Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

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The use of large and small subunits of ribosomal DNA in evaluating phylogenetic relationships between species ofCornudiscoidesKulkarni, 1969 (Monogenoidea: Dactylogyridae) from India

Journal of Helminthology ◽

10.1017/s0022149x16000134 ◽

2016 ◽

Vol 91 (2) ◽

pp. 206-214 ◽

Cited By ~ 2

Author(s):

J. Verma ◽

N. Agrawal ◽

A.K. Verma

Keyword(s):

Ribosomal Dna ◽

18S Rrna ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

28S Rrna ◽

Ganges River ◽

Mystus Vittatus ◽

Ribosomal Subunits ◽

18S Rrna Genes ◽

High Degree

AbstractTwo partial regions of ribosomal DNA (28S and 18S) were used to evaluate genetic variations among the species ofCornudiscoides,viz.C. proximus, C. geminusandC. agarwali, all parasites ofMystus vittatus(Bagridae) from River Gomati, Ganges River basin, India. Our findings demonstrated that both the large and small ribosomal subunits are useful for species identification and genetic characterization of parasites, leading to resolution of inter/intra-relationships at generic and specific levels. The secondary structures of all three species for 28S and 18S rRNA genes contained exact pattern matches (EMPs) displaying the high degree of similarity among them. The phylogenetic analyses within the members of Dactylogyridae demonstrated that species ofCornudiscoidescluster together for 28S rRNA and 18S rRNA genes.

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Morphological and molecular characterisation of Helicotylenchus ciceri n. sp. and H. scoticus Boag & Jairajpuri, 1985 (Nematoda: Hoplolaimidae) from Iran

Nematology ◽

10.1163/15685411-00003326 ◽

2020 ◽

Vol 22 (6) ◽

pp. 611-626

Author(s):

Fariba Mohammadi Zameleh ◽

Akbar Karegar ◽

Reza Ghaderi ◽

Abbas Mokaram Hesar

Keyword(s):

New Species ◽

Excretory Pore ◽

18S Rrna ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

28S Rrna ◽

Molecular Characterisation ◽

Closely Related Species ◽

Partial 18S ◽

Molecular Characters

Summary Helicotylenchus ciceri n. sp. and H. scoticus are described and illustrated based on morphological, morphometric and molecular characters. The new species is characterised by a conical and truncated lip region with five or six distinct annuli, stylet 32-37 μm long with anteriorly concave knobs, secretory-excretory pore posterior to the pharyngo-intestinal valve, dorsally convex-conoid tail with a terminal projection, phasmids 14 (7-20) annuli anterior to the level of anus, empty spermatheca and absence of males. Intraspecific variation of 16 populations of H. scoticus, collected from chickpea and lentil fields in Kermanshah province, western Iran, is discussed. The results of the phylogenetic analyses based on the sequences of the partial 18S rRNA, D2-D3 expansion segments of 28S rRNA and ITS rRNA genes are provided for the studied species, confirming their differences from each other and determining the position of them and their relationships with closely related species.

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Genetic diversity in the Alpine flatworm <i>Crenobia alpina</i>

Web Ecology ◽

10.5194/we-17-29-2017 ◽

2017 ◽

Vol 17 (2) ◽

pp. 29-35 ◽

Cited By ~ 1

Author(s):

Martin Brändle ◽

Jan Sauer ◽

Lars Opgenoorth ◽

Roland Brandl

Keyword(s):

18S Rrna ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

Dispersal Ability ◽

European Alps ◽

Habitat Specificity ◽

Limited Dispersal ◽

The Alps ◽

18S Rrna Genes ◽

Species Speciation

Abstract. The freshwater flatworm Crenobia alpina (Platyhelminthes, Tricladida, Planariidae) lives almost exclusively in cold springs and crenal streams and possesses only limited dispersal ability. In this study fragments of the COI and 18S rRNA genes were used to estimate genetic divergences among 37 C. alpina populations from the European Alps. Phylogenetic analyses revealed five geographically and genetically distinct groups and at least 10 distinct lineages of C. alpina across the European Alps. Our study suggests that C. alpina represents a complex of numerous cryptic species. Speciation (allopatric and/or sympatric) may have been facilitated by the orogenetic activity of the Alps and the high habitat specificity.

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First confirmation of the shell-boring oyster parasite Polydora websteri (Polychaeta: Spionidae) in Washington State, USA

10.7287/peerj.preprints.27621v2 ◽

2019 ◽

Author(s):

Julieta Martinelli ◽

Heather Lopes ◽

Lorenz Hauser ◽

Isadora Jimenez-Hidalgo ◽

Teri L King ◽

...

Keyword(s):

18S Rrna ◽

Puget Sound ◽

Washington State ◽

Species Level ◽

Rrna Genes ◽

Mitochondrial Cytochrome ◽

Cytochrome C Oxidase I ◽

Pacific Oysters ◽

Oyster Aquaculture ◽

18S Rrna Genes

Invasions by the spionid polychaete Polydora websteri have resulted in the collapse of oyster aquaculture industries in Australia, New Zealand, and Hawaii. These worms burrow into the shells of bivalves, creating unsightly mud blisters that are unappealing to consumers and, when nicked during shucking, release mud and detritus that can foul oyster meats. Recent sightings of mud blisters on the shells of Pacific oysters (Crassostrea gigas) in Puget Sound, Washington, suggest a new spionid polychaete invasion. To determine the identity of the polychaete causing these mud blisters, we obtained Pacific oysters from two locations in Puget Sound and examined them for blisters and burrows associated with spionid infection. We then extracted polychaetes and sequenced mitochondrial (cytochrome c oxidase I [COI]) and nuclear (18S rRNA) genes to obtain species-level identifications for a subset of these worms. Our data confirm that P. websteri is present in mud blisters of Puget Sound oysters, constituting the first confirmed record of this species in Washington State. The presence of non-native P. websteri could threaten the sustainability of oyster aquaculture in Washington, which currently produces more shellfish than any other US state.

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A new amphibious species of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae) from the Ryukyu Archipelago and Taiwan

Zootaxa ◽

10.11646/zootaxa.4952.3.3 ◽

2021 ◽

Vol 4952 (3) ◽

pp. 465-494

Author(s):

SHO TSUKAMOTO ◽

SHIMPEI F. HIRUTA ◽

KATSUYUKI EGUCHI ◽

JHIH-RONG LIAO ◽

SATOSHI SHIMANO

Keyword(s):

Phylogenetic Analyses ◽

Rrna Genes ◽

Valid Species ◽

28S Rrna ◽

Ryukyu Archipelago ◽

Morphological Examination ◽

Mitochondrial Coi ◽

Molecular Phylogenetic ◽

East And Southeast Asia ◽

18S Rrna Genes

In Japan and Taiwan, five valid species of the genus Scolopendra Linnaeus, 1758 have been described: S. morsitans Linnaeus, 1758, S. subspinipes Leach, 1816, S. mutilans Koch, 1878, S. japonica Koch, 1878, and S. multidens Newport, 1844. Recently, an undetermined species was found in the Ryukyu Archipelago and Taiwan. Using molecular phylogenetic analyses with mitochondrial COI and 16S rRNA and nuclear 28S rRNA and 18S rRNA genes as well as conventional morphological examination, we successfully discriminated this sixth species as an independent lineage from S. subspinipes, S. mutilans, and other named congeners from East and Southeast Asia. Therefore, the species was described as S. alcyona Tsukamoto & Shimano, sp. nov. Several situational evidences suggest that this species prefers streamside environments and exhibits amphibious behavior.

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An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63081-0 ◽

2004 ◽

Vol 54 (5) ◽

pp. 1861-1875 ◽

Cited By ~ 98

Author(s):

David Moreira ◽

Purificación López-García ◽

Keith Vickerman

Keyword(s):

18S Rrna ◽

Phylogenetic Analyses ◽

Pcr Amplification ◽

Rrna Genes ◽

Close Relative ◽

New Classification ◽

Direct Pcr ◽

Scientific Attention ◽

18S Rrna Genes

Given their ecological and medical importance, the classification of the kinetoplastid protists (class Kinetoplastea) has attracted much scientific attention for a long time. Morphology-based taxonomic schemes distinguished two major kinetoplastid groups: the strictly parasitic, uniflagellate trypanosomatids and the biflagellate bodonids. Molecular phylogenetic analyses based on 18S rRNA sequence comparison suggested that the trypanosomatids emerged from within the bodonids. However, these analyses revealed a huge evolutionary distance between the kinetoplastids and their closest relatives (euglenids and diplonemids) that makes very difficult the correct inference of the phylogenetic relationships between the different kinetoplastid groups. Using direct PCR amplification of 18S rRNA genes from hydrothermal vent samples, several new kinetoplastid-like sequences have been reported recently. Three of them emerge robustly at the base of the kinetoplastids, breaking the long branch leading to the euglenids and diplonemids. One of these sequences belongs to a close relative of Ichthyobodo necator (a fish parasite) and of the ‘Perkinsiella amoebae’-like endosymbiont of Neoparamoeba spp. amoebae. The authors have studied the reliability of their basal position and used all these slow-evolving basal-emerging sequences as a close outgroup to analyse the phylogeny of the apical kinetoplastids. They thus find a much more stable and resolved kinetoplastid phylogeny, which supports the monophyly of groups that very often emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences. A new classification of the class Kinetoplastea is proposed based on the results of the phylogenetic analysis presented. This class is now subdivided into two new subclasses, Prokinetoplastina (accommodating the basal species I. necator and ‘Perkinsiella amoebae’) and Metakinetoplastina (containing the Trypanosomatida together with three additional new orders: Eubodonida, Parabodonida and Neobodonida). The classification of the species formerly included in the genus Bodo is also revised, with the amendment of this genus and the genus Parabodo and the creation of a new genus, Neobodo.

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A new species of the genus Pseudocrangonyx (Crustacea: Amphipoda: Pseudocrangonyctidae) from Simbok Cave, Korea

Zootaxa ◽

10.11646/zootaxa.4731.3.2 ◽

2020 ◽

Vol 4731 (3) ◽

pp. 321-334 ◽

Cited By ~ 4

Author(s):

CHI-WOO LEE ◽

KO TOMIKAWA ◽

TAKAFUMI NAKANO ◽

GI-SIK MIN

Keyword(s):

Phylogenetic Analyses ◽

Histone H3 ◽

16S Rrna Genes ◽

Rrna Genes ◽

28S Rrna ◽

Mitochondrial Cytochrome ◽

Molecular Phylogenetic ◽

Subterranean Species ◽

A New Species ◽

Honshu Island

A new subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyx joolaei, is described from the groundwater of a cave in South Korea. Pseudocrangonyx joolaei sp. nov. can be distinguished from its congeners by the number of sternal gills as well as a combination of the antennal sinus, the accessory flagellum of antenna 1, and the terminal article of uropod 3. Molecular phylogenetic analyses based on nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed that P. joolaei sp. nov. formed a clade with P. akatsukai Tomikawa & Nakano, 2018 that inhabits limestone caves in the western Honshu island, Japan.

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First confirmation of the shell-boring oyster parasite Polydora websteri (Polychaeta: Spionidae) in Washington State, USA

10.7287/peerj.preprints.27621v1 ◽

2019 ◽

Author(s):

Heather Lopes ◽

Julieta Martinelli ◽

Lorenz Hauser ◽

Isadora Jimenez-Hidalgo ◽

Teri L King ◽

...

Keyword(s):

18S Rrna ◽

Puget Sound ◽

Washington State ◽

Species Level ◽

Rrna Genes ◽

Mitochondrial Cytochrome ◽

Cytochrome C Oxidase I ◽

Pacific Oysters ◽

Oyster Aquaculture ◽

18S Rrna Genes

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Description of Rotylenchus arasbaranensis n. sp. from Iran with discussion on the taxonomic status of Plesiorotylenchus Vovlas, Castillo & Lamberti, 1993 (Nematoda: Hoplolaimidae)

Nematology ◽

10.1163/15685411-00002827 ◽

2014 ◽

Vol 16 (9) ◽

pp. 1019-1045 ◽

Cited By ~ 5

Author(s):

Mohammad Reza Atighi ◽

Ebrahim Pourjam ◽

Razieh Ghaemi ◽

Majid Pedram ◽

Gracia Liébanas ◽

...

Keyword(s):

18S Rrna ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Original Description ◽

Molecular Data ◽

Rrna Genes ◽

Molecular Studies ◽

18S Rrna Genes ◽

First Time ◽

Partial 18S

Rotylenchus arasbaranensis n. sp., a new monosexual species is described and illustrated based on morphological, morphometric and molecular studies. The new species is characterised by having an offset and hemispherical lip region with 5-6 annuli, 32-36 μm long stylet, vulva located at 43.9-59.2% with a single epiptygma and rounded tail, rarely bilobed, with 6-8 annuli. The species R. striaticeps and the male of R. buxophilus are reported for the first time from Iran and R. fragaricus is reported and studied for the second time after its original description. The results of the phylogenetic analyses based on the sequences of the D2-D3 expansion region of the 28S, ITS1-rRNA and the partial 18S rRNA genes were provided for the studied species, confirming their differences from each other and determining the position of them and their relationships with closely related taxa. Also, the validity of Plesiorotylenchus is discussed on the basis of molecular data and its synonymisation (with only one sequence) with Rotylenchus is accepted.

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Phylogenetic analysis using rDNA reveals polyphyly of Oplophoridae (Decapoda:Caridea)

Invertebrate Systematics ◽

10.1071/is09049 ◽

2010 ◽

Vol 24 (2) ◽

pp. 172 ◽

Cited By ~ 15

Author(s):

Tin-Yam Chan ◽

Ho Chee Lei ◽

Chi Pang Li ◽

Ka Hou Chu

Keyword(s):

Phylogenetic Analysis ◽

18S Rrna ◽

Morphological Characters ◽

The Other ◽

Rrna Genes ◽

Deep Channel ◽

The Family ◽

Molecular Phylogenetic ◽

18S Rrna Genes ◽

Molar Process

Molecular phylogenetic analysis on nine of the ten genera in the caridean family Oplophoridae Dana, 1852, as well as 14 other caridean families using mitochondrial 16S and nuclear 18S rRNA genes, does not support the monophyletic status of Oplophoridae. Two disparate groups of oplophorids are revealed, with different morphological characters and ecology. It is proposed that the family Oplophoridae is restricted to the three genera Oplophorus, Systellaspis and Janicella. These three genera tend to be distributed in shallower water than the other oplophorid genera, and can also be distinguished from them by certain morphological characters. They have a thicker integument, superficial cuticular photophores and larger eyes, and the molar process of their mandibles is greatly reduced or bears a deep channel. The family Acanthephyridae Bate, 1888 is resurrected for the other seven genera, which are generally distributed in deeper water and are characterised by red soft integument, no cuticular photophores, smaller eyes and well-developed molar process of the mandibles without a deep channel. The relationships between these two families and other caridean families could not be clearly resolved in this study.

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