Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

Garvin, Michael R.; Bielawski, Joseph P.; Gharrett, Anthony J.

doi:10.1371/journal.pone.0024127

Cited by 87 publications

(89 citation statements)

References 70 publications

(97 reference statements)

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“…For example, a recent study analyzed mtDNA sequences from hundreds of Atlantic salmon individuals from many populations and found a pattern of positive selection in ND1, ND3, and ND4 that correlated with latitudinal gradients (Consuegra et al, 2015). Interestingly, similar results were also found in Pacific salmon (Garvin et al, 2011) and killer whales (Foote et al, 2011) suggesting these patterns of positive selection in mitochondrial genes could be driven by different metabolic demands in the lower temperatures of higher latitudes. Surfperches are certainly a good system to examine this pattern as they range from warmer waters off Southern California and Baja, Mexico to cooler waters off Alaska, but here we only have data from three individuals each representing separate species.…”

Section: Substitution Rates and Dn/dssupporting

confidence: 70%

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

et al. 2016

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The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae) The complete 16,515 bp nucleotide sequence of the mitochondrial genome was determined for the black surfperch, Embiotoca jacksoni (Perciformes: Embiotocidae). The black surfperch mitochondrial genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (Dloop), the gene order of which is identical to that observed in most vertebrates. The protein-coding gene sequences of E. jacksoni mitochondrial DNA were compared with two other embiotocid surfperches with available complete mitochondrial genomes, Cymatogaster aggregata and Ditrema temminckii. Across all mitochondrial protein-coding genes in surfperches the weighted average substitution rate was 2.079% per My and average dN/dS ratios for each protein-coding gene ranged from 0.016 in CytB to 0.608 in ND3. Substitution rates and dN/dS ratios were relatively high for ATP8 compared to other protein-coding genes. Although most protein-coding genes showed signals of purifying selection, we found evidence for positive selection in ND3 in E. jacksoni.

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Section: Substitution Rates and Dn/dssupporting

confidence: 70%

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

et al. 2016

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“…This position is situated close to two fixed changes between American and European eels (positions 544 and 548; Figure 2) and is situated in a region of the ND5 gene, a 'piston' arm, which previously has been suggested to be under positive selection in pacific salmon (Oncorhynchus sp.) (Supplementary Figure S2); (Garvin et al, 2011). However, similar mutations were observed in two individuals of independent ancestry (Figure 2) and the derived valine amino acid has almost identical physiochemical properties to the ancestral isoleucine.…”

Section: Genetic Variation and Demographic Historysupporting

confidence: 57%

Speciation and demographic history of Atlantic eels (Anguilla anguilla and A. rostrata) revealed by mitogenome sequencing

et al. 2014

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Processes leading to speciation in oceanic environments without obvious physical barriers remain poorly known. European and American eel (Anguilla anguilla and A. rostrata) spawn in partial sympatry in the Sargasso Sea. Larvae are advected by the Gulf Stream and other currents towards the European/North African and North American coasts, respectively. We analyzed 104 mitogenomes from the two species along with mitogenomes of other Anguilla and outgroup species. We estimated divergence time between the two species to identify major events involved in speciation. We also considered two previously stated hypotheses: one where the ancestral species was present in only one continent but was advected across the Atlantic by ocean current changes and another where population declines during Pleistocene glaciations led to increasing vicariance, facilitating speciation. Divergence time was estimated to B3.38 Mya, coinciding with the closure of the Panama Gateway that led to reinforcement of the Gulf Stream. This could have advected larvae towards European/North African coasts, in which case American eel would be expected to be the ancestral species. This scenario could, however, not be unequivocally confirmed by analyses of dN/dS, nucleotide diversity and effective population size estimates. Extended bayesian skyline plots showed fluctuations of effective population sizes and declines during glaciations, and thus also lending support to the importance of vicariance during speciation. There was evidence for positive selection at the ATP6 and possibly ND5 genes, indicating a role in speciation. The findings suggest an important role of ocean current changes in speciation of marine organisms.

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“…Garvin et al [21] detected a strong signal of positive selection in the ND2 and ND5 genes between species of Pacific salmon. Specifically, they linked the significant sites on the ND5 gene to the structural piston arm of a proton pump and suggest the possibility that changes in the proton pump may have influenced fitness during the evolution of the salmon species studied.…”

Section: Discussionmentioning

confidence: 99%

Evidence of Positive Selection in Mitochondrial Complexes I and V of the African Elephant

et al. 2014

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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.

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Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

Cited by 87 publications

References 70 publications

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

Speciation and demographic history of Atlantic eels (Anguilla anguilla and A. rostrata) revealed by mitogenome sequencing

Evidence of Positive Selection in Mitochondrial Complexes I and V of the African Elephant

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