Phylogeography and genomic adaptation of penguins across a wide latitudinal distribution from the Tropics to Antarctica

Penguins are widely distributed across latitudes along the southern hemisphere, from Equator to the pole. They differ in biology, ecology, population dynamics, adaptation and speciation timing. We studied several molecular markers (mtDNA, nuclear introns, MHC, and microsatellites), SNPs along the whole genome sequencing (n=12) and ddRAD to assess population genetic structure, phylogeography and adaptation of Pygoscelis (Antarctic and Sub-Antarctic region) and Spheniscus (South America) species. Spheniscus species exhibited reduced population genetics structure. Likewise, P. adeliae and P. antarcticus show similar patterns, with high gene flow between Antarctica and a sub-Antarctic island for the latter species. P. papua show a completely different pattern, with significant population genetics structure and high lineages divergence between Antarctica and each sub-Antarctic island. Comparing the nucleotide diversity on the CDS of genomes, the intraspecific diversity of 3635 genes between the five species of Spheniscus and Pygoscelis were similar, however, for the 35 genes related to thermoregulation, the highest diversity was observed in S. magellanicus and the lowest in P. adeliae, suggesting better adaptive capacities of S. magellanicus in response to climate change. MHC (major histocompatibility complex) genes in S. humboldti and S. magellanicus, exhibited high diversity for MHCI and MHCII, lack of local adaptation due high gene flow or weak selection. This high MHC diversity enhances the adaptive ability of both species to respond to pathogens. This molecular comparative approach allows understanding the differences in ecology between penguin species and how species may potentially respond to global changes based on the genetic diversity.