Cytochrome b gene based phylogeny and genetic divergence of Tetraophasis of China

2010 ◽  
Vol 60 (2) ◽  
pp. 133-144 ◽  
Author(s):  
Longying Wen ◽  
Naifa Liu
Keyword(s):  
Cytochrome B ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Divergence Time ◽  
Tibet Plateau ◽  
Phylogenetic Study ◽  
Sequence Difference ◽  
Molecular Clock Estimate ◽  
Mitochondrial Cytochrome B

AbstractTetraophasis (Galliformes; Phasianidae) includes T. obscurus and T. szechenyii, which are endemic and distributed in the west and central parts of China. The phylogenetic status of Tetraophasis in the Phasianidae and the divergence of the two species are still controversial. We performed a phylogenetic study using DNA sequences of 828bp of the mitochondrial cytochrome b (Cytb) genes of Tetraophasis and of selected species of several other genera of Phasianidae. The phylogenetic trees suggest that Tetraophasis species belong to Phasianinae, which is inconsistent with the traditional taxonomic view that these species belong to Perdicinae. Sequence difference between T. obscurus and T. szechenyii was 3.0-3.1% and the divergence time was 1.88-1.94 Myr based on molecular clock estimate. Compared with other genera, T. obscurus and T. szechenyii should be classified as two distinct species. Our data suggest that the divergence of Tetraophasis may have been induced by the uplift of the Qinghai-Tibet Plateau and by environmental changes.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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).

A molecular phylogenetic study of Hylopetes (Rodentia: Sciuridae) inferred from mitochondrial cytochrome-b gene

Biologia ◽  
2014 ◽  
Vol 69 (12) ◽  
Author(s):  
Farong Yu ◽  
Xiuzhen Lian ◽  
Zuoping Li ◽  
Mingren Xie
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Cytochrome B Gene ◽  
Phylogenetic Study ◽  
Molecular Phylogenetic Study ◽  
Mitochondrial Cytochrome B ◽  
Distinct Genus ◽  
Molecular Phylogenetic ◽  
Close Genetic Relationship ◽  
Tectonic Movements

AbstractTo elucidate the phylogenetic relationships of Hylopetes, the complete cytochrome-b gene sequences (1,140 bp) were determined from degraded museum specimens for phylogenetic study. The large genetic differences (18.1% to 20.7%) separate Eoglaucomys from Hylopetes as a distinct genus. Phylogenetic relationships reconstructed with maximum parsimony, maximum likelihood, and Bayesian methods show that all Hylopetes were genetically clustered as two major groups, the Indochinese Hylopetes group including H. alboniger and H. phayrei, and the Sundaic group consisting of H. lepidus, H. nigripes, and H. spadiceus. The close genetic relationship and the recent divergence suggest that the Indochinese group rapidly extended to their present distributions with the uplifting of the Himalayas last few million years ago, whereas the oceanic tectonic movements during the Pliocene-Pleistocene resulted in the current geographical distributions of the Sundaic group through alteration of dispersal across the islands of the Sunda Shelf.

scholarly journals Phylogenetic relationships among Callosciurus squirrels in the Indochina Peninsula: phylogenetic position of C. pygerythrus from Myanmar

2021 ◽  
Vol 67 (1) ◽  
pp. 87-98
Author(s):  
Tatsuo Oshida ◽  
Wynn Than ◽  
Thida Oo ◽  
Khin Yu Yu Swe ◽  
Hiroaki Saito ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Divergence Times ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Indochina Peninsula ◽  
Mitochondrial Cytochrome B ◽  
Global Cooling ◽  
Mitochondrial Cytochrome B Gene

The phylogenetic relationships among seven Callosciurus species from the Indochina Peninsula, including the C. honkhoaiensis which is endemic to Hon Khoai Island, were studied using complete mitochondrial cytochrome b gene sequences (1140 bases). We primarily focused on the phylogenetic position of C. pygerythrus, which is distributed in the western part of the peninsula. We identified two main lineages: 1) C. caniceps, C. honkhoaiensis, C. inornatus, C. phayrei and C. pygerythrus, and 2) C. erythraeus and C. finlaysonii. Estimated divergence time between the two lineages was at the junction of the Zanclean and Piacenzian in the Pliocene. Within the first linage, the divergence time of sub-lineages corresponded to the Pliocene-Pleistocene boundary, although phylogenetic relationships were unclear. These two divergence times estimated in the present study correspond to episodes of global cooling, suggesting that climate may have contributed to the divergence of these Callosciurus squirrels.

scholarly journals Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4896 ◽  
Author(s):  
Hongying Ma ◽  
Yajiang Wu ◽  
Hai Xiang ◽  
Yunzhou Yang ◽  
Min Wang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
East Asia ◽  
Dna Sequences ◽  
De Novo ◽  
Divergence Time ◽  
Upper Paleolithic ◽  
Phylogenetic Study ◽  
Mitochondrial Genomes ◽  
Domestic Horses ◽  
Matrilineal Inheritance

Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

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.

Molecular phylogeny and divergence time of the Antarctic sea urchin (Sterechinus neumayeri) in relation to the South American sea urchins

2004 ◽  
Vol 16 (1) ◽  
pp. 29-36 ◽  
Author(s):  
YOUN-HO LEE ◽  
MIWHA SONG ◽  
SANGHOON LEE ◽  
ROXANA LEON ◽  
SYLVIA O. GODOY ◽  
...  
Keyword(s):  
South America ◽  
Sea Urchin ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Divergence Time ◽  
Paracentrotus Lividus ◽  
Sequence Evolution ◽  
Tectonic Event ◽  
Sterechinus Neumayeri ◽  
The Antarctic

Sterechinus neumayeri is an abundant regular sea urchin that lives in the shallow Antarctic waters. This organism has been used as a model system in many fields of the Antarctic biology. Yet, understanding of the evolutionary identity of the species, such as its phylogenetic relationships and divergence time, remains limited. Here, we reconstructed the molecular phylogenies of the species together with two sea urchin species in southernmost South America (Loxechinus albus and Pseudechinus magellanicus), a parechinid species (Paracentrotus lividus) and three strongylocentrotid species (Strongylocentrotus purpuratus, S. intermedius, and Hemicentrotus pulcherrimus) using mitochondrial DNA sequences of 12S rDNA-tRNA(gln) region (877nt) and cytochrome oxidase subunit I (COI, 1079nt). The rate of sequence evolution and the divergence time of the species were then estimated from the trees. The phylogenetic trees reveal that S. neumayeri is a sister group to the lineage of L. albus and P. lividus, and separated from the lineage 24–35 million years ago (m.y.a.). The divergence between S. neumayeri and L. albus coincides with the separation of Antarctica from South America, suggesting that the tectonic event must have provoked the cladogenesis of the species through vicariance.

scholarly journals Phylogenetic Trees of Aecial-Stage Rust Fungus, Puccinia paederiae (Dietel) Gorlenko Causing Gall on Paederia linearis Hook f.

2017 ◽  
Vol 15 (10) ◽  
pp. 739-752
Author(s):  
Wuttiwat JITJAK ◽  
Niwat SANOAMUANG
Keyword(s):  
Bayesian Methods ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Rust Fungus ◽  
Large Subunit ◽  
Molecular Data ◽  
Small Subunit ◽  
Phylogenetic Study ◽  
Internal Transcribed Spacer Region

A rust fungus, Puccinia paederiae (Dietel) Gorlenko causing galls on the stem of the skunk vine (Paederia linearis Hook. f. var. linealis and P. linealis var. palida (Craib) Puff) was collected for phylogenetic study as no molecular data was exclusively available for this fungus. Three regions of ribosomal DNA sequences, small subunit (SSU), large subunit (LSU) and internal transcribed spacer region 1 (ITS1) were employed. The results of maximum parsimony and Bayesian methods suggested that among the trees with these sequences, this fungus was nested in Pucciniaceae clades and Puccinia species with supportive statistical values. This is the first report on the phylogenetic analysis using multiple genes of the rust, P. paederiae.

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