generative hyphae with clamp connections; tubular cystidia; two- to four-celled basidia; and allantoid, colorless, thin-walled, smooth, IKI–, CB–, basidiospores (6.5–13.5 × 2.7–5.5 µm). Sequences of ITS and nLSU rRNA gene regions of the specimens were generated, and phylogenetic analyses were carried out with methods of maximum parsimony, maximum likelihood, and Bayesian inference. These phylogenetic analyses inferred from ITS+nLSU indicated that H. niveum is nested in Heteroradulum within Auriculariales. Further study within Heteroradulum on the basis of ITS+nLSU dataset revealed that it formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and then grouped with H. yunnanensis.

Molecular phylogeny of the Annelida

2000 ◽  
Vol 78 (11) ◽  
pp. 1873-1884 ◽  
Author(s):  
Damhnait McHugh
Keyword(s):  
Molecular Analysis ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Gene ◽  
Sister Group ◽  
The Body ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Sister Relationship

Traditionally, the Annelida has been classified as a group comprising the Polychaeta and the Clitellata. Recent phylogenetic analyses have led to profound changes in the view that the Annelida, as traditionally formulated, is a natural, monophyletic group. Both molecular and morphological analyses support placement of the Siboglinidae (formerly the Pogonophora) as a derived group within the Annelida; there is also evidence, based on molecular analysis of the nuclear gene elongation factor-1α, that the unsegmented echiurids are derived annelids. While monophyly of the Clitellata is well-supported by both molecular and morphological analyses, there is no molecular evidence to support monophyly of the polychaete annelids; the Clitellata fall within a paraphyletic polychaete grade. Relationships among groups of polychaete annelids have not yet been resolved by molecular analysis. Within the Clitellata, paraphyly of the Oligochaeta was indicated in a phylogenetic analysis of cytochrome c oxidase I, which supported a sister relationship between the leeches, including an acanthobdellid and a branchiobdellid, and two of the four oligochaetes in the analysis. There is some evidence from analysis of 18S rRNA sequences for a sister-group relationship between the clitellates and the taxon Aeolosoma. There is no agreement regarding the body form of the basal annelid, and while molecular analyses provide strong support for the Eutrochozoa, the identity of sister-group to the Annelida among the Eutrochozoa remains enigmatic. It is recommended that future investigations include additional conserved gene sequences and expanded taxon sampling. It is likely that the most productive approach to resolving annelid phylogeny, and thus increasing our understanding of annelid evolution, will come from combined analyses of several gene sequences.

Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus

2012 ◽  
Vol 25 (6) ◽  
pp. 418 ◽  
Author(s):  
Roy E. Halling ◽  
Mitchell Nuhn ◽  
Todd Osmundson ◽  
Nigel Fechner ◽  
James M. Trappe ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sister Group ◽  
Molecular Data ◽  
Translation Elongation ◽  
Spore Deposit ◽  
Large Subunit Rdna ◽  
Translation Elongation Factor 1Α

Harrya is described as a new genus of Boletaceae to accommodate Boletus chromapes, a pink-capped bolete with a finely scabrous stipe adorned with pink scabers, a chrome yellow base and a reddish-brown spore deposit. Phylogenetic analyses of large-subunit rDNA and translation elongation factor 1α confirmed Harrya as a unique generic lineage with two species, one of which is newly described (H. atriceps). Some Chinese taxa were recently placed in a separate genus, Zangia, supported by both morphology and molecular data. Multiple accessions from Queensland, Australia, support the synonymy of at least three species in a separate Australian clade in the new genus, Australopilus. The truffle-like Royoungia is also supported as a separate lineage in this clade of boletes. Even though it lacks stipe characters, it possesses the deep, bright yellow to orange pigments in the peridium. Additional collections from Zambia and Thailand represent independent lineages of uncertain phylogenetic placement in the Chromapes complex, but sampling is insufficient for formal description of new species. Specimens from Java referable to Tylopilus pernanus appear to be a sister group of the Harrya lineage.

Rediagnosis of the squat lobster genus Gastroptychus Caullery, 1896, with a new genus Sternostylus and a new family Sternostylidae (Crustacea: Decapoda: Anomura: Chirostyloidea)

Zootaxa ◽  
2018 ◽  
Vol 4524 (1) ◽  
pp. 77 ◽  
Author(s):  
KEIJI BABA ◽  
SHANE T. AHYONG ◽  
KAREEN E. SCHNABEL
Keyword(s):  
Type Species ◽  
Anterior Margin ◽  
New Genus ◽  
Sister Group ◽  
Sensu Stricto ◽  
The Other ◽  
Squat Lobster ◽  
Terminal Spine ◽  
New Family ◽  
Left And Right

The chirostyloidean squat lobster genus Gastroptychus Caullery, 1896 is revised and is split into two genera: Gastroptychus sensu stricto (type species, Ptychogaster spinifer A. Milne-Edwards, 1880) and Sternostylus new genus (type species, Ptychogaster formosus Filhol, 1884). Gastroptychus sensu stricto, is restricted to nine species with a sternal plastron, at sternite 3, abruptly demarcated from the preceding sternites (excavated sternum) by a distinct step forming a well-defined transverse or concave anterior margin at the articulation with maxillipeds 3, the maxillipeds 3 widely separated, with the distal parts accommodated in the excavated sternum between the left and right maxillipeds 3 when folded, and the P2–4 dactyli with the terminal spine demarcated by a suture. Sternostylus new genus, represented by 12 species, has the sternite 3 anteriorly bluntly produced medially and steeply sloping anterodorsally to the anterior sternite, with a pair of spines directly behind the anterior margin, the left and right maxillipeds 3 adjacent, and the P2–4 dactyli ending in an indistinctly demarcated corneous spine. The above-mentioned characters of Gastroptychus are consistent with Chirostylidae sensu stricto. Published molecular phylogenies indicate, however, that Sternostylus is the sister group to all the other Chirostylidae, and is designated the type genus of a new family, Sternostylidae. 

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