Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally
generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are
commercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in
warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits to
not only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processes
underlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found that
parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. This
includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributes
to thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, b-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight
Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two
species. Phylogeny-based metrics highlight conservation needs for some of these species.