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.

A new Agonimia from Europe with a flabelliform thallus

2011 ◽  
Vol 44 (1) ◽  
pp. 55-66 ◽  
Author(s):  
Beata GUZOW-KRZEMIŃSKA ◽  
Josef P. HALDA ◽  
Paweł CZARNOTA
Keyword(s):  
Czech Republic ◽  
New Species ◽  
Great Britain ◽  
Dna Sequences ◽  
Sequence Data ◽  
Small Subunit ◽  
The Czech Republic ◽  
Rdna Sequence Data ◽  
Small Subunit Ribosomal Dna ◽  
A New Species

AbstractAgonimia flabelliformis sp. nov. (Verrucariaceae, Ascomycota) is described as a new species from the Czech Republic, Germany and Great Britain. Except for the distinctive, flabelliform to minutely coralloid thallus the species mostly resembles A. allobata. It differs from other related species of Agonimia in the absence of cortical papillae and in ascospore size. The distinctness of the new species and its placement within the genus Agonimia is supported by analyses of mitochondrial small subunit ribosomal DNA sequences from several samples of the taxon, and from many other representatives of Verrucariales including newly sequenced A. repleta and A. vouauxii. Additionally, ITS rDNA sequence data supports the distinction of A. flabelliformis from A. allobata. However, A. allobata was found to be highly variable and relationships, as well as the monophyly of taxa within Agonimia, are still unresolved and need further investigation.

scholarly journals Reconsideration of the ‘well-known’ hypotrichous ciliate Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 (Ciliophora, Sporadotrichida), with notes on its morphology, morphogenesis and molecular phylogeny

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3216-3225 ◽  
Author(s):  
Xiaoteng Lu ◽  
Chen Shao ◽  
Yuhe Yu ◽  
Alan Warren ◽  
Jie Huang
Keyword(s):  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Large Body ◽  
Small Subunit ◽  
Variable Number ◽  
Ssu Rdna ◽  
Intermediate Form ◽  
Rdna Sequence Data

The oxytrichid species Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003, isolated from a tributary of the Yangtze River in the Mudong district of Chongqing, southern China, was reinvestigated with emphasis on its morphology, morphogenesis and small-subunit (SSU) rDNA-based phylogeny. Compared with three previously described populations, the Mudong population of P. curdsi is characterized by its large body size, 170–295 × 65–110 μm in vivo, and by having a variable number of right marginal rows, either two or three. Likewise, the number of right marginal rows anlagen (RMA) is also variable, i.e. usually two, but sometimes several small extra anlagen that give rise to the formation of the third row, are present to the left of the RMAs. We posit that the Mudong population is an intermediate form between the three previously described populations. Phylogenetic analyses based on the SSU rDNA sequence data show that all populations of P. curdsi cluster with the type species of the genus, Pleurotricha lanceolata, in a clade nested within the Oxytrichidae.

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.

Phylogenetic analyses of various euglenoid taxa (euglenozoa) based on 18s rdna sequence data

2000 ◽  
Vol 36 (1) ◽  
pp. 220-226 ◽  
Author(s):  
Angelika Preisfeld ◽  
Silke Berger ◽  
Ingo Busse ◽  
Susanne Liller ◽  
Hans Georg Ruppel
Keyword(s):  
18S Rdna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rdna Sequence ◽  
Rdna Sequence Data ◽  
18S Rdna Sequence

scholarly journals Redescription, Morphogenesis, and Molecular Phylogeny of Pseudosincirra longicirrata nov. comb., With Establishment of a New Genus Pseudosincirra nov. gen. (Ciliophora, Hypotrichia)

2021 ◽  
Vol 12 ◽  
Author(s):  
Qi Gao ◽  
Chen Shao ◽  
Qiuyue Tang ◽  
Jingbao Li
Keyword(s):  
Molecular Phylogeny ◽  
New Genus ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Original Population ◽  
The Family ◽  
Rdna Sequence Data

The morphology and morphogenesis of Pseudosincirra longicirrata nov. gen. and nov. comb., isolated from southern China, were investigated with living observation and protargol staining. Our population is similar to the original population in living characteristics and ciliary patterns. The main determinable morphogenetic features of P. longicirrata nov. comb. are the presence of five frontoventral-transverse cirral anlagen (FVT-anlagen) and a dorsomarginal kinety anlage. According to the origin of FVT-anlagen IV and V in proter, it can be determined that P. longicirrata nov. comb. possesses two frontoventral rows and one right marginal row. Hence, a new genus, Pseudosincirra nov. gen., is proposed, and the diagnosis of P. longicirrata nov. comb. is improved. The new genus is diagnosed as follows: adoral zone of membranelles and undulating membranes is in a Gonostomum pattern; there are three enlarged frontal cirri, one buccal cirrus, and one parabuccal cirrus; postperistomial cirrus and transverse cirri are lacking; there are two more or less long frontoventral rows and one right and two or more left marginal rows; cirri within all rows very widely spaced; dorsal kinety pattern is of Urosomoida type, that is, three dorsal kineties and one dorsomarginal kinety; and caudal cirri are present. Phylogenetic analyses based on the small subunit ribosomal (SSU rDNA) sequence data indicate that P. longicirrata nov. comb. clusters with Deviata and Perisincirra. It is considered that Pseudosincirra nov. gen. and Perisincirra paucicirrata should be assigned to the family Deviatidae; fine cirri, and cirri within all rows being relatively widely spaced, should be considered as plesiomorphies of Deviatidae; and Deviatidae is closely related to Dorsomarginalia or Strongylidium–Hemiamphisiella–Pseudouroleptus.

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.

On the phylogeny of Ophiostoma, Ceratocystis s.s., and Microascus, and relationships within Ophiostoma based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (9) ◽  
pp. 1249-1265 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Small Subunit ◽  
Data Set ◽  
Rdna Sequences ◽  
Morphological Criteria ◽  
Small Subunit Rdna ◽  
Rdna Sequence Data ◽  
Large Subunit Rdna

Phylogenetic analysis of partial rDNA sequences suggests that Ophiostoma should remain the sole genus of the Ophiostomataceae, and this should be the sole family within the Ophiostomatales, whereas Ceratocystis s.s. would be best disposed within the Microascales. Although morphological criteria suggest that the genus Ophiostoma is heterogeneous, analysis of partial small subunit rDNA sequence data shows that Ophiostoma (excluding O. roraimense) represents a monophyletic taxon. Analysis of a partial large subunit rDNA data set, which included sequences from 55 species assignable to Ophiostoma, failed to support the strict subdivision of the genus based on either ascospore characters or the nature of the anamorph. Key words: Ceratocystis, Microascus, Ophiostoma, partial rDNA sequences, phylogeny.

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.

scholarly journals Morphology, Morphogenesis, and Molecular Phylogeny of a New Freshwater Ciliate, Quadristicha subtropica n. sp. (Ciliophora, Hypotrichia)

2021 ◽  
Vol 12 ◽  
Author(s):  
Chen Shao ◽  
Qi Gao ◽  
Alan Warren ◽  
Jingyi Wang
Keyword(s):  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Freshwater Pond ◽  
Small Subunit Ribosomal Dna

The morphology and the regulation of cortical pattern associated with the cell size, division, and phylogenetic position of a new hypotrichous ciliate, Quadristicha subtropica n. sp. collected from a freshwater pond in southern China, were investigated. Quadristicha subtropica n. sp. is characterized as follows: size in vivo 60–115 μm × 25–45 μm; 19–21 adoral membranelles; buccal cirrus near anterior end of endoral and paroral; cirrus IV/3 at about level of buccal vertex; right marginal row begins ahead of buccal vertex; 11–16 right and 12–19 left marginal cirri; and dorsal cilia about 5 μm long. The basic morphogenetic process in Q. subtropica n. sp. is consistent with that of the type species, Quadristicha setigera. Phylogenetic analyses based on small subunit ribosomal DNA sequence data reveal that the systematic position of Q. subtropica n. sp. is rather unstable with low support values across the tree and the genus Quadristicha is not monophyletic.

scholarly journals Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

2015 ◽  
Vol 97 (2) ◽  
pp. 394-404 ◽  
Author(s):  
Juan F. Díaz-Nieto ◽  
Sharon A. Jansa ◽  
Robert S. Voss
Keyword(s):  
Soft Tissue ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Fresh Material

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

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