scholarly journals Phylogeny of certain members of Hyrcanus group (Diptera: Culicidae) in China based on mitochondrial genome fragments

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Hui-Min Zhu ◽  
Shu-Han Luo ◽  
Man Gao ◽  
Feng Tao ◽  
Jing-Peng Gao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Genetic Distances ◽  
Malaria Vectors ◽  
Mitochondrial Genomes ◽  
Neighbor Joining ◽  
Minimum Evolution ◽  
Data Sequence ◽  
Rdna Its2 ◽  
Relationship Of

Abstract Background Species of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear. Methods Five members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood. Findings Four parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)). Conclusions The An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.

Molecular identification of common hard ticks (Acari: Ixodidae) in Xinjiang, China

Zootaxa ◽  
2021 ◽  
Vol 4950 (1) ◽  
pp. 46-60
Author(s):  
QIGUO WANG ◽  
YUJIANG ZHANG ◽  
SURONG SUN ◽  
TAO LUO ◽  
WENTING MOU ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Rhipicephalus Sanguineus ◽  
Genetic Distances ◽  
Neighbor Joining ◽  
Minimum Evolution ◽  
Rdna Genes ◽  
Hard Ticks ◽  
Distance Model ◽  
Two Parameter

We provide data on the cytochrome c oxidase subunit I (COI) and 16S rDNA genes for eight species of common hard ticks in Xinjiang: Dermacentor montanus, D. niveus, Haemaphysalis sulcate, Hyalomma asiaticum asiaticum, Hya. detritum, Hya. scupense, Rhipicephalus sanguineus and R. pumilio. Genetic distances, calculated based on the Kimura two-parameter (K2P) distance model, found the same trend of intraspecies level≤interspecies level<intragenus level. Phylogenetic trees, constructed with the neighbor-joining (NJ) and minimum-evolution (ME) methods, demonstrated that each species clustered into separate clades, thus confirming the usefulness of CO1 and 16S rDNA genes for tick species identification. The genera Dermacentor, Haemaphysalis and Rhipicephalus were all recovered in the phylogenetic analysis, as was the subfamily Rhipicephalinae, but a monophyletic Hyalomma was not. 

scholarly journals Utility of Complete Mitochondrial Genomes in Phylogenetic Classification of the Species of Anopheles (Culicidae: Anophelinae)

2021 ◽  
Author(s):  
Taghi Ghassemi-Khademi ◽  
Mohammad Ali Oshaghi ◽  
Hassan Vatandoost ◽  
Seyed Massoud Madjdzadeh ◽  
Mohammad Amin Gorouhi
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Malaria Vectors ◽  
Mitochondrial Genomes ◽  
Phylogenetic Classification ◽  
Anopheles Mosquitoes ◽  
Blood Sucking ◽  
Complete Mitochondrial Genomes

Background: Among the blood-sucking insects, Anopheles mosquitoes have a very special position, because they transmit parasites of the genus Plasmodium, which cause malaria as one of the main vector-borne disease worldwide. The aim of this review study was to evaluate utility of complete mitochondrial genomes in phylogenetic classification of the species of Anopheles. Methods: The complete mitochondrial genome sequences belonging to 28 species of the genus Anopheles (n=32) were downloaded from NCBI. The phylogenetic trees were constructed using the ML, NJ, ME, and Bayesian inference methods. Results: In general, the results of the present survey revealed that the complete mitochondrial genomes act very accu- rately in recognition of the taxonomic and phylogenetic status of these species and provide a higher level of support than those based on individual or partial mitochondrial genes so that by using them, we can meticulously reconstruct and modify Anopheles classification. Conclusion: Understanding the taxonomic position of Anopheles, can be a very effective step in better planning for controlling these malaria vectors in the world and will improve our knowledge of their evolutionary biology.

scholarly journals Complete mitochondrial genome of Nanorana pleskei (Amphibia: Anura: Dicroglossidae) and evolutionary characteristics

2011 ◽  
Vol 57 (6) ◽  
pp. 785-805 ◽  
Author(s):  
Guiying Chen ◽  
Bin Wang ◽  
Jiongyu Liu ◽  
Feng Xie ◽  
Jianping Jiang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Tandem Duplication ◽  
Complete Mitochondrial Genome ◽  
Gene Organization ◽  
Tibet Plateau ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding

Abstract The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAMet gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the monophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were ((Gymnophiona (Caudata, Anura)). Based on the phylogenetic trees, type 1 was recognized as the ancestral type for amphibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaningful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family.

scholarly journals The mitochondrial genomes of the acoelomorph worms Paratomella rubra and Isodiametra pulchra

2017 ◽  
Author(s):  
Helen E Robertson ◽  
François Lapraz ◽  
Bernhard Egger ◽  
Maximilian J Telford ◽  
Philipp H. Schiffer
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Large Degree ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Long Branch Attraction ◽  
Protein Coding ◽  
Simple Body ◽  
Mitochondrial Sequences ◽  
Marine Worms

AbstractAcoels are small, ubiquitous, but understudied, marine worms with a very simple body plan. Their internal phylogeny is still in parts unresolved, and the position of their proposed phylum Xenacoelomorpha (Xenoturbella+Acoela) is still debated.Here we describe mitochondrial genome sequences from two acoel species: Paratomella rubra and Isodiametra pulchra. The 14,954 nucleotide-long P. rubra sequence is typical for metazoans in size and gene content. The larger I. pulchra mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome.Mitochondrial sequences for both P. rubra and I. pulchra have a unique genome organisation in comparison to other published metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap in P. rubra, with little non-coding sequence making the genome compact. Conversely, the I. pulchra mitochondrial genome has many long non-coding sequences between genes, likely driving the genome size expansion. Phylogenetic trees inferred from concatenated alignments of mitochondrial genes grouped the fast-evolving Acoela and Tunicata, almost certainly due to the systematic error of long branch attraction: a reconstruction artefact that is probably compounded by the fast substitution rate of mitochondrial genes in this taxon.

A phylogenetic approach to the Philippines endemic centipedes of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae), with the description of a new species

Zootaxa ◽  
2018 ◽  
Vol 4483 (3) ◽  
pp. 401
Author(s):  
CARLES DOMÉNECH ◽  
VICTOR M. BARBERA ◽  
EDUARDO LARRIBA
Keyword(s):  
Dna Sequences ◽  
Endemic Species ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Genetic Distances ◽  
The Philippines ◽  
Neighbor Joining ◽  
Separate Species ◽  
Additional Species ◽  
A New Species

The genus Scolopendra Linnaeus, 1758 is represented in the Philippines’ fauna by five species, two of which are endemic. Mitochondrial DNA sequences of gene cytochrome c oxidase subunit I (COI) were obtained from six Scolopendra specimens belonging to two endemic species and a new one, described here as Scolopendra paradoxa Doménech sp. nov. These sequences were analyzed together with another forty-one sequences from GenBank, including additional species of Scolopendra and a few representatives of other Scolopendridae genera. Phylogenetic trees inferred from the COI analysis using maximum likelihood and neighbor joining showed the three Philippines Scolopendra endemic species as a polyphyletic group coherent with their respective morphologies, although the position of S. spinosissima Kraepelin, 1903 varied within the obtained trees. Species delimitation based on standard external morphological characters was also concordant with the observed genetic distances, monophyly and node support, confirming S. subcrustalis Kronmüller, 2009 and S. paradoxa sp. nov. as separate species also at the molecular level, while only the position of S. spinosissima could not be properly established with any of the statistical methods used. In addition, the male genitalia of the three studied species were found to lack gonopods and a penis. Remarks on the ultimate legs prefemoral spinous formula of S. spinosissima plus a key to the species of the genus Scolopendra in the Philippines are provided. 

scholarly journals Genetic diversity and phylogenetic relationship of higher termite Globitermes sulphureus (Haviland)(Blattodea:Termitidae)

Sociobiology ◽  
2021 ◽  
Vol 68 (2) ◽  
pp. 5911
Author(s):  
Nurul Akmar Hussin ◽  
Abdul Hafiz Ab Majid
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Evolutionary Genetics ◽  
Neighbor Joining ◽  
Geographic Isolation ◽  
Neutral Genetic Diversity ◽  
Coii Gene ◽  
Relationship Of

The subterranean higher termite Globitermes sulphureus (Blattodea: Termitidae), is a peridomestic forager and regarded as a significant pest in Southeast Asia. In this study, the populations of G. sulphureus from the USM main campus area were investigated based on partial sequences of the mitochondrial COII gene. The genetic diversity was determined using DnaSP v5 software while the phylogenetic relationship was defined using Neighbor-joining (NJ) and maximum likelihood (ML) methods using Molecular Evolutionary Genetics Analysis (MEGA 7) software. A total of 2 haplotypes were detected among the 5 sample sequences that differed by two variable sites. In addition, both phylogenetic trees gave similar topology and supporting the results from haplotype diversity. Based on the haplotype diversity and molecular phylogeny, it is proposed that geographic isolation and lack of human activities have contributed to the neutral genetic diversity of G. sulphureus.   

scholarly journals FILOGENI POPULASI Haliotis squamata REEVE, 1846 DARI PANTAI SELATAN PULAU JAWA DAN BALI BERDASARKAN SEKUEN CYTOCHROME B DNA MITOKONDRIA

2020 ◽  
Vol 12 (2) ◽  
pp. 585-595
Author(s):  
Syamsul Bachry ◽  
Dedy D. Solihin ◽  
Rudhy Gustiano ◽  
Kadarwan Soewardi ◽  
Nurlisa A. Butet
Keyword(s):  
Genetic Distance ◽  
Cytochrome B ◽  
Phylogenetic Trees ◽  
Parameter Method ◽  
Neighbor Joining ◽  
Southern Coast ◽  
Nucleotide Difference ◽  
Tree Construction ◽  
Relationship Of ◽  
Two Populations

Abalone Haliotis squamata Reeve 1846 is an abalone that has distribution on the southern coast of Java and Bali in Indonesia. The purpose of this study was to analyze the phylogenetic relationship of H. squamata from the southern coast of Java and Bali based on the cytochrome b (Cyt b) mitochondrial DNA sequence. A total of 38 samples were collected from Java (Binuangeun, Pangandaran, Banyuwangi, and Bali (Buleleng). Samples were extracted, applied using method PCR, and sequencing the method Sanger sequencing di 1st BASE Malaysia. Using primary sequences to applied namely forward primers forward AB-Cytb DivF (5'-TAAGCCAATTCGTAAGGTTC-3') dan primer reverse AB-Cytb DivR (5'-AAAATACCACTCTGGCTGAA-3'). Genetic distance was analyzed using the Kimura 2-parameter method and phylogenetic tree construction was carried out by Neighbor-Joining using the MEGA 7. The result showed that a specific nucleotide difference of 81 bp to 820 bp. The genetic distance between H. squamata intraspecies from the southern coast of Java and Bali is 0.96%-1.06%. This genetic distance is high enough to separate the two populations and form their clusters based on phylogenetic trees. The population of Bali seems to form new subpopulations. The data obtained in this study will be very useful for the management of H. squamata abalone genetic resources related to their sustainability and utilization.

scholarly journals Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2)

2023 ◽  
Vol 83 ◽  
Author(s):  
S. Khalid ◽  
R. Siddique ◽  
S. Shaheen ◽  
M. N. Shahid ◽  
Z. Shamim ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Genetic Lineage ◽  
Envelope Membrane ◽  
Neighbor Joining ◽  
Genomic Features ◽  
Novel Coronavirus ◽  
High Level ◽  
Relationship Of ◽  
Full Length Genome

Abstract Novel coronavirus (nCoV) namely “SARS-CoV-2” is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the “SARS-CoV-2” although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among “SARS-CoV-2” and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that “SARS-CoV-2” has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

Morphological and Genetic Relation in Hybrids of Triatomines (Hemiptera: Reduviidae) of the Phyllosoma Complex from Mexico

2020 ◽  
Vol 113 (5) ◽  
pp. 398-406
Author(s):  
Jesus A Davila-Barboza ◽  
Mario C Saucedo-Montalvo ◽  
Susana Favela-Lara ◽  
Gustavo- Ponce-Garcia ◽  
Ildefonso Fernandez-Salas ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Molecular Data ◽  
Genetic Distances ◽  
Morphological Data ◽  
Neighbor Joining ◽  
Phenotypic Characters ◽  
Molecular Approaches ◽  
Dominant Phenotype ◽  
High Dominance ◽  
Relationship Of

Abstract Triatoma longipennis Usinger 1939, Triatoma pallidipennis (Stal, 1872), and Triatoma picturata Usinger 1939 are considered among the species with the highest transmission capacity of Chagas disease in Mexico, with an impact on health mainly in rural zones and places with worn-out dwellings. There have been previous studies on the phylogenetic relationship of these species of the Phyllosoma complex using molecular approaches, in addition to analyzing morphological characters. However, one of the problems in the field is the presence of hybrids that due to the short genetic distance between species, and such organisms have not yet been identified and could be confused with parental organisms. In this work, we analyzed genotypical and phenotypic characters, between the species and the three possible hybrids resulting from the cross between the species. In the analysis of wings morphology, we found that the dominant phenotype in hybrids was that of T. pallidipennis, having a higher dominance than T. longipennis. Besides, the use of the COI marker amplified in DNA of parentals and the three possible hybrids showed by neighbor-joining phylograms a greater association of the hybrids with T. longipennis, in agreement with the analysis of genetic distances and polymorphic sites. Thus, the morphological data demonstrate the high dominance of T. pallidipennis and the molecular data of T. longipennis in its hybrids, in such a way that it is possible to differentiate hybrids from parental species.

scholarly journals Romanian cyprinids phylogeny based on 16S ARN mitochondrial genes

2007 ◽  
Vol 23 (5-6-2) ◽  
pp. 405-411
Author(s):  
C. Luca ◽  
S. Kevorkian ◽  
M. Elvira ◽  
A. Dinischiotu ◽  
M. Costache
Keyword(s):  
Nucleotide Sequence ◽  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Genome Structure ◽  
Mitochondrial Genes ◽  
Model System ◽  
Neighbor Joining ◽  
Base Pairs ◽  
Sequence Comparisons ◽  
Misgurnus Fossilis

The vertebrate mitochondrial genome has been an important model system for studying molecular evolution, organism phylogeny, and genome structure. Phylogenetic relatioships were inferred from analysis of 570 base pairs (bp) of mithocondrial DNA (mtDNA), representing a conserved region of 16S rRNA. We sequenced 13 cyprinids species and one putative outgroup (Misgurnus fossilis) from Romania. Based upon nucleotide sequence comparisons of cyprinid mitochondrial 16SRNA genes, we established the phylogenetic relationships between analyzed species. The phylogenetic trees obtained by two different methods (neighbor-joining and maximum parsimony) have the same topology and show that most species examined have supported the traditional division of the Cyprinidae into two subfamilies: Cyprininae and Leuciscinae.

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