Bulinus species on Madagascar: molecular evolution, genetic markers and compatibility with Schistosoma haematobium

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. 261-275 ◽  
Author(s):  
J. R. STOTHARD ◽  
P. BRÉMOND ◽  
L. ANDRIAMARO ◽  
B. SELLIN ◽  
E. SELLIN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Population Genetic Analysis ◽  
Basal Node ◽  
Pcr Rflp ◽  
Dna Sequence Variation ◽  
Long Time ◽  
Laboratory Infection ◽  
Species Groups ◽  
Nucleotide Divergence

Of the four species of Bulinus found on Madagascar, three species: B. obtusispira, B. liratus and B. bavayi are endemic while the fourth, B. forskalii, is probably a recent introduction from the African mainland. The evolutionary relationships of these species with Bulinus species from Africa were studied by phylogenetic analysis of DNA sequence variation at two mitochondrial loci: cytochrome oxidase subunit I (COI) and large ribosomal subunit (LSU) or 16S. The observed levels of nucleotide divergence within Bulinus were substantial but may underestimate the true levels as there was evidence of ‘saturation' of transitional substitutions at both loci. A putative secondary structure model for the sequenced segment of the 16S was developed. Subsequent phylogenetic analysis using transversional changes only for both loci, showed that there were contrasting levels of divergence within the four species groups. B. obtusispira was consistently placed within the B. africanus group, appearing ancestral to this group and was closest to the basal node within Bulinus. Together with B. bavayi, the two species appear to have been isolated on Madagascar for a long time, contrasting with both B. liratus and B. forskalii that appear more recent colonisers; however, estimate of exact times of divergence is problematic. A PCR-RFLP assay was developed to enable identification and discrimination of B. obtusispira and B. liratus using discriminatory variation within the COI. To enable population genetic analysis within B. obtusispira, microsatellite markers were developed using an enrichment method and 8 primer pairs are reported. Laboratory infection experiments using Madasgacan S. haematobium from the Mahabo area showed that certain populations of B. obtusispira, B. liratus and B. bavayi were compatible.

scholarly journals ANALYSIS OF nrLSU GENE TO SUPPORT IDENTIFICATION OF FUNGUS BELONGING TO Cordyceps GENUS AND CLAVICIPITACEAE FAMILY

2018 ◽  
Vol 55 (1A) ◽  
pp. 91
Author(s):  
Vu Tien Luyen
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Agarose Gel ◽  
Large Ribosomal Subunit ◽  
Pcr Product ◽  
Sequencing Method ◽  
Clear Band ◽  
Molecular Phylogenetic ◽  
Long Time ◽  
Reference Sequences

Nucleotide sequences of the nuclear large ribosomal subunit (nrLSU) have been used in fungal systematics for a long time. nrLSU was also used in Cordyceps and related genera within the Clavicipitaceae family. A previously identified sample by morphology and ITS was used in this research to analyze the ability of nrLSU to support the identification of entomopathogenic fungi. Our results show that we successfully amplified nrLSU gene using the primer pair LR0R and LR5. The PCR product on agarose gel showed a clear band at 950 bp. Sequencing method was then adopted and proofread before molecular phylogenetic analysis was applied with reference sequences obtained from the publication of Sung et al. Once again, this analysis confirms the DL0004 specimen as Cordyceps neovolkiana. 

scholarly journals Multiple Origins of a Mitochondrial Mutation Conferring Deafness

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 771-776 ◽  
Author(s):  
Timothy P Hutchin ◽  
Gino A Cortopassi
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Ribosomal Subunit ◽  
Sensorineural Deafness ◽  
Nucleotide Substitutions ◽  
Mitochondrial Mutation ◽  
Distance Analysis ◽  
Multiple Origins ◽  
Mtdna Haplotypes ◽  
Mtdna Sequence

A point mutation (1555G) in the smaller ribosomal subunit of the mitochondrial DNA (mtDNA) has been associated with maternally inherited traits of hypersensitivity to streptomycin and sensorineural deafness in a number of families from China, Japan, Israel, and Africa. To determine whether this distribution was the result of a single or multiple mutational events, we carried out genetic distance analysis and phylogenetic analysis of 10 independent mtDNA D-loop sequences from Africa and Asia. The mtDNA sequence diversity was high (2.21%). Phylogenetic analysis assigned 1555G-bearing haplotypes at very divergent points in the human mtDNA evolutionary tree, and the 1555G mutations occur in many cases on race-specific mtDNA haplotypes, both facts are inconsistent with a recent introgression of the mutation into these races. The simplest interpretation of the available data is that there have been multiple origins of the 1555G mutation. The genetic distance among mtDNAs bearing the pathogenic 1555G mutation is much larger than among mtDNAs bearing either evolutionarily neutral or weakly deleterious nucleotide substitutions (such as the 4336G mutation). These results are consistent with the view that pathogenic mtDNA haplotypes such as 1555G arise on disparate mtDNA lineages which because of negative natural selection leave relatively few related descendants. The co-existence of the same mutation with deafness in individuals with very different nuclear and mitochondrial genetic backgrounds confirms the pathogenicity of the 1555G mutation.

Cladistic analysis of the Zethus (Zethoides) (Hymenoptera, Vespidae, Eumeninae) species groups with insights on the current subgeneric classification of Zethus Fabricius, 1804

2018 ◽  
Vol 49 (2) ◽  
pp. 103-129 ◽  
Author(s):  
Rogério Botion Lopes ◽  
Fernando Barbosa Noll
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Species Groups

Zethus is the largest genus in Eumeninae, with over 250 species. Currently, it is divided in four subgenera: Z. (Zethus), Z. (Zethusculus), Z. (Zethoides) and Z. (Madecazethus). Z. (Zethoides), with 42 species, is subdivided in eight species groups, each considered a phylogenetic unit, that were created without any phylogenetic analysis. Eighteen species of Z. (Zethoides) corresponding to different groups were examined, altogether with terminals from distinct lineages of Zethus, Zethini and Eumenini, to perform a cladistics analysis to verify the proposed divisions. Zethus (Zethoides) and all of its species groups, except for the Z. biglumis group, were monophyletic. Zethus s.s. was paraphyletic in relation to Z. (Madecazethus), Z. (Zethoides) and Ctenochilus. Z. (Zethusculus) was also retrieved paraphyletic. Despite the subgeneric incongruences, the outgroups were too poorly represented to carry a taxonomic modification. Thus, the only alteration was the inclusion of the Z. clypearis group in the Z. biglumis group.

scholarly journals Genetic identification of bovine leukaemia virus

2018 ◽  
Vol 6 (2) ◽  
pp. 314-324 ◽  
Author(s):  
Irina Donnik ◽  
Irina Donnik ◽  
Ramil Vafin ◽  
Ramil Vafin ◽  
Aram Galstyan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Research Methods ◽  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Genetic Identification ◽  
Gene Fragment ◽  
Phylogenetic Classification ◽  
Pcr Rflp

Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.

A phylogenetic revision of Calydna and relatives (Lepidoptera: Riodinidae)

2002 ◽  
Vol 33 (2) ◽  
pp. 185-237 ◽  
Author(s):  
Jason P.W. Hall
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Male And Female ◽  
Basal Clade ◽  
Two New Species ◽  
Group A ◽  
Species Groups ◽  
First Time ◽  
The Relationship ◽  
Phylogenetic Revision

AbstractA phylogenetic revision of the Neotropical riodinid genus Calydna Doubleday and relatives is presented. A phylogenetic analysis for all twenty species of Calydna using thirty-eight characters of adult morphology generated four most parsimonious cladograms. Calydna is characterised to contain eighteen species, divided here into three monophyletic species groups with the relationship caieta group + (thersander group + hiria group). A new genus Echydna Hall gen. n. is described for the most basal clade, containing chaseba Hewitson and punctata C. & R. Felder, which are transferred from Calydna (combs. n.). The taxonomy, morphology, biogeography and biology of both genera are discussed, locality data is listed and mapped, and the adults and male and female genitalia are illustrated for all species. Concealed male abdominal androconial scales, which phylogenetically unite the thersander and hiria groups, are reported for the first time outside of the tribes Symmachiini and Nymphidiini. Two new species are described, Calydna jeannea sp. n. and Calydna nicolayi sp. n., and the replacement name fissilisima is provided for the unavailable name fissilis Stichel; maculosa Bates is transferred from Calydna to Callistium Stichel (comb. n.).

scholarly journals Sarcocystis sp. parasites in the Mexican Great-tailed Grackle (Quiscalus mexicanus), Bronzed Cowbird (Molothrus aeneus), and Stripe-headed Sparrow (Aimophila ruficauda)

2014 ◽  
Vol 1 (2) ◽  
Author(s):  
Félix Domingo Sánchez-Godoy ◽  
Fernando Chávez-Maya ◽  
Adriana Méndez-Bernal ◽  
Gary García-Espinosa ◽  
Cristina Guerrero-Molina ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Transcribed Spacer ◽  
Sequence Similarity ◽  
Bird Species ◽  
The United States ◽  
Histopathological Analysis ◽  
Biological Studies ◽  
Pcr Rflp ◽  
Molothrus Aeneus ◽  
Specific Fragment

The objective of this study was to describe the morphological and ultraestructural characteristics, the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) results, the sequences and the phylogenetic analysis of a specific fragment of internal transcribed spacer 1 (ITS-1), amplified using the 25/396 primers, of the Sarcocystis sp. parasites identified in the muscles of wild great-tailed grackles, bronzed cowbirds, and stripe-headed sparrows in Mexico. Fifteen birds with sarcocystosis in their skeletal muscles were studied: 7 great-tailed grackles (Quiscalus mexicanus), 6 bronzed cowbirds (Molothrus aeneus), and 2 stripe-headed sparrows (Aimophila ruficauda). Histopathological analysis revealed thin-walled mature parasite cysts. Ultrastructurally, the cyst wall consisted of a granular layer with villar protrusions and numerous microtubules. The bradyzoites measured 4.1 × 1.6 µm, and micronemes appeared in the anterior third of the conoid. For molecular identification, PCR-RFLP was performed using sequences of a specific fragment of internal transcribed spacer 1 (ITS-1) using the primers 25/396 and Hinf I. Hind III did not cut this fragment. The sequencing results indicated a 100% similarity among the Sarcocystis parasites from the three bird species, and a BLAST search revealed 96% sequence similarity with S. neurona. The phylogenetic analysis shows that the sequences studied are topologically distant to those sequences reported for S. neurona in the United States and in South America and are not related to any group previously reported. Although our morphological and molecular analysis data provide strong evidence that S. neurona uses these bird species as intermediate hosts, future molecular studies with additional DNA fragments, combined with biological studies, will ultimately allow us to convincingly identify these parasites. This is the first report of a Sarcocystis sp. parasite in wild birds in Mexico that may be S. neurona.

Diversity of the internal transcribed spacer of rDNA in morels

1999 ◽  
Vol 45 (9) ◽  
pp. 769-778 ◽  
Author(s):  
Daniel Wipf ◽  
Anne Fribourg ◽  
Jean Charles Munch ◽  
Bernard Botton ◽  
François Buscot
Keyword(s):  
Internal Transcribed Spacer ◽  
Great Distance ◽  
Sequence Analyses ◽  
Putative Species ◽  
Intraspecific Variations ◽  
Morchella Conica ◽  
Morchella Esculenta ◽  
Pcr Rflp ◽  
Species Groups ◽  
Its1 And Its2

The internal transcribed spacer (ITS) of rDNA was analysed by PCR/RFLP in 66 strains belonging to 11 putative species of the Morchellaceae and 3 species of the Discinaceae. For certain taxa, in particular Morchella esculenta, Morchella conica, and Morchella elata, isolates from distant geographical origins were available. Nevertheless, no intraspecific variations of ITS length and restriction was noted. All genera were separated and within Morchella; four putative species could be clearly distinguished in the group of the yellow morels (sectio adnatae). In contrast, no distinction could be obtained between the compared taxa in the group of the black morels (sectio distantes). Sequence analyses of the ITS were performed in one strain of seven putative Morchella. The sequence comparison confirmed the distinctions within the yellow morels and allowed us to separate one putative taxon from the others in black morels. Only the 5,8 gene could be aligned in all sequenced samples. The ITS1 and ITS2 sectors could only be aligned within the black and yellow morels, respectively. The genetic and phylogenetic distances between black and yellow morels, respectively revealed by maximum parsimony and neighbour joining analyses, both confirm the great distance between these species groups and address the question of a separation in the genus Morchella.Key words: Morchellaceae, Discinaceae, ITS.

scholarly journals Structure of the small ribosomal subunit RNA of the pulmonate snail,Limicolaria kambeul, and phylogenetic analysis of the Metazoa

FEBS Letters ◽  
1992 ◽  
Vol 309 (2) ◽  
pp. 123-126 ◽  
Author(s):  
Birgitta Winnepennickx ◽  
Thierry Backeljau ◽  
Yves van de Peer ◽  
Rupert De Wachter
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Small Ribosomal Subunit ◽  
Pulmonate Snail

Phylogenetic analysis of the Neotropical Pristimantis leptolophus species group (Anura: Craugastoridae): molecular approach and description of a new polymorphic species 

Zootaxa ◽  
2017 ◽  
Vol 4242 (2) ◽  
pp. 313
Author(s):  
MAURICIO RIVERA-CORREA ◽  
CARLOS JIMÉNEZ-RIVILLAS ◽  
JUAN M. DAZA
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Reconstruction ◽  
Morphological Diversity ◽  
Molecular Data ◽  
Species Group ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Molecular Evidence ◽  
Polymorphic Species ◽  
Species Groups

Pristimantis, distributed throughout the New World tropics, is the most speciose vertebrate genus. Pristimantis presents an enormous morphological diversity and is currently divided into several demonstrably non-monophyletic phenetic species groups. With the purpose of increasing our understanding of Pristimantis systematics, we present the first phylogenetic analysis using molecular evidence to test the monophyly and infer evolutionary relationships within the Pristimantis leptolophus group, an endemic group of frogs from the highlands of the Colombian Andes. Our phylogenetic reconstruction recovers the group as monophyletic with high support, indicating general concordance between molecular data and morphological data. In addition, we describe a new polymorphic species lacking conspicuous tubercles, a regular attribute among species of the P. leptolophus species group and endemic from the Páramo de Sonsón complex (Antioquia, Colombia). The phylogenetic position of the new species is inferred and other systematic implications in the light of our results are discussed. 

The placement of the spider genus Periegops and the phylogeny of Scytodoidea (Araneae: Araneomorphae)

Zootaxa ◽  
2012 ◽  
Vol 3312 (1) ◽  
pp. 1 ◽  
Author(s):  
FACUNDO M. LABARQUE ◽  
MARTÍN J. RAMÍREZ
Keyword(s):  
Phylogenetic Analysis ◽  
Sister Group ◽  
Median Lobe ◽  
Posterior Median ◽  
The Third ◽  
The Family ◽  
Long Time

The relationships of Scytodoidea, including the families Drymusidae, Periegopidae, Scytodidae and Sicariidae, have been con-tentious for a long time. Here we present a reviewed phylogenetic analysis of scytodoid spiders, emphasizing Periegops, theonly genus in the family Periegopidae. In our analysis the Scytodoidea are united by the fusion of the third abdominal entapo-physes into a median lobe, the presence of female palpal femoral thorns and associated cheliceral stridulatory ridges, a mem-branous lobe on the cheliceral promargin, and the loss of minor ampullate gland spigots. A basal split within Scytodoideadefines two monophyletic groups: Sicariidae and a group formed by Scytodidae as the sister group of Periegopidae plus Dry-musidae, all united by having bipectinate prolateral claws on tarsi I–II, one major ampullate spigot accompanied by a nubbin,and the posterior median spinnerets with a mesal field of spicules. Periegops is the sister group of Drymusidae, united by the regain of promarginal cheliceral teeth and a triangular cheliceral lamina, which is continuous with the paturon margin.

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