Phylogenetic analysis of Gyrodactylus spp. (Platyhelminthes: Monogenea) using ribosomal DNA sequences

1999 ◽  
Vol 77 (9) ◽  
pp. 1439-1449 ◽  
Author(s):  
J Cable ◽  
P D Harris ◽  
R C Tinsley ◽  
C M Lazarus
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Species Group ◽  
Internal Transcribed Spacers ◽  
Base Pairs ◽  
Separate Species ◽  
5.8S Rdna ◽  
Complete Sequences

Species of the viviparous monogenean genus Gyrodactylus are difficult to identify morphologically and relationships within the genus are unclear. Partial or complete sequences were obtained for the internal transcribed spacers (ITS-1 and ITS-2) and 5.8S ribosomal DNA (rDNA) of 11 Gyrodactylus species (G. kobayashii, G. gurleyi, G. pungitii, G. rogatensis, G. gasterostei, G. derjavini, G. salaris, G. rarus, G. turnbulli, G. bullatarudis, and G. arcuatus) and the related Gyrdicotylus gallieni. Phylogenetic analyses (parsimony, distance, and maximum likelihood) separated species of the Gyrodactylus wageneri species-group (with a long ITS-1) from those of the Gyrodactylus eucaliae and G. arcuatus species-groups (with a short ITS-1). This subdivision into species with a long (610-630 base pairs (bp)) or short (300-500 bp) ITS-1 was also apparent with 5.8S rDNA and ITS-2 data. No support could be found for the hypothesis that G. salaris is a member of a separate species group, as this species clustered within the G. wageneri group. The morphologically homogeneous G. wageneri group was subdivided by our molecular data into five species that infect cottids, gasterosteids, and salmonids and two species that infect cyprinid fishes. Overall, the ITS-2, combined with the 5.8S rDNA (an alignment of 668 bp), appeared to be the most informative indicator of phylogenetic relationships within the genus Gyrodactylus. The potential importance of this technique for future gyrodactylid systematics is discussed.

Phylogenetic relationships among Coregonus species inferred from the DNA sequence of the first internal transcribed spacer (ITS1) of ribosomal DNA

1997 ◽  
Vol 54 (7) ◽  
pp. 1494-1503 ◽  
Author(s):  
S L Sajdak ◽  
R B Phillips
Keyword(s):  
Ribosomal Dna ◽  
North American ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Base Pairs ◽  
Phylogenetic Hypotheses ◽  
Northwestern North America ◽  
Hybridization And Introgression

Phylogenetic analyses based on morphometrics, data on protein electrophoresis, and mitochondrial DNA have given conflicting phylogenetic hypotheses for the subfamily Coregoninae (Prosopium, Coregonus, and Stenodus). To resolve these conflicts, phylogenetic analysis of 13 taxa of Coregoninae was done using a nuclear gene, the first internal transcribed spacer (ITS1) of the ribosomal DNA (rDNA). ITS1 sequences of all North American ciscoes were identical. In agreement with analyses based on other molecular data, the genus Stenodus was included in Coregonus, and there was no support for the monophyly of the ciscoes. The analysis based on rDNA also placed C. peled as the sister species to C. lavaretus, but this may represent a case of hybridization and introgression. A length polymorphism involving a repeating unit of 65-67 base pairs was found in the ITS1. All ciscoes except C. peled had one copy of the repeat. Coregonus peled, C. lavaretus, and Eurasian and Beringian C. clupeaformis had two copies of the repeat, while the other North American C. clupeaformis had three copies, suggesting that C. clupeaformis of northwestern North America is a form of C. lavaretus.

scholarly journals Integrative Studies on a New Ciliate Campanella sinica n. sp. (Protista, Ciliophora, Peritrichia) Based on the Morphological and Molecular Data, With Notes on the Phylogeny and Systematics of the Family Epistylididae

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhe Wang ◽  
Tong Wu ◽  
Borong Lu ◽  
Yong Chi ◽  
Xue Zhang ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Lsu Rdna ◽  
5.8S Rdna ◽  
Freshwater Pond ◽  
The Family

During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, Campanella sinica n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao, China. Specimen observations of this species were performed both in vivo and using silver staining. C. sinica n. sp. is characterized by the appearance of the mature colony, which is up to 2 cm high and contains more than 1,000 zooids, the asymmetric horn-shaped zooids, strongly everted and multi-layered peristomial lip, the slightly convex peristomial disc, and the well-developed haplokinety and polykinety, which make more than four circuits of the peristome before descending into the infundibulum. The small subunit ribosomal DNA (SSU rDNA), 5.8s rDNA and its flank internal transcribed spacers (ITS1-5.8s rDNA-ITS2), and large subunit ribosomal DNA (LSU rDNA) are sequenced and used for phylogenetic analyses which reveal that the family Epistylididae Kahl, 1933 is non-monophyletic whereas the genus Campanella is monophyletic and nests within the basal clade of the sessilids. The integrative results support the assertion that the genus Campanella represents a separate lineage from other epistylidids, suggesting a further revision of the family Epistylididae is needed. We revise Campanella including the transfer into this genus of a taxon formerly assigned to Epistylis, which we raise to species rank, i.e., Campanella ovata (Nenninger, 1948) n. grad. & n. comb. (original combination Epistylis purneri f. ovataNenninger, 1948). In addition, we provide a key to the identification of the species of Campanella.

scholarly journals Systematic Relationship of Weeping Katsura Based on Nuclear Ribosomal DNA Sequences

HortScience ◽  
2002 ◽  
Vol 37 (3) ◽  
pp. 595-598 ◽  
Author(s):  
Jianhua Li ◽  
Michael S. Dosmann ◽  
Peter Del Tredici ◽  
Susyn Andrews
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Morphological Evidence ◽  
Separate Species ◽  
Cultivar Group ◽  
Cercidiphyllum Japonicum

Sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA were used to examine genetic divergence of the two species of katsura [Cercidiphyllum japonicum Sieb. & Zucc. and Cercidiphyllum magnificum (Nakai) Nakai] and four clones of weeping katsura (`Amazing Grace', `Tidal Wave', `Pendulum', and `Morioka Weeping'), and to characterize the affinity of these weeping katsura to both species. Our results indicate that C. japonicum and C. magnificum are genetically distinct, supporting the recognition of them as separate species. Based on our DNA sequence data and morphological evidence, all weeping selections are phylogenetically derived from C. japonicum, not C. magnificum; nor are they of a hybrid origin between C. japonicum and C. magnificum. We propose the new cultivar-group Cercidiphyllum japonicum Weeping Group to include all katsura clones of weeping or pendulous habit, and recognize the cultivar epithet `Morioka Weeping' and its application to the excurrent and upright clone obtained from Japan and distributed in North America by the Arnold Arboretum.

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.

Re-description of the Arctic tardigrade Tenuibiotus voronkovi (Tumanov, 2007 (Eutardigrada; Macrobiotidea), with the first molecular data for the genus

Zootaxa ◽  
2016 ◽  
Vol 4196 (4) ◽  
pp. 498 ◽  
Author(s):  
KRZYSZTOF ZAWIERUCHA ◽  
MAŁGORZATA KOLICKA ◽  
ŁUKASZ KACZMAREK
Keyword(s):  
Original Description ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
The Arctic ◽  
Morphological Description ◽  
28S Rrna ◽  
Morphometric Data ◽  
Additional Material ◽  
Svalbard Archipelago ◽  
5.8S Rdna

Tardigrada is phylum of micrometazoans widely distributed throughout the world, because of old descriptions and insufficient morphometric data, many species currently need revision and re-description. Tenuibiotus voronkovi (Tumanov, 2007) is tardigrade previously only recorded from the Svalbard archipelago. This species’ original description was based on two individuals with destroyed claws on the fourth pair of legs and a lack of complete morphometric data for buccal tube and claws. In this paper, we present a re-description of T. voronkovi, supplementing the original description using the original paratype and additional material from Svalbard: Spitsbergen, Nordaustlandet and Edgeøya. This species is characterised by two macroplacoids and a microplacoid, claws of Tenuibiotus type, dentate lunules under claw IV, and faint granulation on legs I–III and strong granulation on the legs IV. We include a new morphological description with microphotographs, morphometric, and molecular data (including: mitochondrial cytochrome c oxidase subunit I (COI), internal transcribed spacers (ITS1–5.8S rDNA–ITS2), and nuclear ribosome subunits 28S rRNA and 18S rRNA). These are the first published molecular data for the genus Tenuibiotus Pilato and Lisi, 2011, analysis of which indicated an affiliation of Tenuibiotus to the family Macrobiotidae. We found no differences in body size between individuals from different islands (Nordaustlandet and Edgeøya), but did observe variability in the eggs. After revision of the literature and the published figures, we concluded that Dastych’s (1985) report of T. willardi (Pilato, 1976) from Svalbard, was actually T. voronkovi, which has the greater distribution in Svalbard, and other Arctic locations, than previously believed. 

scholarly journals A re-examination of the molecular systematics and phylogeography of taxa of the Peromyscus aztecus species group, with comments on the distribution of P. winkelmanni

Therya ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 331-346
Author(s):  
C. William Kilpatrick ◽  
Nelish Pradhan ◽  
Ryan W Norris
Keyword(s):  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Molecular Study ◽  
Molecular Data ◽  
Species Group ◽  
Cytb Sequence ◽  
Voucher Specimen ◽  
Cranial Measurements ◽  
Mitochondrial Cytochrome B ◽  
Isthmus Of Tehuantepec

The objectives of this study are to examine the available molecular data from the mitochondrial cytochrome-b gene (Cytb) and a concatenated dataset with this gene and two nuclear introns (Adh-1-I2 and Fgb-I7) to reexamine the systematic and phylogeographic conclusions reached by Sullivan et al. (1997) concerning the Peromyscus aztecus species group. The divergence of samples of P. aztecus oaxacensis across the Isthmus of Tehuantepec are further examined and taxonomic revisions are suggested. In addition, this study reviews the sources of data that lead to the conclusion that P. winkelmanni occurred in the Sierra Madre del Sur in Guerrero including a morphometric examination of a reported voucher. Bayesian and maximum likelihood analyses were conducted on a dataset of 31 Cytb sequences of all taxa in the P. aztecus group except for P. a. cordillerae and a concatenated dataset including five individuals of this group. Representative taxa of the P. boylii, P. mexicanus, and P. truei groups were included in both analyses. Body and cranial measurements of the voucher of the P. winkelmanni from Guerrero from which a Cytb sequence is reported to have been obtained was compared with measurements from specimens taken from the vicinity of Dos Aguas, Michoacán, including the type locality. We identified seven instances involving problematic identifications in GenBank. Once these issues were addressed, well-supported monophyletic sister clades of the P. aztecus and P. boylii species groups were recovered from phylogenetic analyses of Cytb sequences (Fig 1). Phylogenetic analyses of the Cytb and the concatenated datasets recover similar topologies that support the relationships of taxa of the aztecus group proposed by an earlier molecular study. Populations of P. a. oaxacensis southeast of the Isthmus of Tehuantepec represent a distinct species. Measurements of the voucher from Guerrero identified as the source of a P. winkelmanni Cytb sequence are smaller than P. winkelmanni for several characters. The divergent populations of P. a. oaxacensis from southeast of the Isthmus of Tehuantepec are recognized as two subspecies of P. cordillerae, P. c. cordillerae and P. c. hondurensis, whereas those northwest of the Isthmus are retained as P. a. oaxacensis. The lack of genetic divergence observed between P. a. evides and P. a. oaxacensis questions whether these two taxa should continue to be recognized as separate subspecies. Northern and southern populations of P. spicilegus demonstrate moderate divergence and additional examination of morphological and molecular differentiation within this taxon is warranted. The distribution of P. winkelmanni should be restricted to the vicinity of Dos Aguas, Michoacán, due to the lack of a voucher specimen that would confirm its reported occurrence in Guerrero.

scholarly journals The genus Parasola in Pakistan with the description of two new species

MycoKeys ◽  
2018 ◽  
Vol 30 ◽  
pp. 41-60 ◽  
Author(s):  
Shah Hussain ◽  
Habib Ahma ◽  
Sadiq Ullah ◽  
Najam-Ul-Sehar Afshan ◽  
Donald H. Pfister ◽  
...  
Keyword(s):  
New Species ◽  
Elongation Factor ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Side View ◽  
Germ Pore ◽  
5.8S Rdna ◽  
Rdna Its ◽  
Two New Species ◽  
Morphological And Molecular Data

Parasola is a genus of small, veil-less coprinoid mushrooms in the family Psathyrellaceae (Agaricales). The genus is not well documented in Asia, specifically in Pakistan. In this study we describe two new species Parasolaglabra and P.pseudolactea from Pakistan, based on morphological and molecular data. Phylogeny based on three DNA regions: nuc rDNA region encompassing the internal transcribed spacers 1 and 2 along with the 5.8S rDNA (ITS), nuc 28S rDNA D1-D2 domains (28S) and translation elongation factor 1α gene (TEF1α) show that the new taxa are clustered in a clade formed by the members of section Parasola of genus Parasola. Parasolaglabra with grayish pileus, slightly depressed pileal disc, lamellae separated from the stipe by pseudocollarium, basidiospores 14.5–16.5 × 9.5–11.5 × 8.0–10.5 µm, in front view broadly ovoid to oblong, some with rhomboidal outline, in side view ellipsoid, with eccentric germ-pore of 1.5 µm diameter. Parasolapseudolactea with yellowish brown to dull brown pileus, disc indistinctly umbonate, lamellae free, pseudocollarium absent, basidiospores 13.5–14.5 × 10.5–12.0 × 9.5–10.5 µm, in face view rounded triangular to heart shaped, rarely ovoid to subglobose, in side view ellipsoid to oblong, with eccentric germ-pore of 1.5 µm diam. In addition to these new species, P.auricoma and P.lilatincta were also studied. Morphological descriptions for the new species and comparison with known Parasola species are provided. Our observations highlight the diversity of Parasola in northern Pakistan and further document the need for additional systematic focus on the region’s fungi.

Aspergillus affinis sp. nov., a novel ochratoxin A-producing Aspergillus species (section Circumdati) isolated from decomposing leaves

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 1007-1015 ◽  
Author(s):  
Domenico Davolos ◽  
Anna Maria Persiani ◽  
Biancamaria Pietrangeli ◽  
Alessandra Ricelli ◽  
Oriana Maggi
Keyword(s):  
Ochratoxin A ◽  
Dna Sequences ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Chain Gene ◽  
Protein Coding ◽  
5.8S Rdna ◽  
Rdna Gene ◽  
Molecular Phylogenetic

Two ochratoxin A (OTA)-producing Aspergillus isolates, recently collected from submerged riparian decomposing leaves in Italy, were found to have a similar morphology to Aspergillus cretensis (subgenus Circumdati, section Circumdati). However, marked differences emerged between these two novel isolates and A. cretensis as the former displayed different colony features and had larger vesicles, metulae, phialides and conidia, as well as a distinct sclerotial form and size. In order to determine the taxonomic status and to infer the evolutionary relationships of these two morphologically identical isolates, a molecular phylogenetic analysis was performed on all the officially recognized lineages in the section Circumdati. The DNA sequences and the deduced amino acid residues from the nuclear loci were analysed. Both rRNA and protein coding genes were assessed, which are widely used to differentiate taxa belonging to genus Aspergillus at various evolutionary levels. The 5.8S rDNA gene and internal transcribed spacers (ITS), the D1/D2 domains of the 28S rDNA gene, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and then sequenced. The analysis of the rRNA regions and of the benA and cmd sequence data indicated that the two isogenic isolates belonged to a genetically distinct OTA-producing species of the genus Aspergillus. The isolates are proposed as representing a novel species, Aspergillus affinis sp. nov., with the type strain ATCC MYA-4773T ( = CBS 129190 = 417). Phylogenetically, A. affinis sp. nov. appeared to be very closely related to A. cretensis, from which it could be distinguished by means of a morphological trait analysis.

A redefinition of the genus Troglocharinus Reitter, 1908, with description of new species (Coleoptera, Leiodidae, Cholevinae, Leptodirini)

Zootaxa ◽  
2021 ◽  
Vol 4926 (2) ◽  
pp. 151-188
Author(s):  
JAVIER FRESNEDA ◽  
VALERIA RIZZO ◽  
JORDI COMAS ◽  
IGNACIO RIBERA
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Valid Species ◽  
Distribution Area ◽  
Undescribed Species ◽  
Separate Species ◽  
Male And Female ◽  
New Material

We redefine the genus Troglocharinus Reitter, 1908 based on a phylogenetic analysis with a combination of mitochondrial and molecular data. We recovered the current Speonomites mengeli (Jeannel, 1910) and S. mercedesi (Zariquiey, 1922) as valid, separate species within the Troglocharinus clade, not directly related to Speonomites Jeannel, 1910, a finding corroborated by a detailed study of the male and female genitalia. In consequence, we reinstate Speonomus mercedesi Zariquiey, 1922 stat. nov. as a valid species, transfer both of them to the genus Troglocharinus, T. mengeli (Jeannel, 1910) comb. nov. and T. mercedesi (Zariquiey, 1922) comb. nov., and redescribe the genus. The study of new material from the distribution area of the former S. mengeli revealed the presence of two undescribed species, T. sendrai sp. nov. and T. fadriquei sp. nov., which we describe herein. We designate the lectotype of Speonomus vinyasi Escolà, 1971 to fix its identity, as among its syntypes there are two different species. In agreement with the results of the phylogenetic analyses we establish the synonymy between the genus Speonomites and Pallaresiella Fresneda, 1998 syn. nv. 

The Akodon boliviensis species group (Rodentia: Cricetidae: Sigmodontinae) in Argentina: species limits and distribution, with the description of a new entity

Zootaxa ◽  
2010 ◽  
Vol 2409 (1) ◽  
pp. 1 ◽  
Author(s):  
J. PABLO JAYAT ◽  
PABLO E. ORTIZ ◽  
JORGE SALAZAR-BRAVO ◽  
ULYSES F. J. PARDIÑAS ◽  
GUILLERMO D’ELÍA
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Species Group ◽  
Species Limits ◽  
Northwestern Argentina ◽  
Semiarid Environments ◽  
Central Argentina ◽  
The Andes ◽  
Mountain System ◽  
Living Species

Akodon, with about 42 living species, is the most diverse genus of the subfamily Sigmodontinae. The Akodon boliviensis species group includes small-bodied, morphologically similar forms inhabiting Altiplano grasslands and grassland/forest ecotones of the eastern slope of the Andes, from central Peru to central Argentina. Northwestern Argentina contains the largest diversity of species of the group; the taxonomic treatment of these species has been based largely on unsupported and some weakly based opinions as underscored by recurrent changes. Based on morphologic and molecular data we assessed species limits among Argentinean populations of the Akodon boliviensis species group. We conclude that four species of the A. boliviensis species group inhabit northwestern Argentina. These are: A. boliviensis; A. caenosus (under which we synonymyze A. aliquantulus); A. spegazzinii (of which the nominal forms alterus, leucolimnaeus, and tucumanensis are junior synonyms); and A. sylvanus. Additionally, we described here a new species of the A. boliviensis species group, Akodon polopi, which inhabits central Argentina. This is the only species of the A. boliviensis species group inhabiting the Sierras Grandes range (ca. 2000 m), mountain system of medium height, isolated (ca., 600 km) from the main Andean chain by low elevation arid and semiarid environments. Additionally, our phylogenetic analyses suggests that the Akodon varius species group is polyphyletic.

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