Ascomal evolution of filamentous ascomycetes: evidence from molecular data

1995 ◽  
Vol 73 (S1) ◽  
pp. 811-815 ◽  
Author(s):  
Joseph W. Spatafora
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Small Subunit ◽  
Filamentous Ascomycete ◽  
Group 4 ◽  
Nucleotide Data ◽  
Group 2 ◽  
Parsimony Trees

Phylogenetic analyses of nucleotide data from partial sequences (1150 bp) of the small subunit ribosomal DNA (SSU rDNA) were performed on 30 taxa representing several orders of Hymenoascomycetes and Loculoascomycetes. These analyses detected four major groups of filamentous ascomycetes: group 1, pyrenomycetes (Hypocreales, Microascales, Diaporthales, Sordariales) and loculoascomycetes (Pleosporales); group 2, operculate discomycetes (Pezizales); group 3, inoperculate discomycetes (Geoglossaceae); and group 4, plectomycetes (Eurotiales, Onygenales) and loculoascomycetes (Chaetothyriales). Well-supported clades, which correspond to groupings based on ascomal morphology, were resolved; however, the monophyly of the classes Hymenoascomycetes and Loculoascomycetes was rejected. The placement of the root on the filamentous ascomycete ingroup proved more problematic than resolving the ingroup relationships. Three alternative rooting possibilities, which were identified in suboptimal parsimony trees, were not significantly less likely in maximum likelihood ratio tests. Nonetheless, the most likely topology obtained from fastDNAml was identical to the most parsimonious tree. Key words: filamentous ascomycetes, Hymenoascomycetes, Loculoascomycetes, parsimony, maximum likelihood, ribosomal DNA.

Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽  
2003 ◽  
Vol 5 (5) ◽  
pp. 699-711 ◽  
Author(s):  
Peter Mullin ◽  
Timothy Harris ◽  
Thomas Powers
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Nominal Species ◽  
Competing Hypotheses ◽  
Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

Progress toward a phylogenetic classification of the Polyporaceae through parsimony analysis of mitochondrial ribosomal DNA sequences

1995 ◽  
Vol 73 (S1) ◽  
pp. 853-861 ◽  
Author(s):  
David S. Hibbett ◽  
Michael J. Donoghue
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Brown Rot ◽  
Small Subunit ◽  
Higher Order ◽  
Group 4 ◽  
Group 3 ◽  
Group 5 ◽  
Group 2

We used sequence data from mitochondrial small-subunit ribosomal DNA to infer phylogenetic relationships of the Polyporaceae. We examined 62 species representing 14 families of Aphyllophorales and Agaricales. Parsimony analyses of these sequences suggest that the Polyporaceae are polyphyletic. Higher order relationships are poorly resolved, but seven groups of species are generally well supported (as measured by bootstrapping) or are congruent with previous taxonomic hypotheses. Group 1 includes Polyporus s.str., seven other genera of Polyporaceae, Lentinus, and Ganoderma. Because this clade contains the type species of Polyporus, it may serve as the core for a future recircumscription of the Polyporaceae. Group 2 is morphologically and ecologically diverse, but all members have amyloid, ornamented spores (with the possible exception of Heterobasidion). This group includes Bondarzewia, Heterobasidion, Hericium, Echinodontium, Lentinellus, Auriscalpium, and Russula. Group 3 includes five exemplars of the Hymenochaetaceae, as well as Oxyporus and Trichaptum. Trichaptum and members of the Hymenochaetaceae are unusual among the holobasidiomycetes in their possession of imperforate parenthosomes. Group 4 represents the Boletaceae and includes Boletus and Suillus. Group 5 includes Bjerkandera, which is a polypore, and Pulcherricium and Phanerochaete, which are corticioid. In Group 5 the corticioid habit may have been derived by reduction. Group 6 includes Fomitopsis, Piptoporus, and Daedalea, all of which are brown rot polypores with bipolar mating systems. Group 7 includes Laetiporus and Phaeolus. Laetiporus is classified in Polyporaceae, but Phaeolus has been placed in both the Polyporaceae and Hymenochaetaceae. In general, our results suggest that macromorphology is evolutionarily flexible, but that certain anatomical and physiological characters, while not free from homoplasy, contain clues to higher order relationships of polypores. Key words: Aphyllophorales, basidiomycetes, classification, phylogeny, Polyporaceae, ribosomal DNA.

Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽  
2021 ◽  
Vol 511 (3) ◽  
Author(s):  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Growth Habit ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Two New Species ◽  
Thin Walled ◽  
Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

scholarly journals Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yi-Fan Cao ◽  
Hui-Xia Chen ◽  
Yang Li ◽  
Dang-Wei Zhou ◽  
Shi-Long Chen ◽  
...  
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Sister Relationship ◽  
Tibetan Antelope ◽  
A New Species

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.

scholarly journals Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Vol 285 (1893) ◽  
pp. 20181632 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

Molecular characterisation of, and new data on, two populations of Xiphinema ingens Luc & Dalmasso, 1964 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 125-138
Author(s):  
Sohrab Mirzaei ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Morphological Variation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
28S Rdna ◽  
Molecular Characterisation ◽  
Morphometric Data ◽  
Two Populations

Two populations of Xiphinema ingens were recovered and characterised based on morphological, morphometric and molecular data. Interesting morphological variation was observed on the nature of differentiation in uterus of females between both populations, i.e. one population had only a pseudo-Z-organ in the shape of globular bodies, whilst the second population had a similar pseudo-Z-organ but also had crystalloids which varied in size and number and were located near the pseudo-Z-globules or sometimes at some distance from them towards the vagina. Variation was also observed in the shape of tail of juveniles within each population as well as between two recovered populations. Both populations had the same range of morphometric data and formed a fully supported clade in both Bayesian inference (BI) and maximum likelihood (ML) methods of phylogenetic analyses using partial sequences of 28S rDNA D2-D3 and ITS1 regions. The two populations of X. ingens formed a clade with another Xiphinema species native to Iran (X. castilloi) in 28S and two species, X. macroacanthum and X. bernardi, in ITS1 trees.

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.

A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages

2009 ◽  
Vol 42 (1) ◽  
pp. 7-21 ◽  
Author(s):  
Paweł CZARNOTA ◽  
Beata GUZOW-KRZEMIŃSKA
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Small Subunit ◽  
Sister Species ◽  
Phylogenetic Study ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

AbstractThe phylogeny of the Micarea prasina group was investigated using mitochondrial small subunit ribosomal DNA sequences from 14 taxa representing this group, four other members of the genus Micarea, and Psilolechia lucida as an outgroup. A total of 31 new mtSSU rDNA sequences were generated, including 10 from the M. micrococca complex. Bayesian, maximum parsimony (MP) and maximum likelihood (ML) methods were used to analyse the data. The results show that M. micrococca is not monophyletic and forms three strongly supported lineages: 1) M. micrococca s. str., 2) M. byssacea (Th. Fr.) Czarnota, Guzow-Krzemińska & Coppins comb. nov., and 3) a putative taxon that requires further studies. Micarea viridileprosa is a sister species to M. micrococca s. str. and the recently described M. nowakii is a sister species to M. prasina s. str. The placement of M. tomentosa within the M. prasina group is confirmed. Micarea hedlundii appears to be more closely related to the M. micrococca complex than M. prasina s. str. Descriptions, illustrations, taxonomic remarks, distribution and habitat data for M. micrococca s. str. and M. byssacea are provided. A lectotype for Biatora byssacea Hampe non Zwackh and a neotype for Catillaria prasina β [var.] byssacea are selected.

Phylogeny of the Micareaceae inferred from nrSSU DNA sequences

2004 ◽  
Vol 36 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Heidi L. ANDERSEN ◽  
Stefan EKMAN
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Confidence Set ◽  
Tree Topologies ◽  
Small Subunit Ribosomal Dna

The phylogeny of the Micareaceae and the genus Micarea Fr. was studied using 39 nuclear small subunit ribosomal DNA sequences. Phylogenetic analyses were carried out using maximum parsimony, maximum likelihood, and Bayesian inference. A confidence set of trees was estimated using expected likelihood weights to investigate a series of hypotheses of monophyly. Tree topologies were very similar between methods and differed only in the placement of a few poorly supported branches. The results indicate that the Micareaceae in its current circumscription belongs in the Lecanorales, but that it is not monophyletic. Psilolechia, Micarea with a ‘non-micareoid’ photobiont, Micarea sensu stricto and Byssoloma form a paraphyletic grade in this study. Micarea sensu stricto and Byssoloma (Pilocarpaceae) form a strongly supported monophyletic group, which constitutes the sister group to the Bacidiaceae. Scoliciosporum A. Massal has sometimes been considered close to Micarea, but no support was found for that hypothesis.

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.

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