Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians

Abstract

Abstract:We investigated three single nucleotide polymorphisms (SNPs) in the mitochondrial sub-haplogroups of the Pima Indians to determine the effect of selection on each SNP and on metabolic efficiency. The SNPs are within genes encoding proteins in electron transport and oxidative phosphorylation, and may affect the efficiency of energy metabolism, including resting metabolic rate (RMR) and respiratory quotient (RQ). They may be adaptations toward an energy-efficient metabolism when this population migrated to the desert and adopted a restricted caloric intake, and they may currently contribute to obesity. We found that two of the three recent SNPs affect RMR and/or RQ. Using the analytical software TreeSAAP, we inspected selection throughout mammalian evolution in 107 species, and characterized the biochemical shift produced by the amino acid substitutions. Our results suggest that two SNPs were affected by selection during mammalian evolution in a manner consistent with the effects on metabolic efficiency in Pima Indian SNP's. Therefore, evolutionary selection favors the recent Pima Indian mutations that result in amino acid substitutions consistent with increased efficiency of energy metabolism, with consequent effects on RMR and RQ.

Evolutionary Pressure on Mitochondrial Cytochrome b Is Consistent with a Role of CytbI7T Affecting Longevity during Caloric Restriction

“…These sequences were aligned and used for phylogenetic analysis (Supplementary Figure S1). The cytb gene sequences for the 107 mammalian species and the phylogenetic tree created from all 13 mtDNA genes were used as input for TreeSAAP as in Chamala et al [26].…”

“…When a SNP fails to share characteristics with the historical adaptations of the group, that SNP is more likely have a detrimental effect. Conversely, if a SNP has much in common with the adaptations of the group, that SNP may have a similar adaptive effect [26].…”

Evolution for extreme living: variation in mitochondrial cytochrome c oxidase genes correlated with elevation in pikas (genus Ochotona)

“…We used the algorithm implemented in TreeSAAP (selection on amino acid properties) (Woolley et al 2003) to identify significant amino acid changes within cox genes of the genus Ochotona. Ascertaining positive selection using physicochemical amino acid properties, such as in TreeSAAP, is a much more sensitive approach and allows individual amino acid changes and their effects on protein characteristics to be assessed (Chamala et al 2007). TreeSAAP compares the observed distribution of amino acid changes inferred from a phylogenetic tree with a random distribution of amino acid changes under neutral conditions.…”

“…We made alignments 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 for each of these 3 genes using Geneious 7.1.4. In combination with the phylogenetic tree created by Chamala et al (2007) (Fig. S1), we analyzed alignments using TreeSAAP in the same way as described above.…”

Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software

“…The use of amino acid properties results in a high degree of resolution that is more sensitive than the dN/dS approach [12], [16], and allows for the detailed diagnosis of individual amino acid changes in the context of the structure and function of proteins [1]. This alternative approach for detecting selection also exhibits great promise as a tool in the area of biomedical research [4], [14], [10].…”