scholarly journals First DNA Barcoding Based Record of Lysiosquillina Maculata (Fabricius, 1793) (Crustacea: Stomatopoda) From Chennai Coast, Tamil Nadu, India

2022 ◽  
Author(s):  
Babu C ◽  
Silambarasan K ◽  
Anrose A ◽  
Tiburtius A
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Tamil Nadu ◽  
Mitochondrial Gene ◽  
Neighbor Joining ◽  
Closely Related Species ◽  
Protein Coding ◽  
Mantis Shrimp ◽  
Varied Form ◽  
Mitochondrial Cytochrome Oxidase

Abstract Taxonomic identification of mantis shrimp Lysiosquillina maculata through DNA barcoding analysis collected from Kasimedu fisheries harbour, Chennai coast, Tamil Nadu, India. The mitochondrial cytochrome oxidase sub unit I gene (mtcoI) with 650 bp region was sequenced for phylogenetic analysis. The present record, mitochondrial gene sequences were used to identify the mantis shrimp Lysiosquillina maculata. This is the first confirmed record of Indian waters and the mt COI sequence was deposited in GenBank. The neighbor joining method was used for phylogenetic analysis. The pair wise genetic distance calculated with 08 closely related species varied form 0.03-0.404%. Phylogenetic tree based on 13 protein coding genes shows that Lysiosquillina maculata has a closer phylogenetic relationship to Harpiosquilla harpax.

scholarly journals Abundant Mitochondrial Genome Diversity, Population Differentiation and Convergent Evolution in Pines

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1605-1614
Author(s):  
Junyuan Wu ◽  
Konstantin V Krutovskii ◽  
Steven H Strauss
Keyword(s):  
Mitochondrial Dna ◽  
Population Differentiation ◽  
Mitochondrial Gene ◽  
Dna Polymorphisms ◽  
Neighbor Joining ◽  
Closely Related Species ◽  
Breeding Programs ◽  
Length Polymorphisms ◽  
Polymerase Chain ◽  
Mitochondrial Genome Diversity

Abstract We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and θ) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

scholarly journals The first representatives of the millipede family Glomeridellidae (Diplopoda, Glomerida) recorded from China and Indochina

ZooKeys ◽  
2020 ◽  
Vol 954 ◽  
pp. 1-15
Author(s):  
Weixin Liu ◽  
Sergei Golovatch
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Barcoding ◽  
Southern China ◽  
Mitochondrial Gene ◽  
Guizhou Province ◽  
The Family ◽  
Structural Details ◽  
Molecular Phylogenetic ◽  
A New Species

A new species of glomeridellid millipede is described from Guizhou Province, southern China: Tonkinomeris huzhengkunisp. nov. This new epigean species differs very clearly in many structural details, being sufficiently distinct morphologically and disjunct geographically from T. napoensis Nguyen, Sierwald & Marek, 2019, the type and sole species of Tonkinomeris Nguyen, Sierwald & Marek, 2019, which was described recently from northern Vietnam. The genus Tonkinomeris is formally relegated from Glomeridae and assigned to the family Glomeridellidae, which has hitherto been considered strictly Euro-Mediterranean in distribution and is thus new to the diplopod faunas of China and Indochina. Tonkinomeris is re-diagnosed and shown to have perhaps the basalmost position in the family Glomeridellidae. Its relationships are discussed, both morphological and zoogeographical, within and outside the Glomeridellidae, which can now be considered as relict and basically Oriental in origin. Because of the still highly limited array of DNA-barcoding sequences of the COI mitochondrial gene available in the GenBank, the first molecular phylogenetic analysis of Glomerida attempted here shows our phylogram to be too deficient to consider meaningful.

Morphological description and DNA barcoding of Chaetocladius (Chaetocladius) elisabethae sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Moscow Region

Zootaxa ◽  
2018 ◽  
Vol 4403 (2) ◽  
pp. 378 ◽  
Author(s):  
EUGENYI A. MAKARCHENKO ◽  
MARINA A. MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
DMITRY M. PALATOV
Keyword(s):  
Dna Barcoding ◽  
Mitochondrial Gene ◽  
Interspecific Variation ◽  
Instar Larva ◽  
Molecular Data ◽  
Genetic Distances ◽  
Moscow Region ◽  
Morphological Description ◽  
Closely Related Species ◽  
Male Pupa

Illustrated descriptions of the adult male, pupa and fourth instar larva, as well as DNA barcoding results of Chaetocladius (Chaetocladius) elisabethae sp. nov. in comparison with closely related species of Chaetocladius s. str. from the Moscow Region are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between C. (s. str.) elisabethae sp. nov. and other species of the subgenus produced K2P genetic distances of 0.11–0.16, values well associated with interspecific variation. The barcodes of the new species were identical to the Chaetocladius sp. 2ES in BOLD systems. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str. 

scholarly journals DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae)

2007 ◽  
Vol 274 (1619) ◽  
pp. 1731-1739 ◽  
Author(s):  
T.L Whitworth ◽  
R.D Dawson ◽  
H Magalon ◽  
E Baudry
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Mitochondrial Gene ◽  
Introgressive Hybridization ◽  
Species Number ◽  
Closely Related Species ◽  
Endosymbiotic Bacteria ◽  
Limited Success ◽  
Mtdna Introgression ◽  
Mtdna Haplotype

In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora , known to be infected with the endosymbiotic bacteria Wolbachia . We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia -associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.

scholarly journals New records of two Lutjanus species (Teleostei: Perciformes: Lutjanidae) with re-description of six lutjanids from Saint Martin’s Island of the Bay of Bengal, Bangladesh

2018 ◽  
Vol 46 (2) ◽  
pp. 239-253 ◽  
Author(s):  
Shilpi Saha ◽  
Sanjay Chakraborty ◽  
Subrina Sehrin ◽  
Abdullah Al Masud ◽  
Kazi Ahsan Habib ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bay Of Bengal ◽  
Related Species ◽  
Genetic Divergence ◽  
New Records ◽  
Morphological Differentiation ◽  
Morphological Characters ◽  
Mitochondrial Cytochrome ◽  
Closely Related Species ◽  
Mitochondrial Cytochrome Oxidase

Investigations on Snapper fish of the genus Lutjanus were conducted from October 2015 to April 2016 in the coral ecosystem of St. Martin’s Island, Bangladesh. Twenty one individuals of 8 species of Lutjanus were collected from local fishermen. Both morphological characters and DNA barcoding approach by mitochondrial cytochrome oxidase I subunit (COI) were used to confirm the identification of all species. Present study recorded the first national occurrence of two reef associated Lutjanus species (L. xanthopinnis and L. indicus). In addition six species (L. rivulatus, L. lutjanus, L. vitta, L. lemniscatus, L. fulviflamma and L. johnii) were re-described. Distinct morphological differentiation were found between more closely related species L. xanthopinnis, L. vitta and L. lutjanus. Three different appearances of L. johnii, two different appearances of L. rivulatus and L. lemniscatus were confirmed as same species. Phylogenetic analysis showed monophylotic clade for conspecific individuals and paraphyletic clade for congeneric individuals. Average genetic divergence for intraspecific level was 1.5% and 12.5% for interspecific level. Current study increased the number of Lutjanus species in Bangladesh from 15 to 17 and extended the distribution range of those new recorded species in northeastern part of the Bay of Bengal. Bangladesh J. Zool. 46(2): 239-253, 2018

A new species of Dendrobates (Anura: Dendrobatidae) from the Amazonian lowlands in Perú

Zootaxa ◽  
2006 ◽  
Vol 1152 (1) ◽  
pp. 45 ◽  
Author(s):  
JASON L. BROWN ◽  
RAINER SCHULTE ◽  
KYLE SUMMERS
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Related Species ◽  
Repetition Rate ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Closely Related Species ◽  
Mean Frequency ◽  
Amazonian Lowlands ◽  
A New Species

We describe a new species of poison frog from Amazonian Peru. Dendrobates uakarii, sp. nov. is distinguished by the presence of paired parallel dorsolateral lines: one yellow oblique lateral and one red dorsolateral (on each flank), with one vertebral line, similar in color to the dorsolateral lines. Phylogenetic analysis show that D. uakarii, sp. nov. and closely related taxa (D. ventrimaculatus sp. aff. Shreve from Porto Walter, Brazil and another from Amazonas, Brazil) form the sister group to D. fantasticus Boulenger. This new species can be distinguished from its sister taxa on the basis of 19 unique mitochondrial gene nucleotide site substitutions. Comparisons between closely related species show a slight difference in call repetition rate and mean frequency.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

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