scholarly journals Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences

2011 ◽  
Vol 57 (6) ◽  
pp. 758-767 ◽  
Author(s):  
Xiaoli Wang ◽  
Jiangyong Qu ◽  
Naifa Liu ◽  
Xinkang Bao ◽  
Sen Song
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Control Region ◽  
Divergence Time ◽  
Population Expansion ◽  
Middle Pleistocene ◽  
Distribution Analysis ◽  
D Loop ◽  
Limited Gene Flow ◽  
Partial Isolation

Abstract Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T. himalayensis. The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced, and 57 polymorphic positions defined 37 haplotypes. A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations. In the phylogenetic tree, all haplotypes grouped into four groups: clade A (Kunlun Mountains clade), clade B (Northern Qinghai-Tibetan Plateau clade), clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade). We found a low level of gene flow and significant genetic differentiation among all populations. Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation, and expansion occurred in the glaciation. Analysis of mtDNA D-loop sequences confirmed demographic population expansion, as did our non-significant mismatch distribution analysis. In conclusion, limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T. himalayansis based on the analysis on mtDNA D-loop sequences.

scholarly journals Maternal variability of Croatian Spotted goat (Capra hircus)

2019 ◽  
Vol 64 (No. 6) ◽  
pp. 248-254
Author(s):  
Ivana Drzaic ◽  
Ino Curik ◽  
Dinko Novosel ◽  
Vlatka Cubric-Curik
Keyword(s):  
Mitochondrial Dna ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Capra Hircus ◽  
Phylogeographic Structure ◽  
Goat Breed ◽  
Loop Region ◽  
D Loop ◽  
Mtdna Diversity

Abstract: This study provides the first characterization of maternal ancestry and mitochondrial DNA (mtDNA) diversity in the Croatian Spotted goat (CSG), the most important autochthonous goat breed in Croatia. CSG (n = 25) were randomly sampled from seven herds and a 660-bp fragment from the mtDNA D-loop region was sequenced. Those sequences were compared with 122 corresponding GenBank sequences from goat populations in Albania, Austria, Egypt, Greece, Italy, Romania and Switzerland. CSG showed a great polymorphism (only three out of 17 haplotypes were shared) with high a haplotype (Hd = 0.967 ± 0.019) and nucleotide diversity (π = 0.01305 ± 0.00068). When compared with Mediterranean and ancient goats, all of the 25 CSG were randomly scattered inside haplogroup A showing the weak phylogeographic structure with within-breed variance accounting for 91.76% of the genetic variation. In addition, population expansion tests (mismatch distribution and Fu’s Fs statistic) supported these results suggesting at least one population expansion.

Profound Length Heteroplasmic Alterations in Mitochondrial DNA Control Region From Primary AML Cells: Implication of Impaired Mitochondrial Replication and Demonstration of ‘vicious cycle’ Hypothesis.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3116-3116
Author(s):  
Myung-Geun Shin ◽  
Hye Ran Kim ◽  
Hyeoung-Joon Kim ◽  
Hoon Kook ◽  
Tai Ju Hwang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Copy Number ◽  
Regulatory Region ◽  
Mtdna Control Region ◽  
Vicious Cycle ◽  
Mtdna Copy Number ◽  
Length Heteroplasmy ◽  
Region Length ◽  
D Loop

Abstract Abstract 3116 Poster Board III-53 Mitochondrial DNA (mtDNA) control region (displacement (D)-loop including HV1 and HV2) is a non-coding region of 1124 bp (nucleotide positions, np 16 024–576), which acts as a promoter for both the heavy and light strands of mtDNA, and contains essential transcription and replication elements (Blood 2004;103:4466-77). Importantly, mutations in the D-loop regulatory region might change mtDNA replication rate by modifying the binding affinity of significant trans-activating factors (Eur J Cancer 2004;40:2519-24). Thus, length heteroplasmic alterations of mtDNA control region may be related with mitochondrial dysfunction resulting in ‘vicious cycle’ (Mol Med Today 2000;6:425-32). In an attempt to investigate profiling of mtDNA length heteroplasmic alterations in primary AML cells, we carried out a quantitative size-based PCR product separation by capillary electrophoresis (ABI 3130XL Genetic Analyzer and ABI Prism Genotyper version 3.1) using six targets (np 303-315 poly C, np 16184-16193 poly C, np 514-511 CA repeats, np 3566-3572 poly C, np 12385-12391 poly C and np 12418-12426 poly A). Length heteroplasmy was further confirmed by cloning and sequencing. Quantitative analysis of mtDNA molecules was performed using the QuantiTect SYBR Green PCR kit (Qiagen) and Rotor-Gene 3000 (Corbett Research). Forty-eight AML bone marrow samples were collected after receiving Institutional Review Board approval and informed consent. There were profound alterations of mtGI in 303 poly C, 16184 poly C and 514 CA repeats. The length heteroplasmy pattern of 303 poly C tract in the HV2 region disclosed mixture of 7C, 8C, 9C and 10C mtDNA types. In the HV2 region, length heteroplasmy in poly-C tract at np 303 - 309 exhibited 5 variant peak patterns: 7CT6C+8CT6C (50.0%), 8CT6C+9CT6C (14.0%), 8CT6C+ 9CT6C+ 10CT6C (10.4%), 9CT6C+10CT6C+11CT6C (8.3%) 9CT6C + 10CT6C + 11CT6C+12CT6C (2.1%). The length heteroplasmy pattern of 514-523 CA repeats in the HV2 region exhibited 2 variant peak patterns: CACACACACA (56.3%) and CACACACA (43.7%). In the HV1 region, length heteroplasmy in the poly-C tract at np 16184 - 16193 exhibited 9 variant peak patterns: 5CT4C+5CT3C (31.0%), 6CT4C+6CT3C (2.1%), 9C+10C+11C+12C (16.7%), 9C+10C+11C (2.1%), T4CT4C+5CT3C (4.2%), 9C+10C+11C+12C+13C (2.1%), 3CTC4C+5CT3C (2.1%), 10C+11C+12C+13C (4.2%), 8C+9C+10+11C (2.1%). Primary AML cells revealed decreased enzyme activity in respiratory chain complex I, II and III. AML cells had about a two-fold decrease in mtDNA copy number compared with normal blood mononuclear cells. Current study demonstrates that profound length heteroplasmic alterations in mtDNA control region of primary AML cells may lead to impairment of mitochondrial biogenesis (reduction of mtDNA copy number) and derangement of mitochondrial ATP synthesis. During this perturbation, mitochondria in primary AML cells might produce a large amount of reactive oxygen species, which causes the vicious cycle observed in chronic inflammatory diseases and cancers as well. Disclosures No relevant conflicts of interest to declare.

Genetic variation of microsatellite and mitochondrial DNA markers in broad whitefish (Coregonus nasus) in the Colville and Sagavanirktok rivers in northern Alaska

1997 ◽  
Vol 54 (7) ◽  
pp. 1548-1556 ◽  
Author(s):  
J C Patton ◽  
B J Gallaway ◽  
R G Fechhelm ◽  
M A Cronin
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Gene Flow ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Nuclear Genome ◽  
Pcr Amplification ◽  
Colville River ◽  
Limited Gene Flow ◽  
Northern Alaska

There has been concern that a causeway leading to oil production facilities in the Alaskan Beaufort Sea could affect the extent of emigration from, and immigration into, a population of broad whitefish (Coregonus nasus) in the Sagavanirktok River. To assess this, we analyzed the genetic relationships of the broad whitefish populations in the Sagavanirktok River, and the nearest adjacent population, in the Colville River. Three microsatellite loci from the nuclear genome, and the NADH-1 gene of mitochondrial DNA (mtDNA), were analyzed. Diploid genotypes were determined with PCR amplification of the microsatellite loci, and mtDNA genotypes were identified with PCR amplification followed by sequencing of 798 nucleotides. Several alleles were identified at each locus and both populations had high levels of genetic variation. There is significant differentiation of the Sagavanirktok River and Colville River broad whitefish stocks for the three microsatellite loci (FST = 0.031) but not mtDNA (FST < 0.001). Possible explanations for the lower level of differentiation of mtDNA than microsatellites include female-mediated gene flow between populations, skewed sex ratios, natural selection, or mutation. The results indicate that there is limited gene flow between the Colville and Sagavanirktok rivers, which represent semi-isolated spawning populations.

scholarly journals Detection of somatic mutations in the mitochondrial DNA control region D‑loop in brain tumors: The first report in Malaysian patients

2017 ◽  
Author(s):  
Abdul Mohamed Yusoff ◽  
Khairol Mohd Nasir ◽  
Khalilah Haris ◽  
Siti Mohd Khair ◽  
Abdul Abdul Ghani ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Brain Tumors ◽  
Control Region ◽  
Somatic Mutations ◽  
Mitochondrial Dna Control Region ◽  
First Report ◽  
D Loop

scholarly journals Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria

2016 ◽  
Vol 113 (30) ◽  
pp. E4276-E4285 ◽  
Author(s):  
Gokhan Akman ◽  
Radha Desai ◽  
Laura J. Bailey ◽  
Takehiro Yasukawa ◽  
Ilaria Dalla Rosa ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Mitochondrial Disease ◽  
Genetic Information ◽  
Disease Mechanism ◽  
Dna Segregation ◽  
D Loop ◽  
Mitochondrial Dna Replication ◽  
Pathological Variant ◽  
Potential Substrate

The genetic information in mammalian mitochondrial DNA is densely packed; there are no introns and only one sizeable noncoding, or control, region containing key cis-elements for its replication and expression. Many molecules of mitochondrial DNA bear a third strand of DNA, known as “7S DNA,” which forms a displacement (D-) loop in the control region. Here we show that many other molecules contain RNA as a third strand. The RNA of these R-loops maps to the control region of the mitochondrial DNA and is complementary to 7S DNA. Ribonuclease H1 is essential for mitochondrial DNA replication; it degrades RNA hybridized to DNA, so the R-loop is a potential substrate. In cells with a pathological variant of ribonuclease H1 associated with mitochondrial disease, R-loops are of low abundance, and there is mitochondrial DNA aggregation. These findings implicate ribonuclease H1 and RNA in the physical segregation of mitochondrial DNA, perturbation of which represents a previously unidentified disease mechanism.

Abundant genetic diversity and maternal origins of modern horses

2019 ◽  
Vol 99 (4) ◽  
pp. 929-934
Author(s):  
Hongzhao Lu ◽  
Hao Bai ◽  
Ling Wang ◽  
Tao Zhang
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Gene Flow ◽  
Domestic Horse ◽  
European Regions ◽  
Geographical Regions ◽  
D Loop ◽  
Ancient Times

To clarify the origin and genetic diversity of modern horses, mitochondrial DNA (mtDNA) D-loop sequences were generated for 3965 horses from 12 geographical regions. From these sequences, we observed 439 haplotypes defined by 138 polymorphic nucleotide sites. All horses were genetically diverse (HD = 0.973 ± 0.001, π = 0.0243 ± 0.0005), which showed that maternal lineages of the domestic horse are worldwide highly diverse. In general, all 18 haplogroups were presented in the Asian horse. The majority of modern horse sequences belong to haplogroups L, Q, and A. At the same time, 194 archaeological samples from four geographical regions were obtained. Indeed, haplogroup distributions are overlapping in modern and ancient samples, indicating that most haplogroups were already present in ancient times at least in Europe and Asia. The network showed that breeds of Asian and Europe regions overlapped, suggesting that extensive gene flow had occurred between different horse breeds in Asian and European regions.

scholarly journals High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1680
Author(s):  
Nattakan Ariyaraphong ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
Thitipong Panthum ◽  
Syed Farhan Ahmad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Dairy Cattle ◽  
Large Scale ◽  
Genetic Relationships ◽  
Extensive Study ◽  
Distribution Analysis ◽  
Cattle Breeds ◽  
D Loop

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

scholarly journals Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9679
Author(s):  
Noorhani Syahida Kasim ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Rumeaida Mat Piah ◽  
Wahidah Mohd Arshaad ◽  
Siti Azizah Mohd Nor ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Pacific Ocean ◽  
Goodness Of Fit ◽  
Demographic History ◽  
Population Expansion ◽  
Seasonal Migration ◽  
Likelihood Method ◽  
Recent Population Expansion ◽  
D Loop ◽  
Longtail Tuna

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989–1.000; ND5 = 0.848–0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019–0.025; ND5 = 0.0017–0.003), “star-like” haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

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