Phylogeny of the genus Scathophaga (Diptera: Scathophagidae) inferred from mitochondrial DNA sequences

2001 ◽  
Vol 79 (3) ◽  
pp. 517-524 ◽  
Author(s):  
M V Bernasconi ◽  
J Pawlowski ◽  
C Valsangiacomo ◽  
J -C Piffaretti ◽  
P I Ward
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Coi Gene ◽  
Similar Species ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Protein Coding ◽  
Scathophaga Stercoraria ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Scathophaga stercoraria has been used for a large number of studies in animal ecology and evolution. Morphological phylogenetic work on the relationships among flies of the family Scathophagidae in general, and the genus Scathophaga in particular, has led to limited or incomplete conclusions. We addressed these relationships by sequencing 810 base pairs (bp) from the mitochondrial cytochrome oxidase subunit I (COI) gene and 738 bp of the mitochondrial cytochrome b (Cyt b) gene in 16 species of Scathophagidae. Phylogenetic analysis of these two protein-coding genes allows us to resolve relatively well the relationships within the genus Scathophaga, using both separate and combined (COI + Cyt b) data. Most of the phylogenetic trees generated by our data support the following relationships: (((S. analis + S. inquinata) + S. lutaria) + S. cineraria + (S. taeniopa + S. suilla + S. incola) + S. furcata + S. tropicalis). The most noteworthy findings are that (i) S. obscura and S. tinctinervis, which were formerly placed in the genus Coniosternum, form a sibling species cluster; (ii) S. taeniopa and S. suilla, which are morphologically very similar species, are clearly distinct taxa; (iii) S. analis, considered a doubtful species in the Catalogue of Palearctic Diptera, could be a synonym of S. inquinata; and (iv) the South American S. tropicalis and the Old World S. stercoraria are not sister-species.

scholarly journals Kajian Penanda Genetik Gen Sitokrom b DNA Mitokondria Ikan Lais dari Sungai Kampar Riau

2018 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Roza Elvyra ◽  
Dedy Duryadi Solihin
Keyword(s):  
Species Diversity ◽  
Molecular Marker ◽  
Phylogenetic Relationship ◽  
Cytochrome B ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Phylogenetic Marker ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

The mitochondrial cytochrome b (cyt-b) gene as a phylogenetic marker of lais fish Kryptopterus schilbeides from Kampar River in Riau has been studied. This is a prelimininary research on the utility of cyt-b gene as a molecular marker to obtain species diversity and phylogenetic relationship among Kryptopterus fishes from Kampar River. The primers of L14841 and H15149 were used to amplify the cyt-b gene. The results showed that K. schilbeides has isoleusine at site-81 and metionine at site-114; K. schilbeides from Kampar River and K. schilbeides from GenBank form a phylogeny cluster at 45% value.

scholarly journals Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh

2019 ◽  
Vol 5 (1) ◽  
pp. 25-30
Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam
Keyword(s):  
Genetic Diversity ◽  
Cytochrome B ◽  
Tissue Sample ◽  
Sequence Similarity ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Multiple Sequence ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30

scholarly journals Molecular detection of cattle and buffalo species meat origin using mitochondrial cytochrome b (Cyt b) gene

2016 ◽  
Vol 2 (2) ◽  
pp. 177-182
Author(s):  
Sirazum Munira ◽  
Fatema Tuz Jahura ◽  
Md Munir Hossain ◽  
Mohammad Shamsul Alam Bhuiyan
Keyword(s):  
Cytochrome B ◽  
Genomic Dna ◽  
Molecular Technique ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Dna Yield ◽  
Mitochondrial Cytochrome B ◽  
Meat Samples ◽  
Species Specific ◽  
Cyt B Gene

The study was conducted to adopt PCR based technique for identification of species origin from meat samples of cattle and buffalo using mitochondrial cytochrome b (Cyt b) gene fragment. A total of 42 ear tissue and meat samples were collected from different slaughterhouses and farms of Mymensingh, Bogra and Rangpur districts and stored in 96% ethanol at room temperature. Genomic DNA was extracted from all samples using GeNet Bio genomic DNA isolation kit. The average DNA yield of considered samples was found 204.57 ng/?l where the purity ranged from 1.82–1.99. Two (2) pair species-specific primers were used to amplify Cyt b gene fragments of 472 bp and 124 bp for cattle and buffalo, respectively. The PCR results revealed different species specific amplified fragments which could discriminate between cattle (472 bp) and buffalo (124 bp) species precisely from pure and mixed samples of those species. This study suggests an accurate molecular technique for identification of cattle and buffalo species meat origin and differentiates species present in adulterated meat samples. In conclusion, this DNA based technique could be utilized for prevention of malpractice in slaughterhouse and chain shops and thereby to protect consumer’s right.Asian J. Med. Biol. Res. June 2016, 2(2): 177-182

A phylogenetic analysis of Neotoma varia (Rodentia: Cricetidae), a rediscovered, endemic, and threatened rodent from Datil Island, Sonora, Mexico

Zootaxa ◽  
2010 ◽  
Vol 2647 (1) ◽  
pp. 51 ◽  
Author(s):  
SERGIO TICUL ÁLVAREZ-CASTAÑEDA ◽  
EVELYN RIOS
Keyword(s):  
Gulf Of California ◽  
Optimality Criteria ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene ◽  
Tree Topologies ◽  
Endangered Population ◽  
Low Levels ◽  
Cyt B Gene

The systematics of the rediscovered and threatened rodent, Neotoma varia, from Datil Island in the Gulf of California, was assessed using sequences from the mitochondrial cytochrome b gene (Cyt b) regarding specimens of N. albigula from Tiburon Island and populations on the mainland off Datil Island. Neotoma varia was originally described as a species and subsequently considered a subspecies, relegated to subspecific status based on morphologic characters and few specimens; no genetic analyses have been published. Bayesian inference, maximum-parsimony, maximumlikelihood, and distance optimality criteria based on 828-bp of the Cyt b gene from individuals representing 11 populations, converged on essentially identical tree topologies, consistent with the inclusion of N. varia within N. albigula. The population of Datil Island is related to specimens from Tiburon Island and the adjacent mainland populations showing low levels of genetic differentiation with other subspecies of N. albigula (0.2–1.4%). Previous morphologic analyses indicated inconstancy in characters regarding the holotype; however, N. varia is morphologically different in the oclusal view of the upper molars. Under these conditions, we consider N. varia as a subspecies of N. albigula. N. a. varia has a very specific habitat and is present only on a very small part of the island; in spite of low divergence regarding other N. albigula subspecies, N. a. varia possesses a genetic identity and needs to be considered as a critically endangered population.

scholarly journals Molecular detection of goat and sheep meat origin using mitochondrial cytochrome b gene

2016 ◽  
Vol 45 (2) ◽  
pp. 41-45
Author(s):  
FT Jahura ◽  
S Munira ◽  
AKFH Bhuiyan ◽  
MR Hoque ◽  
MSA Bhuiyan
Keyword(s):  
Cytochrome B ◽  
Molecular Technique ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Mitochondrial Cytochrome B ◽  
Indigenous Goat ◽  
Meat Species ◽  
Meat Samples ◽  
Species Specific ◽  
Cyt B Gene

The present study was conducted to discriminate between sheep and goat species meat origin utilizing mitochondrial cytochrome b (Cyt b) gene fragment. A total of 46 ear tissue and meat samples were collected from different slaughterhouses and farms of Mymensingh and Rangpur districts. Genomic DNA was extracted using GeNet Bio DNA isolation kit and DNA concentration and purity was quantified by NanoDrop spectrophotometer. Two pairs species specific primer were used to amplify Cyt b gene fragments. Selected primers were highly conserved across the breed within a species and worked well with the species of indigenous goat and sheep resulting similar size of the amplicons 330 and 585 bp respectively. The duplex PCR condition would enable to detect adulteration from goat and sheep mixed samples which revealed by two precise bands (330 and 585 bp) in a single reaction. This study suggests an accurate molecular technique for identification of sheep and goat meat species origin and differentiates species present in adulterate meat samples. In conclusion, this DNA based marker could be used for prevention of fraudulent practice in slaughterhouse and chain shops in Bangladesh.Bang. J. Anim. Sci. 2016. 45 (2): 41-45

Phylogeny of Old and New World Vultures (Aves: Accipitridae and Cathartidae) Inferred from Nucleotide Sequences of the Mitochondrial Cytochrome b Gene

1995 ◽  
Vol 50 (11-12) ◽  
pp. 868-882 ◽  
Author(s):  
Michael Wink
Keyword(s):  
Cytochrome B ◽  
New World ◽  
Genetic Relatedness ◽  
Nucleotide Sequences ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Old World ◽  
Mitochondrial Cytochrome B ◽  
Close Relationship ◽  
Cyt B Gene

Abstract The molecular phylogeny of 11 Old World and 5 New World vultures was inferred from nucleotide sequences of the mitochondrial cytochrome b (cyt b) gene. According to this analysis carrion-feeding has evolved independently at least three times during evolution: 1.) In the New World vultures, which are clearly separated from vultures of the family Accipitridae; 2.) in the Neophron-Gypaetus clade which is positioned at the base of the Accipitrid tree and 3.) in the Gyps-Aegypius-complex which encloses the largest group of Old World vultures. Thus the genetic data clearly show that the carrion-feeding lifestyles and associated morphologies shared by New and Old World vultures are rather based on convergence than on close genetic relatedness. Employing the cyt b sequences of 12 other members of the Falconiformes and 10 members of the Ciconiiformes (sensu Sibley and Monroe, 1990) the phylogenetic relationship between the three clades of vultures and these other taxa was assessed. New World Vultures appear to share distant ancestry with storks but a close relationship is unlikely.

scholarly journals Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

2020 ◽  
Vol 13 (1) ◽  
pp. 96-103
Author(s):  
Dorothea Vera Megarani ◽  
Herjuno Ari Nugroho ◽  
Zahrah Prawita Andarini ◽  
Yura Dwi Risa B. R. Surbakti ◽  
Rini Widayanti
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cytochrome B ◽  
Genetic Characterization ◽  
Phylogenetic Study ◽  
Cyt B ◽  
Phylogenetic Structure ◽  
Mitochondrial Cytochrome B ◽  
Sperata Seenghala ◽  
Cyt B Gene

Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

scholarly journals A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽  
2020 ◽  
Vol 4748 (1) ◽  
pp. 182-194 ◽  
Author(s):  
JING ZHANG ◽  
ERNST BROCKMANN ◽  
QIAN CONG ◽  
JINHUI SHEN ◽  
NICK V. GRISHIN
Keyword(s):  
Dna Sequences ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Type Specimens ◽  
African Species ◽  
Protein Coding ◽  
Coding Regions ◽  
As Species ◽  
Close Relatives ◽  
Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]). 

scholarly journals Allele-Specific PCR for the Detection of Azoxystrobin Resistance in Didymella bryoniae

Plant Disease ◽  
2014 ◽  
Vol 98 (12) ◽  
pp. 1681-1684 ◽  
Author(s):  
Mavis J. Finger ◽  
Venkatesan Parkunan ◽  
Pingsheng Ji ◽  
Katherine L. Stevenson
Keyword(s):  
Dna Sequences ◽  
Cyt B ◽  
Didymella Bryoniae ◽  
Specific Pcr ◽  
Pcr Product ◽  
Allele Specific ◽  
Polymerase Chain ◽  
Sensitive Allele ◽  
Cyt B Gene ◽  
Allele Specific Pcr

Gummy stem blight (GSB), caused by the fungus Didymella bryoniae, is considered the most widespread and destructive disease of watermelon in the southeastern United States. The quinone outside-inhibiting (QoI) fungicide azoxystrobin (AZO), which inhibits mitochondrial respiration by binding to the outer, quinone-oxidizing pocket of the cytochrome bc1 (cyt b) enzyme complex, was initially very effective in controlling GSB. However, resistance to AZO has been observed in D. bryoniae in many watermelon-producing regions. In this study, the DNA sequences of partial cyt b genes of four AZO-resistant (AZO-R) and four AZO-sensitive (AZO-S) isolates of D. bryoniae confirmed the amino acid substitution of glycine by alanine at the 143 codon (G143A) in the AZO-R isolates tested. Allele-specific primers were designed to detect the resistant or sensitive allele at codon 143 of the cyt b gene, which amplified a 165-bp polymerase chain reaction (PCR) product from genomic DNA of nine AZO-R and nine AZO-S isolates of D. bryoniae, respectively. The primer pairs did not amplify DNA from other pathogens tested in the study. The results indicated that the PCR assays developed in the study were specific in differentiating AZO-R and AZO-S isolates and could facilitate AZO resistance detection in D. bryoniae.

scholarly journals A Nation-wide Phylogenetic and Phylogeographic Investigation of the Endemic New Zealand Oyster Borers, Haustrum scobina and Haustrum albomarginatum

2021 ◽  
Author(s):  
Seamus O'Mahony
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Shell Morphology ◽  
Ice Age ◽  
Coi Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Migration Route ◽  
Outgroup Species

The endemic New Zealand sea snails Haustrum scobina and Haustrum albomarginatum are rocky shore intertidal dogwhelks of the Muricidae family. They have direct developing young and are carnivores. Their radula is used to drill into the shells of their prey, and they are commonly referred to as oyster borers. The taxonomic status of these species is still unresolved and therefore the name Haustrum scobina sensu lato is used.<br><br>The overall goal of this thesis research was to investigate the phylogeny and phylogeography of Haustrum scobina sensu lato using mitochondrial DNA sequences. Comparisons made to phylogeographic studies of ecologically similar species such as Cominella spp. provide an opportunity to identify the common environmental determinates of population migration route, genetic differentiation and speciation whenever similar patterns are found.<br><br>A nation-wide collection of samples was used to generate 277 new sequences from a 610 bp portion of the cytochrome c oxidase subunit I (COI) gene. This enabled the formation of a dataset of 654 DNA sequences, which was comprised of the 277 new sequences, 16 retrieved from a published study that deposited them in GenBank, and 361 from a previous unpublished thesis study. An unexpectedly diverse phylogeny of 58 COI haplotypes from 31 sample sites was recovered. These formed three clusters using K-means clustering by pairwise mutational distance. The in-group species did not form reciprocal monophyly groups, and the expected closest outgroup species (Haustrum haustorium) appeared to be as similar to the in-group clusters as they were to each other. A dataset of 27 DNA sequences from an 827 bp portion of the large sub-unit 28S nuclear rRNA gene was produced with the intention of corroborating the findings from the analyses of the COI dataset. This consisted of 26 new sequences and one sequence from a published study that deposited the sequence on GenBank. The expected taxonomic arrangement of Haustrum scobina sensu lato could not be matched by COI sequences due to incongruence with the 28S phylogeny and shell morphology. <br><br>The 28S dataset and shell morphology indicated there are two species in Haustrum scobina sensu lato. These are most likely Haustrum scobina and Haustrum albomarginatum, but they could not clearly be identified in the COI data. As a result, the phylogeographic certainty was limited when using the COI dataset because of the lack of clarity between the haplotypes of the two putative species. Possible reasons for the complicated COI dataset are discussed. Phylogenetic analysis of both the 28S and COI datasets did not support the expected conclusion that members of Haustrum scobina sensu lato are each other’s closest relatives. Haustrum haustorium was the expected immediate outgroup species but formed a polytomy with the in-group. A decrease in COI haplotype diversity was observed in southern samples when they were compared to the samples collected at northern locations. Taranaki sites shared a haplotype with multiple South Island sites that had no haplotype diversity. This suggested post-glacial re-colonisation of southern sites after displacement by ice-age conditions from these locations, a hypothesis consistent with results from studies of the Cominella genus. Association between Purau Bay in Lyttleton Harbour, Titahi Bay, Port Ahuriri and Kawau Island with no associated haplotypes between these locations suggested human-mediated translocation events. A genetic disjunction was also apparent between the south Wellington/Wairarapa coast and the eastern Wairarapa coast. This pattern was consistent with one study of Cominella maculosa and other studies have attributed similar patterns of other species in the region to recent uplift events affecting coastal community composition. The phylogeny of Haustrum scobina sensu lato will require further investigation before it can be used to more confidently resolve the phylogeographic history of the species.

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