Landscape Genomics: Natural Selection Drives the Evolution of Mitogenome in Penguins

• Published in: BMC Genomics
• Main Authors: Ramos, Barbara, González-Acuña, Daniel, Loyola, David, Johnson, Warren, Parker, Patricia, Massaro, Melanie, Dantas, Gisele, Miranda, Marcelo, Vianna, Juliana
• Format: Text
• Language: unknown
• Published: IRL @ UMSL 2018
• Subjects: Bioinformatics; Biology; Genomics; Antarc*; Antarctica; Pygoscelis adeliae
• Online Access: https://irl.umsl.edu/biology-faculty/113; https://doi.org/10.1186/s12864-017-4424-9; https://irl.umsl.edu/context/biology-faculty/article/1112/viewcontent/.pdf

BackgroundMitochondria 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.ResultsWe 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 < 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 ...