R EPORTS Effects of Purifying and Adaptive Selection on Regional Variation

Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, CA 92697-3940, USA.
Science (Impact Factor: 33.61). 02/2004; 303(5655):223-6. DOI: 10.1126/science.1088434
Source: PubMed


A phylogenetic analysis of 1125 global human mitochondrial DNA (mtDNA) sequences permitted positioning of all nucleotide substitutions according to their order of occurrence. The relative frequency and amino acid conservation of internal branch replacement mutations was found to increase from tropical Africa to temperate Europe and arctic northeastern Siberia. Particularly highly conserved amino acid substitutions were found at the roots of multiple mtDNA lineages from higher latitudes. These same lineages correlate with increased propensity for energy deficiency diseases as well as longevity. Thus, specific mtDNA replacement mutations permitted our ancestors to adapt to more northern climates, and these same variants are influencing our health today.

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    • "However, intra-and interspecific variations in mitochondrial genome are very useful markers to study the evolution of animals even human, especially in taxonomy, systematics, ecology, and population biology (Avise et al. 1987, Moritz et al. 1987, Malyarchuk et al. 2010). Mitochondrial DNA analyses based on partial nucleotide sequences usually assume that most of the variations conform to a neutral model of molecular evolution, but some experimental studies and human mitochondrial genome data have suggested that selective forces might act upon mitochondrial DNA (William et al. 1995, Ruiz-Pesini et al. 2004). The complete mitochondrial genome sequences have been determined for >300 species of insects so far and the order Hemiptera is the largest group of the hemimetabolous insects (Schuh and Slater 1995, Zhang et al. 2013). "
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    ABSTRACT: Planthoppers in the genus Nilaparvata Distant are serious pests of rice and many other crops in tropical and temperate Asia, and northern Australia. In this study, the mitochondrial genomes of four Nilaparvata planthoppers were sequenced, three in Nilaparvata lugens Stål and one in Nilaparvata muiri China. Mitochondrial genome of Nilaparvata contain the standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The nucleotide composition of Nilaparvata mitochondrial sequence is biased toward adenine and thymine, and the amino acid composition is affected to a similar degree by the bias to AT. We compare the four mitochondrial genomes and find intra- and interspecific variation in gene length, base composition, nucleotide and amino acid substitutions, intergenic spacer length, and gene overlap. The intra- and interspecific variations reveal that nucleotide and amino acid substitutions in mitochondrial protein-coding genes make a contribution to the formation of various insect biotypes in one species. Furthermore, the accumulation of nonsynonymous substitutions in the mitochondrial protein-coding genes, as well as differences in start codons, the length of intergenic spacers, and gene overlap regions contribute to differences between the two species investigated here. In addition, cox is the most conserved gene family and nad4-nad4l cluster is variable in Nilaparvata mitochondrial genes for the intra- and interspecific variation.
    Journal of Economic Entomology 05/2015; 108(4). DOI:10.1093/jee/tov122 · 1.51 Impact Factor
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    • "ROS have been implicated in inflammatory cytokine production, suggesting a connection between oxidative stress and inflammatory processes [23]. MtDNA haplogroups may also affect the coupling of the respiratory chain [24], which can result in increased endogenous ROS in mitochondria [25]. Recent work has demonstrated that mtDNA haplogroups modify the relationship of traffic-related air pollution exposures with systemic biomarkers of inflammation [26], suggesting a role of mitochondrial haplogroups on systemic inflammation. "
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    ABSTRACT: Background Traffic-related air pollution has been linked with impaired cognition in older adults, possibly due to effects of oxidative stress on the brain. Mitochondria are the main source of cellular oxidation. Haplogroups in mitochondrial DNA (mtDNA) mark individual differences in oxidative potential and are possible determinants of neurodegeneration. The aim of this study was to investigate whether mtDNA haplogroups determined differential susceptibility to cognitive effects of long-term exposure to black carbon (BC), a marker of traffic-related air pollution. Methods We investigated 582 older men (72 ± 7 years) in the VA Normative Aging Study cohort with ≤4 visits per participant (1.8 in average) between 1995–2007. Low (≤25) Mini Mental State Examination (MMSE) was used to assess impaired cognition in multiple domains. We fitted repeated-measure logistic regression using validated-LUR BC estimated in the year before their first visit at the participant’s address. Results Mitochondrial haplotyping identified nine haplogroups phylogenetically categorized in four clusters. BC showed larger effect on MMSE in Cluster 4 carriers, including I, W and X haplogroups, [OR = 2.7; 95% CI (1.3-5.6)], moderate effect in Cluster 1, including J and T haplogroups [OR = 1.6; 95% CI: (0.9-2.9)], and no effect in Cluster 2 (H and V haplogroups) [OR = 1.1; 95% CI: (0.8-1.5)] or Cluster 3 (K and U haplogroups) [OR = 1.0; 95% CI: (0.6-1.6)]. BC effect varied only moderately across the I, X, and W haplogroups or across the J and T haplogroups. Conclusions The association of BC with impaired cognition was worsened in carriers of phylogenetically-related mtDNA haplogroups in Cluster 4. No BC effects were detected in Cluster 2 and 3 carriers. MtDNA haplotypes may modify individual susceptibility to the particle cognitive effects.
    Environmental Health 05/2014; 13(1):42. DOI:10.1186/1476-069X-13-42 · 3.37 Impact Factor
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    • "The selective neutrality assumption of mtDNA has been empirically tested and refuted across a broad range of organisms [12]. Recent studies have found evidence for molecular adaptations in the 13 protein-coding genes in the mtGenome [13], [14]. Some mutations have been associated with pathogenic disorders in humans and mice including exercise intolerance, neurological diseases and myopathy [15], [16], while others have been shown to have positive outcomes including greater aerobic energy metabolism [17]. "
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    ABSTRACT: As species evolve, they become adapted to their local environments. Detecting the genetic signature of selection and connecting that to the phenotype of the organism, however, is challenging. Here we report using an integrative approach that combines DNA sequencing with structural biology analyses to assess the effect of selection on residues in the mitochondrial DNA of the two species of African elephants. We detected evidence of positive selection acting on residues in complexes I and V, and we used homology protein structure modeling to assess the effect of the biochemical properties of the selected residues on the enzyme structure. Given the role these enzymes play in oxidative phosphorylation, we propose that the selected residues may contribute to the metabolic adaptation of forest and savanna elephants to their unique habitats.
    PLoS ONE 04/2014; 9(4):e92587. DOI:10.1371/journal.pone.0092587 · 3.23 Impact Factor
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