Clarification of the systematic position ofCercariaeum crassumWesenberg-Lund, 1934 (Digenea), based on karyological analysis and DNA sequences

2011 ◽  
Vol 86 (3) ◽  
pp. 293-301 ◽  
Author(s):  
R. Petkevičiūtė ◽  
V. Stunžėnas ◽  
G. Stanevičiūtė
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Developmental Stages ◽  
Sequence Divergence ◽  
Sister Group ◽  
Systematic Position ◽  
Life Cycles ◽  
Significant Information ◽  
Rdna Sequences ◽  
Species Specific

AbstractChromosome set and rDNA sequences of the larval digeneanCercariaeum crassumwere analysed in order to clarify its systematic position and possible adult form. Parasites were obtained from the sphaeriid bivalvePisidium amnicum, collected in Lithuanian and Finnish rivers. The karyotype is shown to consist of five pairs (2n = 10) of large, up to 14 μm, chromosomes. Complement, composed of a low diploid number of exclusively bi-armed elements, presumably arose through Robertsonian fusions of acrocentric chromosomes. Consistent with a Robertsonian-derived karyotype, one or two small, metacentric, mitotically stable B chromosomes were detected in the cells of parthenitae isolated from some host individuals. A phylogenetic analysis using rDNA internal transcribed spacer 2 (ITS2) and 28S sequences corroborates the allocation ofC. crassumto the family Allocreadiidae. In neighbour-joining and maximum parsimony phylogenetic treesC. crassumclusters into one clade withAllocreadiumspp., and is the closest sister group in relation toA. isoporum; the level of rDNA sequence divergence between them (2.67% for ITS2 and 1.16% for 28S) is consistent with the level expected for intrageneric variation. The present study adds significant information to a database for establishing species-specific characters for confident characterization of different developmental stages of allocreadiid species, clarification of their life cycles and evaluation of intra- and interspecific variability.

Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3423 (1) ◽  
pp. 61 ◽  
Author(s):  
JERZY A. LIS ◽  
PAWEŁ LIS ◽  
DARIUSZ J. ZIAJA ◽  
ANNA KOCOREK
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Sister Group ◽  
Systematic Position ◽  
Bayesian Phylogenetic Analysis ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Affinity ◽  
The Moment

Mitochondrial 12S and 16S rDNA sequences of five species of Dinidoridae Stål, 1868, a largely Paleotropical family, and 16 other shield bugs (Pentatomoidea) were studied. This was the first molecular examination of the systematic position of this family within the superfamily Pentatomoidea using more than a single dinidorid species. Phylogenetic trees obtained from the Bayesian inference of 12S and 16S sequences of these mitochondrial DNA, identified Dinidoridae as the monophylum and a sister group to the Tessaratomidae. Moreover, results of the study suggested a close molecular affinity of the genus Eumenotes to representatives of the subfamily Dinidorinae, which contradicts all previous morphological analyses that placed it within the subfamily Megymeninae. We suggest restoring taxonomic status of the tribe Eumenotini and removing it from the synonymy of Megymenini, leaving the genus with no subfamilial assignment for the moment.

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.

Molecular characterisation of some species of Mylonchulus (Nematoda: Mononchida) from Japan and comments on the status of Paramylonchulus and Pakmylonchulus

Nematology ◽  
2009 ◽  
Vol 11 (3) ◽  
pp. 337-342 ◽  
Author(s):  
Masaaki Araki ◽  
Wasim Ahmad ◽  
Majid Olia ◽  
Nobuhiro Minaka
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Preliminary Investigation ◽  
Sister Group ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequences ◽  
The Status ◽  
Molecular Relationships ◽  
The Relationship

AbstractComparative analyses of different regions of ribosomal DNA have become a popular tool in understanding the relationship among different species and genera and nematodes are no exception to this. In this study, molecular relationships were inferred from a nearly complete small subunit (SSU) of total 16 OTUs for five species of Mylonchulus, Paramylonchulus and Pakmylonchulus collected from various parts of Japan with two out-group taxa (Mononchus aquaticus and Clarkus papillatus) to examine the relationship among these species. Out of 1685 bp SSU rDNA sequences, phylogenetic trees using distance (NJ), parsimony and likelihood algorithms were performed. Obtained tree topologies were stable across algorithms and sequence data show that populations of the same species clustered together and four out of five species (M. brachyuris, M. hawaiiensis, M. oceanicus, M. sigmaturus) formed a monophyletic assemblage while M. mulveyi formed a sister group. Populations of species lacking subventral teeth but with a double gonad (M. oceanicus) stand with other Mylonchulus species, thereby confirming the synonymy of Pakmylonchulus, while populations with a narrow buccal cavity with few rows of denticles, no subventral teeth and a single prodelphic gonad (M. mulveyi = Paramylonchulus mulveyi) support to some extent the validity of the genus Paramylonchulus. Though a preliminary investigation, it is the first report on molecular relationships in Mylonchulus, probably a paraphyletic genus. Our results suggest that SSU rDNA sequence data are useful in understanding the relationship between genera and species.

Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis

2005 ◽  
Vol 54 (11) ◽  
pp. 1031-1035 ◽  
Author(s):  
Niclas Grahn ◽  
Mounira Hmani-Aifa ◽  
Karin Fransén ◽  
Peter Söderkvist ◽  
Hans-Jürg Monstein
Keyword(s):  
16S Rdna ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Limited Information ◽  
Rdna Sequences ◽  
Biopsy Specimens ◽  
16S Rdna Pcr ◽  
H Pylori ◽  
Species Specific ◽  
Pyrosequencing Analysis

Seroepidemiological studies have indicated that Helicobacter pylori infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not Helicobacter species are present in CRC tissues. In this study the presence of Helicobacter DNA in 77 CRC biopsies was investigated by means of a Helicobacter species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of Helicobacter DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA sequences corresponding to H. pylori 26695 and H. pylori J99 were most commonly found. Intriguingly, one sequence belonged to Helicobacter mustelae, previously identified in ferrets. No significant correlations were found in the prevalence of Helicobacter DNA between colon and rectum tumour biopsies (P = 0.815), nor between Dukes’ classes A/B and C/D (P = 0.262). 16S rDNA PCR amplification combined with pyrosequencing analysis of 16S rDNA variable V3 regions provides a powerful molecular tool to identify Helicobacter species in human biopsy specimens.

scholarly journals Annonaceae substitution rates: a codon model perspective

2014 ◽  
Vol 36 (spe1) ◽  
pp. 108-117 ◽  
Author(s):  
Lars Willem Chatrou ◽  
Michael David Pirie ◽  
Robin Van Velzen ◽  
Freek Theodoor Bakker
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
High Ratio ◽  
Molecular Dating ◽  
Codon Model ◽  
Synonymous Substitutions ◽  
Branch Lengths

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Challenges for Diadromous Fishes in a Dynamic Global Environment

2009 ◽  
Keyword(s):  
Life Cycle ◽  
Phylogenetic Trees ◽  
Sister Group ◽  
Life Cycles ◽  
Character State ◽  
Freshwater Species ◽  
Larval Stages ◽  
Ancestral Character State ◽  
Coastal Marine ◽  
Group Relationships

<em>Abstract</em>.-We develop the view, based on life cycle differences and recently published sister group relationships, that the freshwater life cycle was the ancestral character state leading to anadromy among salmoniforms, whereas the marine life cycle was the ancestral character state leading to anadromy among osmeriforms. In contrast to most salmonid fishes, the reproductive migrations of smelts are generally characterized by brief excursions to spawn in freshwater, and larvae may spend no more than 24 h in freshwater before being transported to coastal marine or estuarine environments. We reconstructed the phylogeny of the suborder Osmeroidei to establish the phylogenetic relationships among anadromous, marine, and freshwater species of this taxon. We mapped these life cycles onto phylogenetic trees of osmeriforms and salmoniforms and applied character-reconstruction methodology based on simple parsimony and likelihood methodologies. A freshwater origin of salmonids was supported by our analyses, whereas either marine or anadromous life cycles characterized the evolution of osmeroids. The possibility that the evolution of anadromy in salmonids and osmeroids followed separate paths requires a reconsideration of some generalizations concerning anadromy. We hypothesize that anadromy in osmeroids may be first and foremost an adaptation to place embryos and the early larval stages in reproductive safe sites to maximize their survival. The evolution of exclusive freshwater species of osmeriforms has occurred via anadromy through the various processes associated with landlocking. Freshwater amphidromy in osmeroids is most likely a consequence of anadromy rather than a precursor and may be contingent upon the availability of food resources in freshwater. Finally, marine osmeroids have been derived from anadromous ancestors and are "safe-site" specialists, exploiting principally the upper intertidal zone for reproduction. We also suggest that such contrasting evolutionary pathways to anadromy may provide insight into the evolution of partial migration, observed uniquely in salmonids, and the nature and extent of population genetic structure found in the two groups of fishes.

Phylogenetic relationships in Neonectria species having Cylindrocarpon anamorphs inferred from mitochondrial ribosomal DNA sequences

2001 ◽  
Vol 79 (3) ◽  
pp. 334-340 ◽  
Author(s):  
Feky R Mantiri ◽  
Gary J Samuels ◽  
James E Rahe ◽  
Barry M Honda
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Divergence ◽  
Small Subunit ◽  
New Combinations ◽  
Rdna Sequences ◽  
Informal Groups

Mitochondrial small subunit (mtSSU) rDNA sequences elucidated phylogenetic relationships in Neonectria Wollenw. (anamorphs = Cylindrocarpon Wollenw.; Ascomycetes, Hypocreales). Twelve isolates representing seven species in five taxonomically informal groups of Neonectria were subjected to phylogenetic analysis. Fusarium inflexum R. Schneid. (teleomorph: Gibberella) and Nectria cinnabarina (Fr.) Fr. (= Nectria s.str.) were outgroups. All of the Neonectria species formed a strongly supported clade with respect to the outgroups, indicating a single ascomycete genus for the holomorphs of Cylindrocarpon. Within the Neonectria clade there were three well-supported subclades that only partially corresponded to phenotype-defined groups. DNA sequence divergence among the twelve Neonectria isolates, 2.3-7.4%, was sufficient to resolve them. The results suggest that the mtSSU rDNA region is appropriate for phylogenetic analysis of Neonectria and Cylindrocarpon. The following new combinations are proposed: Neonectria coronata, Neonectria discophora, Neonectria neomacrospora, Neonectria radicicola, Neonectria rugulosa, Neonectria veuillotiana.Key words: Ascomycetes, Hypocreales, Nectria, systematics, tree pathogens.

scholarly journals Comparative transcriptomics across nematode life cycles reveal gene expression conservation and correlated evolution in adjacent developmental stages

2020 ◽  
Author(s):  
Min R. Lu ◽  
Cheng-Kuo Lai ◽  
Ben-Yang Liao ◽  
Isheng Jason Tsai
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Nematode Species ◽  
Strongyloides Stercoralis ◽  
Life Cycles ◽  
Host Immune System ◽  
Larval Stages ◽  
Highly Correlated ◽  
Species Specific ◽  
The Relationship

AbstractNematodes are highly abundant animals with diverse habitats and lifestyles. Some are free-living while others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. Although parasitism has independently arisen multiple times over evolutionary history, common pressures of parasitism—such as adapting to the host environment, evading and subverting the host immune system, and changing environments across life cycles—have led phenotypes and developmental stages among parasites to converge. To determine the relationship between transcriptome evolution and morphological divergences among nematodes, we compared 48 transcriptomes of different developmental stages across eight nematode species. The transcriptomes were clustered broadly into embryo, larva, and adult stages, suggesting that gene expression is conserved to some extent across the entire nematode life cycle. Such patterns were partly accounted for by tissue-specific genes—such as those in oocytes and the hypodermis—being expressed at different proportions. Although nematodes typically have 3-5 larval stages, the transcriptomes for these stages were found to be highly correlated within each species, suggesting high similarity among larval stages across species. For the Caenorhabditis elegans-C. briggsae and Strongyloides stercoralis-S. venezuelensis comparisons, we found that around 50% of genes were expressed at multiple stages, whereas half of their orthologues were also expressed in multiple but different stages. Such frequent changes in expression have resulted in concerted transcriptome evolution across adjacent stages, thus generating species-specific transcriptomes over the course of nematode evolution. Our study provides a first insight into the evolution of nematode transcriptomes beyond embryonic development.

The cereal rust mite Abacarus hystrix (Acari: Eriophyoidea) is a complex of species: evidence from mitochondrial and nuclear DNA sequences

2009 ◽  
Vol 100 (3) ◽  
pp. 263-272 ◽  
Author(s):  
A. Skoracka ◽  
M. Dabert
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
28S Rdna ◽  
Host Specialization ◽  
Coi Gene ◽  
Grass Species ◽  
Data Set ◽  
Eriophyoid Mites ◽  
Region Data

AbstractThe cereal rust mite Abacarus hystrix (Nalepa), a significant pest of grasses, has been regarded as one of a few exceptions among eriophyoid mites with reference to the pattern of host plant utilization. At least 60 grass species have been recorded as its hosts. Thus, the mite has long been considered as a host generalist in which host specialization would not be likely to evolve. However, recent studies have revealed that host-associated specialization is possible in A. hystrix. Here, we aimed to discriminate between the three populations of A. hystrix associated with the different hosts (namely quackgrass, ryegrass and smooth brome) on the basis of mitochondrial (COI) and nuclear (D2 region of 28S rDNA) DNA sequences. The phylogenetic trees obtained with the maximum likelihood analysis of both COI and D2 region data sets showed that host-adapted strains of A. hystrix form distinct clades. Furthermore, on the COI nucleotide tree, the quackgrass- and brome-associated strains were internally divided each into two well-supported monophyletic clusters. The nucleotide D2 region data set tree showed that brome-associated strain is polyphyletic in origin. There is clear co-variation of DNA results with earlier morphological and ecological traits, as well as the results of crossing experiments. We showed that reproductively incompatible strains of A. hystrix exhibit more than 20% sequence divergence in the COI gene and 0.2% sequence divergence in the D2 28S rDNA. Our results did not confirm the placement of three host-associated strains of A. hystrix within one, ostensibly generalist, species.

Exploring species diversity of lissorchiid trematodes (Digenea: Lissorchiidae) associated with the gravel snail, Lithoglyphus naticoides, in European freshwaters

2020 ◽  
Vol 94 ◽  
Author(s):  
R. Petkevičiūtė ◽  
G. Stanevičiūtė ◽  
V. Stunžėnas
Keyword(s):  
Developmental Stages ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rutilus Rutilus ◽  
Life Cycles ◽  
Species Identity ◽  
Generic Level ◽  
Rdna Sequences ◽  
28S Rdna Sequence ◽  
Lithoglyphus Naticoides

Abstract Comparative analysis using complete ITS2 and partial 28S rDNA sequence data revealed that cercariaeum developing in rediae in Lithoglyphus naticoides represent two different lissorchiid species. One morphotype of cercariaeum is conspecific with adult Palaeorchis incognitus from European roach, Rutilus rutilus. The other cercariaeum is attributable to the genus Asymphylodora, but the species identity is not yet determined. We also generate the first rDNA sequences for Asymphylodora progenetica based on new collections from Bithynia tentaculata from Lithuania. Phylogenetic analyses of the newly generated sequences, together with information for other lissorchiids available on GenBank, showed that all representatives of Lissorchiidae form a strongly supported clade. Three monophyletic lineages, Asymphylodora, Palaeorchis and Lissorchis, were recognized at the generic level. Karyological analysis of the chromosome set of larval P. incognitus revealed a diploid number of 2n = 20. Its karyotype with subtelocentric chromosomes prevailing can be regarded as comparatively ‘primitive’, which is consistent with the basal position of P. incognitus in the 28S tree relative to the representatives of the genus Asymphylodora. The present study adds significant new information for establishing species-specific markers for the confident characterization of different developmental stages of lissorchiid species and clarification of their life cycles.

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