Further phylogenetic studies of the Polychaeta using 18S rDNA sequence data

2004 ◽  
Vol 84 (5) ◽  
pp. 949-960 ◽  
Author(s):  
Kathryn A. Hall ◽  
Pat A. Hutchings ◽  
Donald J. Colgan
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Data ◽  
Phylogenetic Studies ◽  
Rdna Sequence Data ◽  
Substantial Progress ◽  
18S Rdna Sequence

The integration of molecular and morphological approaches has produced substantial progress in understanding the higher classification of most major invertebrate groups. The striking exception to this is the Polychaeta. Neither the membership nor the higher classification of this group has been robustly established. Major inconsistencies exist between the only comprehensive cladistic analysis of Polychaeta using morphological data and the DNA sequence studies covering all or part of the taxon.We have compiled a dataset of available nearly complete 18S ribosomal DNA sequences and collected an additional 22 sequences (20 Polychaeta in 19 taxa, one Myzostomida and one Phoronida) to obtain more comprehensive coverage of polychaete diversity for this gene. Analyses of the data do not resolve all inconsistencies among current hypotheses of polychaete phylogeny. They do support the recognition (in whole or part) of some clades such as the Eunicida, Phyllodocida and Terebellida that have been proposed on morphological grounds. Our analyses contradict the Canalipalpata and the Scolecida. Although the polychaete sister-group to the Clitellata is not clearly resolved in our analyses, the clitellates are always recovered as a derived clade within the Polychaeta. Increased taxon sampling is required to elucidate further the phylogeny of the Polychaeta.

Phylogeny and higher classification of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea)*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 413-425 ◽  
Author(s):  
P. J. GULLAN ◽  
L. G. COOK
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Dna ◽  
Sister Group ◽  
Scale Insect ◽  
Scale Insects ◽  
Morphological Data ◽  
Adult Males ◽  
Plant Feeding ◽  
Phylogenetic Studies

The superfamily Coccoidea contains nearly 8000 species of plant-feeding hemipterans comprising up to 32 families divided traditionally into two informal groups, the archaeococcoids and the neococcoids. The neococcoids form a monophyletic group supported by both morphological and genetic data. In contrast, the monophyly of the archaeococcoids is uncertain and the higher level ranks within it have been controversial, particularly since the late Professor Jan Koteja introduced his multi-family classification for scale insects in 1974. Recent phylogenetic studies using molecular and morphological data support the recognition of up to 15 extant families of archaeococcoids, including 11 families for the former Margarodidae sensu lato, vindicating Koteja’s views. Archaeococcoids are represented better in the fossil record than neococcoids, and have an adequate record through the Tertiary and Cretaceous but almost no putative coccoid fossils are known from earlier. In contrast, the sister group of the scale insects (Aphidoidea) has a more informative Jurassic and Triassic record. Relationships among most scale insect families are unresolved in phylogenetic trees based on nuclear DNA sequences, and most nodes in trees based on morphological data, including those from adult males, are poorly supported. Within the neococcoids, the Eriococcidae is not monophyletic and the monophyly of the Coccidae and Diaspididae may be compromised by the current family-level recognition of a few species-poor autapomorphic groups.

Generic delimitations in the family Stictidaceae (Ostropales, Ascomycota): the Stictis–Conotrema problem

2005 ◽  
Vol 37 (1) ◽  
pp. 67-75 ◽  
Author(s):  
Mats WEDIN ◽  
Heidi DÖRING ◽  
Kristina KÖNBERG ◽  
Gunnar GILENSTAM
Keyword(s):  
Sequence Data ◽  
Sister Group ◽  
Lsu Rdna ◽  
Infrageneric Classification ◽  
Rdna Its ◽  
The Family ◽  
Rdna Sequence Data ◽  
Natural Groups ◽  
High Support

The family Stictidaceae (Ostropales, Ascomycota) contains both lichenized and non-lichenized fungi. Here, we test if Conotrema (lichenized) and Stictis (non-lichenized) as currently delimited are distinct monophyletic genera, by parsimony and parsimony jackknifing analyses of combined nuclear rDNA (ITS and partial LSU rDNA) and mitochondrial SSU rDNA sequence data matrices. The study includes four species of Stictis, three species of Conotrema, and representatives of the related Schizoxylon (lichenized), Odontotrema, Carestiella (at least sometimes associated with algae), Cryptodiscus and Thelotrema (lichenized). In all analyses, the Conotrema species were nested within Stictis with high support. Thus, we conclude that Conotrema are only lichenized representatives of Stictis. The type species of the two generic names, C. urceolatum and S. radiata, are sister taxa in our analyses. Furthermore, the analysis gave no support for the present infrageneric classification of Stictis. Carestiella socia (the type of Carestiella) and the two representatives of Schizoxylon studied were also nested within Stictis s. lat. The Odontotremataceae is the sister group to the Stictidaceae, and Cryptodiscus foveolaris groups with Thelotrema rather than with the Stictidaceae. We conclude that lichenization in the Stictidaceae does not characterize natural groups, and that Conotrema should be considered a synonym to Stictis, as predicted by anatomical characteristics. The new combinations Stictis urceolatum and Stictis populorum are made.

Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)

Zootaxa ◽  
2007 ◽  
Vol 1522 (1) ◽  
pp. 1-68 ◽  
Author(s):  
THOMAS KNEBELSBERGER ◽  
MICHAEL A. MILLER
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Coi Gene ◽  
Parthenogenetic Species ◽  
Mediterranean Countries ◽  
Coi Sequences

Until recently the subaptera-group of Phyllodromica contained only one species. The revision of the subaptera-group  herein consists of the two newly described bisexual species, P. iberica and P. quadracantha, endemic to the Iberian Peninsula and a parthenogenetic species, P. subaptera (Rambur, 1838), which is widely distributed over most of the Mediterranean countries and islands. Within P. iberica three conspecific morphotypes are distinguished. The morphological characteristics of the subaptera-group are described. The species and their distributions are described and depicted. A key for the morphological determination of P. quadracantha and the morphotypes of P. iberica is given. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene are included in the species descriptions. The sequence data are suitable for species identification (DNA barcodes). A cladistic analysis of the morphological data and a phylogenetic analysis of the DNA sequences were performed to infer the phylogenetic relationships between the species of the subaptera-group.

Molecular and morphological phylogenetic analysis and taxonomic revision of the genus Orleanesia (Laeliinae, Epidendroideae, Orchidaceae)

Phytotaxa ◽  
2019 ◽  
Vol 392 (1) ◽  
pp. 1
Author(s):  
GABRIEL F. GONÇALVES ◽  
ANNA VICTORIA S. R. MAUAD ◽  
GIULIANA TAQUES ◽  
ERIC C. SMIDT ◽  
FÁBIO DE BARROS
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Morphological Data ◽  
Data Sets ◽  
New Synonyms ◽  
Nuclear Its

In order to evaluate the monophyly of the genus Orleanesia (Orchidaceae) and to assess its position within Laeliinae, a phylogenetic analysis was performed using molecular (nuclear ITS and plastid matK DNA sequences) and morphological data. A taxonomic revision of Orleanesia was also performed, with a description of the genus and its species using fresh living plants and 115 exsiccates from 31 herbaria. All phylogenetic analyses were highly congruent, and thus the sequence data from all three data sets were combined. The resulting phylogeny corroborated the monophyly of Orleanesia, with two strongly supported clades, and confirmed Caularthron as its sister group. Character analysis was not very informative due to a high degree of homoplasy. Two lectotypifications and three new synonyms were proposed for the genus, thereby reducing the number of accepted species to six. Although none of the species of Orleanesia are considered endangered, it is clear that some populations are threatened with deforestation and habitat reduction.

Description and experimental transmission of Tetracapsuloides vermiformis n. sp. (Cnidaria: Myxozoa) and guidelines for describing malacosporean species including reinstatement of Buddenbrockia bryozoides n. comb. (syn. Tetracapsula bryozoides)

Parasitology ◽  
2016 ◽  
Vol 144 (4) ◽  
pp. 497-511 ◽  
Author(s):  
SNEHA PATRA ◽  
ASHLIE HARTIGAN ◽  
DAVID J. MORRIS ◽  
ALENA KODÁDKOVÁ ◽  
ASTRID S. HOLZER
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Morphological Characters ◽  
Experimental Transmission ◽  
Rdna Sequence Data ◽  
Differential Characters ◽  
Present Description ◽  
Fredericella Sultana ◽  
18S Rdna Sequence ◽  
Molecular Characters

SUMMARYThis paper provides the first detailed description of a Tetracapsuloides species, Tetracapsuloides vermiformis n. sp., with vermiform stages in the bryozoan host, Fredericella sultana, and its experimental transmission from F. sultana to Cyprinus carpio. The suitability of morphological, biological and 18S rDNA sequence data for discrimination between malacosporean species is reviewed and recommendations are given for future descriptions. Presently, malacosporean species cannot be differentiated morphologically due to their cryptic nature and the lack of differential characters of spores and spore-forming stages in both hosts. We examined biological, morphological and molecular characters for the present description and for revising malacosporean taxonomy in general. As a result, Buddenbrockia plumatellae was split into two species, with its sac-like stages being ascribed to Buddenbrockia bryozoides n. comb. In addition to ribosomal DNA sequences multiple biological features rather than morphological characters are considered essential tools to improve malacosporean taxonomy in the future according to our analysis of the limited traits presently available.

Phylogenetic relationships of Nygolaimina and Dorylaimina (Nematoda: Dorylaimida) inferred from small subunit ribosomal DNA sequences

Nematology ◽  
2005 ◽  
Vol 7 (1) ◽  
pp. 59-79 ◽  
Author(s):  
Peter G. Mullin ◽  
Timothy S. Harris ◽  
Thomas O. Powers
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Sister Taxon ◽  
Monophyletic Lineage ◽  
Rdna Sequence Data ◽  
The Common ◽  
Small Subunit Ribosomal Dna ◽  
18S Rdna Sequence

Abstract Phylogenetic reconstructions based on 18S rDNA sequence data indicate that Dorylaimida, comprising the suborders Nygolaimina and Dorylaimina, is a monophyletic lineage, but that there is a deep division within Nygolaimina, giving rise to the possibility that Nygolaimina is paraphyletic. A well-supported clade comprising members of the traditional orders Mermithida and Mononchida (including Bathyodontina) forms the sister taxon to the Dorylaimida. Inferred relationships within this clade indicate that Mermithida shares more recent common ancestry with Mononchina than does Bathyodontina. Vertebrate parasites within Dorylaimia (Dioctophymida and Trichinellida) are reconstructed in a sister-taxon relationship with the Mononchida/Dorylaimida lineage. The enigmatic order Isolaimida (represented by Isolaimium) appears to be ancestral to all other Dorylaimia sampled. Expanded taxon sampling for phylogenetic analyses of the subclass raises new possibilities for the reconstruction of hypothetical character states in the common ancestor of Dorylaimia.

Molecular phylogeny of the Platyhelminthes

2004 ◽  
Vol 82 (2) ◽  
pp. 168-193 ◽  
Author(s):  
Jaume Baguñà ◽  
Marta Riutort
Keyword(s):  
Molecular Phylogeny ◽  
Hox Genes ◽  
Sequence Data ◽  
Sister Group ◽  
Main Difficulty ◽  
Rdna Sequence Data ◽  
Corroborative Evidence ◽  
18S Rdna Sequence ◽  
Basal Position ◽  
Molecular Characters

The phylum Platyhelminthes has traditionally been considered the most basal bilaterian taxon. The main difficulty with this placement is the lack of convincing synapomorphies for all Platyhelminthes, which suggest that they are polyphyletic. Recent molecular findings based on 18S rDNA sequence data and number and type of Hox genes strongly suggest that the majority of Platyhelminthes are members of the lophotrochozoan protostomes, whereas the Acoelomorpha (Acoela + Nemertodermatida) fall outside of the Platyhelminthes as the most basal bilaterian taxon. Here we review phylum-wide analyses based on complete ribosomal and other nuclear genes addressed to answer the main issues facing systematics and phylogeny of Platyhelminthes. We present and discuss (i) new corroborative evidence for the polyphyly of the Platyhelminthes and the basal position of Acoelomorpha; (ii) a new consensus internal tree of the phylum; (iii) the nature of the sister group to the Neodermata and the hypotheses on the origin of parasitism; and (iv) the internal phylogeny of some rhabditophoran orders. Some methodological caveats are also introduced. The need to erect a new phylum, the Acoelomorpha, separate from the Platyhelminthes (now Catenulida + Rhabditophora) and based on present and new morphological and molecular characters is highlighted, and a proposal made.

Molecular phylogeny of Diploschistes inferred from ITS sequence data

2003 ◽  
Vol 35 (1) ◽  
pp. 27-32 ◽  
Author(s):  
María P. Martín ◽  
Scott LaGreca ◽  
H. Thorsten Lumbsch
Keyword(s):  
Sequence Data ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Data ◽  
Bootstrap Support ◽  
Evolutionary Trend ◽  
5.8S Rdna ◽  
Rdna Sequences ◽  
Strong Bootstrap Support ◽  
Nuclear Its

AbstractThe phylogeny of the genus Diploschistes was investigated using nucleotide sequences of the nuclear ITS rDNA region (ITS1, ITS2 and 5.8S rDNA). Sequences of 22 Diploschistes species were aligned to those of six other species of Thelotremataceae, Graphis scripta and Aspicilia cinerea, with the last used as an outgroup. The alignment was analysed cladistically using maximum parsimony. In the most parsimonious trees, Diploschistes is monophyletic, with D. ocellatus being a sister group to the remaining Diploschistes spp. (= Diploschistes s. str.). A previous cladistic analysis of morphological data suggested an evolutionary trend within the genus from perithecioid to urceolate ascomata. The present ITS data suggest the opposite: perithecioid ascomata are apparently an apomorphic character within the genus, with the actinostomus group forming a derived monophyletic clade. However, the topology within Diploschistes s. str. Lacks strong bootstrap support.

Phylogenetic relationships among taxa in the Jahnulales inferred from 18S and 28S nuclear ribosomal DNA sequences

2007 ◽  
Vol 85 (9) ◽  
pp. 873-882 ◽  
Author(s):  
Jinx Campbell ◽  
Astrid Ferrer ◽  
Huzefa A. Raja ◽  
Somsak Sivichai ◽  
Carol A. Shearer
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Molecular Study ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Rdna Sequence Data ◽  
28S Rdna Sequence ◽  
Important Character

Jahnulales is an order of freshwater, lignicolous, bitunicate ascomycetes characterized by wide (10–40 μm), brown, septate hyphae, stalked and (or) sessile ascomata, ascomal walls of 2–6 layers of large cells, and 1-septate ascospores. A variety of ascospore modifications are represented among the species in the order, including wall roughening, gelatinous sheaths, appendages and (or) pads, and apical caps or spines. To clarify generic boundaries and phylogenetic relationships within the Jahnulales and to assess the taxonomic significance of various morphological characters, a molecular study was carried out using 18S and 28S rDNA sequence data from 15 species representing the four genera in the order. In addition, Brachiosphaera tropicalis Nawawi and Xylomyces chlamydosporus Goos, R.D. Brooks & Lamore, two mitosporic species that co-occur with Jahnula Kirschst., species and have wide (>10 μm), brown, septate hyphae were included in the study to determine whether these species are members of this order. Maximum likelihood analyses confirmed the monophyly of the Jahnulales and resolved four clades. Two robustly supported clades comprise the genera Aliquandostipite Inderb. and Megalohypha A. Ferrer & Shearer. A third well-supported clade encompassed species of Brachiosphaera , Jahnula , and Xylomyces . The fourth clade contained isolates of the type species of the genus Jahnula, Jahnula aquatica (Plöttn. & Kirschst.) Kirschst., and two other members of this genus, but this clade was weakly supported. Our data suggest that the presence of very wide, brown, septate hyphae is an important character defining the Jahnulales. Based on molecular and morphological data, we propose the transfer of Jahnula siamensiae Sivichai & E.B.G. Jones and Patescospora separans Abdel-Wahab & El-Shar. to Aliquandostipite and emend the description of the Jahnulales.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

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