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Background  Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera ( Spheniscus, Pygoscelis ,  Eudyptula ,  Eudyptes  and  Aptenodytes ). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species.    Results  We identified the complete mtDNA genomes of several penguin species, including  ND6  and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in  COX  genes. The lowest evolutionary divergence among species was between Humboldt ( Spheniscus humboldti ) and Galapagos ( S. mendiculus ) penguins (0.004) ,  while the highest was observed between little penguin ( Eudyptula minor ) and Adélie penguin ( Pygoscelis adeliae ) (0.097). We identified a signature of purifying selection (Ka/Ks &lt; 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on  ATP8  (Fixed-Effects Likelihood, FEL) and  ND4  (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast,  COX1  had a signature of strong negative selection.  ND4  Ka/Ks ratios were highly correlated with SST (Mantel,  p -value: 0.0001; GLM,  p -value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation.    Conclusions  These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4424-9) contains supplementary material, which is available to authorized users.

Landscape genomics: natural selection drives the evolution of mitogenome in penguins