scholarly journals Altitude-wise analysis of co-occurrence networks of mitochondrial genome in Asian population

2019 ◽  
Author(s):  
Rahul K Verma ◽  
Cristina Giuliani ◽  
Alena Kalyakuina ◽  
Ajay Deep Kachhvah ◽  
Mikhail Ivanchenko ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Altitude ◽  
Dna Sequences ◽  
Group Analysis ◽  
Asian Population ◽  
The Tibetan Plateau ◽  
Mt Dna ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
The Impact

ABSTRACTFinding mechanisms behind high altitude adaptation in humans at the Tibetan plateau has been a subject of evolutionary research. Mitochondrial DNA (mt-DNA) variations have been established as one of the key players in understanding the biological mechanisms at the basis of adaptation to these extreme conditions. To explore cumulative effects and dynamics of the variations in mitochondrial genome at varying altitudes, we investigated human mt-DNA sequences from NCBI database at different altitudes by employing co-occurrence motifs framework. We constructed co-occurrence motifs by taking into account variable sites for each altitude group. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between a lower and a higher altitude region. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral marker 10398 was found to co-occur only at higher altitudes supporting the fact that a separate root of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence motifs at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding role of co-occurrence of mitochondrial variations in high altitude adaptation.

scholarly journals Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rahul K. Verma ◽  
Alena Kalyakulina ◽  
Cristina Giuliani ◽  
Pramod Shinde ◽  
Ajay Deep Kachhvah ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Altitude ◽  
Dna Sequences ◽  
Large Scale ◽  
Framework Analysis ◽  
Mt Dna ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
The Impact

AbstractNetworks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mtDNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects of variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral ‘RSRS50’ variant 10,398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.

scholarly journals Genetic signatures of high-altitude adaptation in Tibetans

2017 ◽  
Vol 114 (16) ◽  
pp. 4189-4194 ◽  
Author(s):  
Jian Yang ◽  
Zi-Bing Jin ◽  
Jie Chen ◽  
Xiu-Feng Huang ◽  
Xiao-Man Li ◽  
...  
Keyword(s):  
High Altitude ◽  
Methylenetetrahydrofolate Reductase ◽  
The Tibetan Plateau ◽  
High Altitude Adaptation ◽  
Drift Model ◽  
Genome Wide ◽  
A Genome ◽  
Altitude Adaptation ◽  
Genetic Signatures ◽  
Genome Wide Study

Indigenous Tibetan people have lived on the Tibetan Plateau for millennia. There is a long-standing question about the genetic basis of high-altitude adaptation in Tibetans. We conduct a genome-wide study of 7.3 million genotyped and imputed SNPs of 3,008 Tibetans and 7,287 non-Tibetan individuals of Eastern Asian ancestry. Using this large dataset, we detect signals of high-altitude adaptation at nine genomic loci, of which seven are unique. The alleles under natural selection at two of these loci [methylenetetrahydrofolate reductase (MTHFR) and EPAS1] are strongly associated with blood-related phenotypes, such as hemoglobin, homocysteine, and folate in Tibetans. The folate-increasing allele of rs1801133 at the MTHFR locus has an increased frequency in Tibetans more than expected under a drift model, which is probably a consequence of adaptation to high UV radiation. These findings provide important insights into understanding the genomic consequences of high-altitude adaptation in Tibetans.

scholarly journals High altitude adaptation mitigates anemia risk associated with diabetes among the Mosuo of Southwest China

2018 ◽  
Author(s):  
M Su ◽  
K Wander ◽  
MK Shenk ◽  
T Blumenfield ◽  
H Li ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
High Altitude ◽  
Market Integration ◽  
Hypoxia Inducible Factor ◽  
Human Populations ◽  
The Tibetan Plateau ◽  
Low Oxygen ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Hb Concentration

AbstractHuman populations native to high altitude regions (≥2500 m) exhibit numerous adaptations to hypoxic stress. On the Tibetan Plateau, these include modifications of the hypoxia inducible factor (HIF) pathway to essentially uncouple erythropoiesis (red blood cell production) and blood hemoglobin (Hb) concentration—which normally increase in response to low oxygen—from hypoxia. Uncoupling of erythropoiesis and hypoxia is also observed among people with diabetes due to damage to kidney tissues. This is hypothesized to result in elevated risk for anemia among diabetics, which increases risk for cardiovascular disease and death. We tested the hypothesis that the independence of erythropoiesis from HIF among high-altitude adapted populations of the Tibetan Plateau may protect against diabetes-associated anemia. We investigated this hypothesis among the Mosuo, a population living in Yunnan Province, China (at ~2800 m altitude) that is undergoing rapid market integration and lifestyle change, with concomitant increase in risk for type 2 diabetes. We found that, although diabetes (glycated hemoglobin, HbA1c ≥6.5%) is associated with anemia (females: Hb<12g/dl; males: Hb<13g/dl) among the Chinese population as a whole (N: 5,606; OR: 1.48; p: 0.008), this is not the case among the Mosuo (N: 316; OR: 1.36; p: 0.532). Both pathways uncoupling hypoxia from erythropoiesis (diabetic disease and high altitude adaptation) are incompletely understood; their intersection in protecting Mosuo with diabetes from anemia may provide insight into the mechanisms underlying each. Further, these findings point to the importance of understanding how high-altitude adaptations interact with chronic disease processes, as populations like the Mosuo experience rapid market integration.

High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses

Gene ◽  
2013 ◽  
Vol 517 (2) ◽  
pp. 169-178 ◽  
Author(s):  
Yali Li ◽  
Zhumei Ren ◽  
Andrew M. Shedlock ◽  
Jiaqi Wu ◽  
Luo Sang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Altitude ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Genome Analyses

scholarly journals High‐altitude adaptation in vertebrates as revealed by mitochondrial genome analyses

2021 ◽  
Author(s):  
Xibao Wang ◽  
Shengyang Zhou ◽  
Xiaoyang Wu ◽  
Qinguo Wei ◽  
Yongquan Shang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Altitude ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Genome Analyses

High Altitude Adaptation and Phylogenetic Analysis of Tibetan Horse Based on the Mitochondrial Genome

2007 ◽  
Vol 34 (8) ◽  
pp. 720-729 ◽  
Author(s):  
Shuqing Xu ◽  
Jiangbai Luosang ◽  
Sang Hua ◽  
Jian He ◽  
Asan Ciren ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
High Altitude ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

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