The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 874-883 ◽  
Author(s):  
Nikolas Nikolaidis ◽  
Zacharias G. Scouras
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Dna Analysis ◽  
Restriction Site ◽  
Species Group ◽  
The Other ◽  
Complex Species ◽  
Restriction Site Maps ◽  
Montium Subgroup

Mitochondrial DNA (mtDNA) restriction site maps for three Drosophila montium subgroup species of the melanogaster species group, inhabiting Indian and Afrotropical montium subgroup territories, were established. Taking into account previous mtDNA data concerning six oriental montium species, a phylogeny was established using distance-matrix and parsimony methods. Both genetic diversity and mtDNA size variations were found to be very narrow, suggesting close phylogenetic relationships among all montium species studied. The phylogenetic trees that were constructed revealed three main lineages for the montium subgroup species studied: one consisting of the Afrotropical species Drosophila seguyi, which is placed distantly from the other species, one comprising the north-oriental (Palearctic) species, and one comprising the southwestern (south-oriental, Australasian, Indian, and Afrotropical) species. The combination of the mtDNA data presented here with data from other species belonging to the melanogaster and obscura subgroups revealed two major clusters: melanogaster and obscura. The melanogaster cluster is further divided into two compact lineages, comprising the montium subgroup species and the melanogaster complex species; the species of the other complex of the melanogaster subgroup, yakuba, disperse among the obscura species. The above grouping is in agreement with the mtDNA size variations of the species. Overall, among all subgroups studied, the species of the montium subgroup seem to be the most closely related. Key words : mtDNA restriction site maps, mtDNA size variations, Drosophila, phylogeny.

The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences

Zootaxa ◽  
2012 ◽  
Vol 3150 (1) ◽  
pp. 59
Author(s):  
XIAOMING GU ◽  
HUI WANG ◽  
RONGRONG CHEN ◽  
YINGZHOU TIAN ◽  
SONG LI
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Species Group ◽  
Close Phylogenetic Relationship

We examined phylogenetic relationships among newst of the genus Paramesotriton using partial mitochondrial gene se-quences, including the ND2-tRNATyr region (1415 bp) and the 12S rDNA-tRNAVal -16S rDNA region (1774 bp), from 42individuals of 10 recognized Paramesotriton species and outgroups by Bayesian inference (BI), Maximum likelihood(ML) and Maximum Parsimony (MP) methods. We found that, (1) Laotriton laoensis is the sister group of Paramesotri-ton, (2) the genus Paramesotriton is monophyletic, composed of either the P. caudopunctatus species group and the P.chinensis species group, or the subgenera Allomesotriton and Paramesotriton (3) P. longliensis and P. zhijinensis shouldbe placed in the P. caudopunctatus species group or subgenus Allomesotriton; (4) P. fuzhongensis is not a junior synonym of P. chinensis, and there is a close phylogenetic relationship between P. fuzhongensis and P. guangxiensis.

scholarly journals Randomly Amplified Polymorphic DNA Analysis in the Genus Hosta

HortScience ◽  
2005 ◽  
Vol 40 (5) ◽  
pp. 1243-1245 ◽  
Author(s):  
Roger J. Sauve ◽  
Suping Zhou ◽  
Yingchun Yu ◽  
Wolfram George Schmid
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Genetic Traits ◽  
Phylogenetic Clustering ◽  
Single Primer ◽  
Cluster 2

A randomly amplified polymorphic DNA (RAPD) technique was used to identify and determine the phylogenetic relationships of 37 hosta accessions representing the major subgenera, sections and groups in the genus Hosta. Results of this study show that RAPD markers were able to differentiate not only the main groups, whose plants shared many genetic traits, but also cultivars within a species. Some accessions were identified by a single primer while others had high intercross linkage and required many markers for their separation. The phylogenetic clustering showed that H. plantaginea, the only night-blooming species, and H. ventricosa, the only known natural tetraploid, are unique and should be classified separately. The four species in the subgenus Bryocles, section Lamellatae H. venusta, H. minor, H. capitata, and H. nakaiana have very low genetic similarity since they do not share many amplified fragments. The other accessions were classified into four main clusters; cluster 1: H. venusta, H. tardiva, H. pycnophylla, H. tsushimensis `Ogon', H. montana, H. tibae, H. montana f. macrophylla, H. kikutii `Kikutii', H. longissima `Longifolia', H. rectifolia `Rectifolia', H. takahashii and H.`Undulata'; cluster 2: H. laevigata, H. sieboldiana, H. pycnophylla × H. longipes f. latifolia, H. longipes `Urajiro' and H. ibukiensis; cluster 3: H. capitata, H. kikutii `Polyneuron', H. nigrescens, H. kikutii `Yakusimensis', H. pachyscapa, H. kikutii `Caput-Avis', H. longipes f. latifolia, H. hypoleuca, H. okamotoi, H. densa and H. takiensis; and cluster 4: H. aequinoctiiantha, H. rupifraga, H. `Amanuma', H. minor and H. kikutii `Densa'.

scholarly journals Mitochondrial DNA Analysis Clarifies Taxonomic Status of the Northernmost Snow Sheep (Ovis nivicola) Population

Life ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 252
Author(s):  
Arsen V. Dotsev ◽  
Elisabeth Kunz ◽  
Veronika R. Kharzinova ◽  
Innokentiy M. Okhlopkov ◽  
Feng-Hua Lv ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Analysis ◽  
Molecular Genetic ◽  
Divergence Time ◽  
Taxonomic Status ◽  
The Other ◽  
Snp Analysis ◽  
Mitochondrial Cytochrome B ◽  
Intraspecific Taxonomy ◽  
High Degree

Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.

Relatedness of three species of Agaricus inferred from restriction fragment length polymorphism analysis of the ribosomal DNA repeat and mitochondrial DNA

Genome ◽  
1989 ◽  
Vol 32 (2) ◽  
pp. 173-178 ◽  
Author(s):  
William E. A. Hintz ◽  
James B. Anderson ◽  
Paul A. Horgen
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
The Other ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Restriction Patterns ◽  
Dna Restriction ◽  
Restriction Fragment Length

The ribosomal DNA (rDNA) repeat of Agaricus brunnescens (= A. bisporus) was cloned and mapped for six restriction endonucleases. The map positions of the 26S, 18S, and 5.8S rRNA genes on the 9.2 kilo base pairs (kbp) repeat were determined by alignment of sites conserved in the rRNA genes of other fungi. The rDNA restriction site maps for six isolates of A. brunnescens, five isolates of A. bitorquis, and three isolates of A. campestris were compared using cloned A. brunnescens (Ag 50) rDNA as a hybridization probe. The rDNA restriction patterns for all six A. brunnescens isolates were identical. The A. bitorquis and A. campestris isolates were subdivided into two groups each, according to rDNA restriction-site polymorphisms. The A. brunnescens and A. bitorquis rDNAs were distinguished by a 0.7 kbp length difference in the noncoding spacer between the 18S and 26S rRNA genes. Despite the almost perfect conservation of the coding region between species, the noncoding spacers of A. campestris and the other two Agaricus species were too divergent to propose a simple series of mutational events to account for the differences. Interstrain and interspecies variation in the mitochondrial DNA was also surveyed. Strain-specific mitochondrial DNA restriction patterns were recognized and fewer differences were observed between the A. brunnescens and A. bitorquis isolates than between A. campestris and the other two species.Key words: Agaricus brunnescens (= A. bisporus), Agaricus, rDNA, mitochondrial DNA, restriction fragment length polymorphism analysis.

scholarly journals Phylogenetic relationships within the Scylla (Portunidae) assessed by the mitochondrial DNA sequence

2017 ◽  
Vol 18 (4) ◽  
pp. 1696-1704
Author(s):  
HURUL ADILA-AIDA MOHAMAD ROSLY ◽  
SITI AZIZAH MOHD NOR ◽  
DARLINA MD. NAIM
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Genetic Distances ◽  
Scylla Paramamosain ◽  
Base Pairs ◽  
Distance Analysis ◽  
Mitochondrial Dna Sequence ◽  
Sampling Locations

Rosly HAAM, Mohd Nor SA, Md. Naim D. 2017. Phylogenetic relationships within the Scylla (Portunidae) assessed by the mitochondrial DNA sequence. Biodiversitas 18: 1696-1704. This study was centered around the phylogenetic of mud crab genus Scylla collected across Malaysia based on a 542 base pairs (bp) section of the mitochondrial cytochrome c oxidase I (COI) from 201 individuals. Sampling locations were nine areas including one location from Borneo (Sabah and Sarawak). The Maximum Parsimony (MP) and Neighbor-Joining (NJ) methods was conducted for phylogenetic analysis and performed in MEGA ver. 5.05. We found that S. olivacea is the plenteous species collected with 111 individuals, followed by S. tranquebarica with 61 individuals. Scylla paramamosain is barely found throughout our sampling locations with only 29 individuals caught in this study. Regrettably, no wild samples of S. serrata was found during our sampling occasions, accordingly life specimens were purchased from restaurants to complete the analysis. Both MP and NJ phylogenetic trees shows a monophyletic relationships among all four species within genus Scylla included in this study. This was also supported by the genetic distance analysis based on Tamura-Nei which indicates that there is high interspecific and low intraspecific genetic distances among and within species of Scylla included in the analysis. This investigation divulged a solid proof that supports the occurrence of three species of Scylla with the nonappearance of S. serrata in Malaysian waters. This current investigations could serve as a guidance for promoting further assessment on aquaculture and conservation management for the species.

scholarly journals Phylogenetic Relationships of Macaques (Cercopithecidae: Macaca) Inferred from Partial Mitochondrial DNA (mtDNA) Cytochrome Oxidase II (COII) gene

1970 ◽  
Vol 4 (1) ◽  
pp. 42-51
Author(s):  
Noor Aisyah Rahim ◽  
Millawati Gani ◽  
Mohd Tajuddin Abdullah
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome Oxidase ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Sister Clade ◽  
Molecular Phylogenetic ◽  
Coii Gene ◽  
Cytochrome Oxidase Ii

The molecular phylogenetic relationships among ten species of macaques were assessed using mitochondrialDNA (mtDNA) cytochrome oxidase II (COII) gene. The 27 individuals comprising of ten species within genusMacaca, namely, M. sylvanus, M. mulatta, M. cyclopis, M. arctoides, M. fascicularis, M. assamensis, M.thibetana, M. nemestrina, M. leonina and M. silenus were used in this study. The phylogenetic trees werereconstructed using neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) methods.Based on our constructed tree, it is suggested that the results from phylogenetic analyses demonstrated fourgroups of macaques. In addition, the trees showed topology of M. sylvanus as a sister clade to all Asianmacaques. The silenus group, which diverged first after M. sylvanus formed their own clade, consisted ofmacaque species M. silenus, M. nemestrina and M. leonina. Meanwhile, the sinica group consisted of M.assamensis and M. thibetana, and the fascicularis group comprised of M. fascicularis, M. arctoides, M. mulattaand M. cyclopis. Our ML tree also showed that M. arctoides is a member of fascicularis group. Our study, alsoindicated that our results neglect the classification based on outer appearances and supports the proposedmolecular work view.

scholarly journals Domestication of the horse: results based on microsatellite and mitochondrial DNA markers

2004 ◽  
Vol 47 (6) ◽  
pp. 517-535
Author(s):  
K. S. Aberle ◽  
O. Distl
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variability ◽  
Microsatellite Markers ◽  
Dna Sequences ◽  
Dna Markers ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Microsatellite Data ◽  
Mtdna Sequences ◽  
The Past

Abstract. Many horse populations suffered severe decreases in numbers in the last century; some, such as the Coldblood horse breeds drastically declined in their population size, while others could be saved at the last minute. It is important to evaluate the amount of genetic variability still present in those populations in order to develop conservation programmes. Furthermore, it is essential to construct phylogenetic trees and to establish the relationships among different horse populations in order to deepen our understanding of the evolution and domestication of the horse. In the past ten years microsatellite markers have been widely used to assess genetic variability within and between different horse breeds. Moreover, attempts have been made to evaluate the phylogenetic relationships of different horse breeds by comparing mitochondrial DNA (mtDNA) sequences. In this paper we give an overview of the latest major findings in studies based on horse microsatellite data and mitochondrial DNA sequences.

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