Cytochrome b sequence variation and a molecular phylogeny of the live-bearing fish genus Gambusia (Cyprinodontiformes: Poeciliidae)

1995 ◽  
Vol 73 (2) ◽  
pp. 213-227 ◽  
Author(s):  
Charles Lydeard ◽  
Michael C. Wooten ◽  
Axel Meyer
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Analyses ◽  
Randomization Tests ◽  
Phylogenetic Information ◽  
Substitution Pattern ◽  
Mitochondrial Cytochrome B ◽  
Replacement Substitution ◽  
Species Groups ◽  
Polymerase Chain ◽  
Taxonomic Groups

Nucleotide sequences for a 402-base segment of the mitochondrial cytochrome b gene were determined from 25 species of live-bearing fishes. A total of 34 sequences representing 24 species of the genus Gambusia and 1 species of Belonesox were generated via the polymerase chain reaction. The levels of overall variation were consistent with those from other genera of fishes. In total, 137 of 402 (34.1%) nucleotides exhibited variation within or among the species. Observed differences at 24 (17.9%) of the 134 cytochrome b codons would result in amino acid replacements. Phylogenetic analyses employing various weighting schemes resulted in several clades representing traditionally recognized taxonomic groups. However, precise relationships among species-groups remained uncertain. Randomization tests indicated that these topologies contained significant nonrandom phylogenetic information. As with other fishes, the overall rate of divergence appeared to be slower than that of other vertebrates and the overall replacement/substitution pattern was suggestive of nonrandom evolutionary input.

The taxonomic status of the Castelo dos Sonhos Hantavirus reservoir, Oligoryzomys utiaritensis Allen 1916 (Rodentia: Cricetidae: Sigmodontinae)

Zootaxa ◽  
2012 ◽  
Vol 3220 (1) ◽  
pp. 1 ◽  
Author(s):  
RODRIGO AGRELLOS ◽  
CIBELE R. BONVICINO ◽  
ELIZABETH SALBÉ T. ROSA ◽  
APARECIDO A.R. MARQUES ◽  
PAULO S. D’ANDREA ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Diploid Number ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sympatric Species ◽  
Junior Synonym ◽  
Natural Reservoir ◽  
Nuclear Intron ◽  
Phylogenetic Reconstructions ◽  
Mitochondrial Cytochrome B

Species of the genus Oligoryzomys are commonly found accross Latin America, and several of them play important rolesas natural reservoirs of Hantaviruses. Here we demonstrate that O. utiaritensis, the natural reservoir of hantavirus Castelodos Sonhos in northwestwern Brazil and previously considered a junior synonym of O. nigripes or O. eliurus, is a validspecies. Morphology, morphometry, karyotyping, and phylogenetic reconstructions based on nuclear (intron 7 of the beta-fibrinogen gene) and mitochondrial (cytochrome b) DNA show that O. utiaritensis differs from O. nigripes and from otherforms of the genus, including the recently described taxon O. moojeni. Oligoryzomys utiaritensis differs in external (whit-ish ventral pelage and tail weakly bicolored) and cranial (incisive foramina never extending posteriorly the alveolus lineof M1) characters from sympatric species. It has the highest diploid number (2n=72) within Oligoryzomys, and is charac-terized by three putative synapomorphies in cytochrome b, and one in intron 7 of beta fibrinogen. We also point to theassignment of Oligoryzomys eliurus as a junior synonym of O. nigripes. Finally, we present phylogenetic analyses of in-trageneric relationships showing that O. utiaritensis is a member of a clade containing Amazonian and Cerrado taxa, including O. moojeni, O. rupestris, and O. delicatus.

scholarly journals New World Nine-Primaried Oscine Relationships: Constructing a Mitochondrial DNA Framework

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 321-336 ◽  
Author(s):  
John Klicka ◽  
Kevin P. Johnson ◽  
Scott M. Lanyon
Keyword(s):  
Cytochrome B ◽  
New World ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Wood Warblers ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Mitochondrial Cytochrome B ◽  
Strong Bootstrap Support ◽  
High Degree

AbstractHistorically, a paucity of comparative morphological characters has led to much debate regarding relationships within and among the major lineages of New World nine-primaried oscines. More recently, DNA-DNA hybridization studies have provided novel and testable hypotheses of relationships, although no consensus has been reached. For 40 songbird taxa, we obtained 1,929 base pairs (bp) of DNA sequence from the mitochondrial cytochrome-b (894 bp) and NADH dehydrogenase subunit 2 (1,035 bp) genes. Phylogenetic analyses confirm the monophyly of this assemblage as traditionally defined. The lineages delineated historically on morphological grounds are retained; finches (Fringillinae) are sister to a well-supported clade (Emberizinae) containing blackbirds (Icterini), sparrows (Emberizini), wood-warblers (Parulini), tanagers (Thraupini), and cardinal-grosbeaks (Cardinalini). However, each tribe individually is either paraphyletic or polyphyletic with respect to most recent songbird classifications. Our results suggest that Euphonia is not a tanager but perhaps represents a derived form of cardueline finch. Piranga, traditionally considered a typical tanager, is a cardinaline in all of our analyses. Calcarius falls outside the sparrow lineage in all of our analyses, but its true affinities remain unclear. Elements of four different AOU families are represented in our clade Thraupini. The inclusion of several “tanager-finches” (Haplospiza, Diglossa, Tiaris, Volatinia, Sporophila) and a nectarivore (Coereba) in this clade is consistent with findings from other molecular phylogenies in suggesting that convergence in feeding specializations among some lineages has confounded traditional morphological classifications. We obtained a novel arrangement of relationships among tribes in our “best” topology; Cardinalini is sister to the rest of the Emberizinae assemblage (as defined by Sibley and Ahlquist [1990]), and Thraupini is sister to a clade containing Icterini, Emberizini, and Parulini. Despite nearly 2,000 bp of sequence for each taxon, and a high degree of stability across most weighting schemes and analytical methods, most nodes lack strong bootstrap support. The ND2 gene provided higher resolution than did cytochrome b, but combining genes provided the most highly supported and resolved topology. We consider the phylogeny a working hypothesis to be used as a guide for further studies within the nine-primaried oscine assemblage.

An ARV1 homologue from a filarial nematode is functional in yeast

2017 ◽  
Vol 93 (1) ◽  
pp. 12-20
Author(s):  
H.M.L.P.B. Herath ◽  
Y.I.N.S. Gunawardene ◽  
M. Pathiranage ◽  
P.D.S.U. Wickramasinghe ◽  
P.G.T.S. Wickramatunge ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Transmembrane Protein ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Temperature Sensitive ◽  
Permissive Temperature ◽  
Phylogenetic Information ◽  
Setaria Digitata ◽  
Gram Staining ◽  
Polymerase Chain

AbstractThe transmembrane protein, ARV1, plays a key role in intracellular sterol homeostasis by controlling sterol distribution and cellular uptake. To date, only the ARV1s from yeast and humans have been characterized to some extent. In this study, the ARV1 of an animal filarial parasite,Setaria digitata(SdARV1), was characterized; its cDNA was 761 bp and encoded a protein of 217 amino acids, with a predicted molecular weight of 25 kDa, containing a highly conserved ARV1 homology domain and three transmembrane domains in the bioinformatic analyses. Information required to cluster members belonging to a particular taxon has been revealed in phylogenetic analyses of ARV1 sequences derived from different organisms. Reverse transcription-polymerase chain reaction (RT-PCR) analyses indicated thatSdARV1was expressed in different developmental stages – microfilariae and adult male and female worms. Experiments carried out with a single copy of theSdARV1under the control of the PMA-1 promoter in a temperature-sensitiveSaccharomyces cerevisiaemutant strain indicated full complementation of the mutant phenotype, with growth at a non-permissive temperature (37°C). Microscopic observations of cellular morphology with Gram staining revealed alteration of the shape from shrunken to oval, in mutant and complemented strains, respectively. Assessment of free sterol levels extracted from mutant yeast and complemented strains indicated that the level of sterol was significantly higher in the former compared to the latter, which had sterol levels similar to those of the wild type. Thus, the results of the current study suggest that SdARV1 is ubiquitously expressed in different developmental stages ofS. digitata, and that it is a true functional homologue of mammalian and yeast ARV1s, which have crucial phylogenetic information that follows classical evolutionary trends. Finally, this is the first study to report the biological function of nematode ARV1.

Detection of Intraspecific.DNA Sequence Variation in the Mitochondrial Cytochrome b Gene of Atlantic Cod (Gadus morhua) by the Polymerase Chain Reaction

1991 ◽  
Vol 48 (1) ◽  
pp. 48-52 ◽  
Author(s):  
Steven M. Carr ◽  
H. Dawn Marshall
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Cytochrome B ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Mitochondrial Cytochrome ◽  
Chain Reaction ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene ◽  
Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for 55 Atlantic cod (Gadus morhua) from Norway and from 10 locations within the Northern Cod complex and adjacent stocks off Newfoundland. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Eleven variable nucleotide positions within a 298 base region defined 12 genotypes. Genotype proportions differed significantly between Newfoundland and Norwegian populations: the majority genotype among Newfoundland populations was present in a minority of Norwegian cod. Newfoundland cod showed less genotypic diversity than those from the eastern Atlantic: nine genotypes were found among all 10 Newfoundland populations, as compared with seven genotypes within the single Norwegian population. An exception was an overwintering, inshore Newfoundland population that showed four genotypes among five fish. As in other vertebrates, third position synonymous transitions predominate over other types of nucleotide changes. However, two amino acid replacement substitutions occur among cod, and the ratio of purine transitions to pyrimidine transitions is significantly higher than in other species. The existence of DNA sequence polymorphism permits the various hypotheses of the distribution and differentiation of Newfoundland cod stocks to be tested, and points to the utility of PCR technology in fishery genetics.

scholarly journals A new species of Gonyosoma Wagler, 1828 (Serpentes, Colubridae), previously confused with G. prasinum (Blyth, 1854)

2021 ◽  
Vol 5 (1) ◽  
pp. 129-139
Author(s):  
Shuo Liu ◽  
Mian Hou ◽  
Ye Htet Lwin ◽  
Qiaoyan Wang ◽  
Dingqi Rao
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Cytochrome B ◽  
Yunnan Province ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Pairwise Distance ◽  
Mitochondrial Cytochrome ◽  
Mitochondrial Cytochrome B ◽  
A New Species

A new species of the genus Gonyosoma Wagler is described from Yunnan Province, China. The new species closely resembles G. prasinum (Blyth), but it is differentiated from the latter species by the following characters: precloacal plate divided, iris blue and inside of mouth greyish-white in life. Based on phylogenetic analyses of mitochondrial cytochrome b sequence data, the new species is recovered as the sister species to G. prasinum by Bayesian Inference and Maximum Likelihood analyses. The uncorrected pairwise distance between the new species and other species of the genus Gonyosoma ranged from 11.78% to 17.07% calculated using the mitochondrial cytochrome b sequence. This discovery increases the number of Gonyosoma species to seven.

Haemoproteus nucleocondensus n. sp. (Haemosporida, Haemoproteidae) from a Eurasian sogbird, the Great Reed Warbler Acrocephalus arundinaceus

Zootaxa ◽  
2012 ◽  
Vol 3441 (1) ◽  
pp. 36 ◽  
Author(s):  
ASTA KRIŽANAUSKIENĖ ◽  
TATJANA A. IEZHOVA ◽  
VAIDAS PALINAUSKAS ◽  
NIKITA CHERNETSOV ◽  
GEDIMINAS VALKIŪNAS
Keyword(s):  
New Species ◽  
Cytochrome B ◽  
Phylogenetic Analyses ◽  
Cytochrome B Gene ◽  
Seasonal Migration ◽  
Great Reed Warbler ◽  
Acrocephalus Arundinaceus ◽  
Reed Warbler ◽  
Gene Sequences ◽  
Mitochondrial Cytochrome B

Haemoproteus (Parahaemoproteus) nucleocondensus n. sp. (Haemosporida, Haemoproteidae) is described from aEurasian songbird, the Great Reed Warbler Acrocephalus arundinaceus based on the morphology of its blood stages andpartial sequences of the mitochondrial cytochrome b gene. Transmission of this haemoproteid occurs in Africa, where theGreat Reed Warblers are infected. Due to unclear reasons, its transmission does not occur at European breeding groundsof this bird, resulting in absence of the parasites in juvenile birds before and during seasonal migration. Haemoproteusnucleocondensus can be readily distinguished from other avian haemoproteids by tiny, compact microgametocyte nucleithat are significantly smaller than macrogametocyte nuclei, a rare character of haemosporidian parasites. By thismorphological feature, the new species is similar to Haemoproteus payevskyi, Haemoproteus micronuclearis, andHaemoproteus nucleofascialis. Haemoproteus nucleocondensus can be readily distinguished from both H. payevskyi andH. micronuclearis, primarily due to its numerous growing gametocytes (size greater than erythrocyte nuclei), which donot touch the envelope of erythrocytes along their entire margin; such gametocytes do not develop in Haemoproteuspayevskyi and H. micronuclearis, but present in H. nucleofascialis. However, microgametocyte nuclei are band-like inshape in the latter parasite; that is not a case in H. nucleocondensus. Illustrations of blood stages of the new species aregiven, and morphological and phylogenetic analyses identify the DNA lineages that are associated with these parasites.Genetic distance between cyt b gene sequences of the new species and H. payevskyi, H. micronuclearis, and H.nucleofascialis is 4.4%, 5.9%, and 8.1%, respectively. Cytochrome b gene sequences (GenBank no. JX026901) can be used for bar-coding in studies of H. nucleocondensus.

scholarly journals Determination of Cattle and Buffalo Skin Crackers Using Polymerase Chain Reaction Restriction Fragment Length Polymorphism

2018 ◽  
Vol 35 (2) ◽  
pp. 184
Author(s):  
Rulli Riana Dewi ◽  
Yuny Erwanto ◽  
Nanung Agus Fitriyanto
Keyword(s):  
Cytochrome B ◽  
Restriction Enzyme ◽  
Cytochrome B Gene ◽  
Universal Primer ◽  
Mitochondrial Cytochrome B ◽  
Pcr Rflp ◽  
Dna Mixture ◽  
Polymerase Chain ◽  
Mixture Samples

The aim of this study was to determine of cattle and buffalo species based on cytochrome b gene using PCR-RFLP. Cattle and buffalo hides were obtained from a slaughterhouse in Yogyakarta and Kudus Regency. To confirm the effectiveness and specificity of this fragment, there are seven of DNA mixture samples in various levels. Isolate DNA samples were amplified using universal primer of cytochrome b gene, then PCR amplicon was digested by RsaI restriction enzyme.. The result showed that mitochondrial cytochrome b gene successfully amplified fragments of 359 bp. RsaI restriction enzyme was able to cleave buffalo cytochrome b gene into two fragment  (326 and 23 bp), while the cytochrome b gene of the skin cattle DNA was uncleaved. . In conclusion, this study indicated that mixture DNA of cattle and buffalo hides could be digested by RsaI restriction enzyme  and determination of the buffalo hides in mixture samples could be detected into  10% level. Furthermore, RsaI enzyme could be used to specific identification buffalo species. PCR-RFLP technology has a potential and reliable method to identify  of the existence of r buffalo hides in the mixture with other hides.

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