Genomic Insights Into the Evolutionary History of Berardius Beaked Whales: Speciation Driven by Resource Specialization, Gigantism and Thermal Barriers?

Understanding the diversity of our oceans is fundamental now more than ever as climate change and human activities put increasing pressure on marine species and ecosystems. Beaked whales (family Ziphiidae) are among the most poorly understood marine mammals, in part due to their affinity to offshore underwater canyons and prolonged diving ability. The ziphiid genus Berardius is comprised of three extant species; however, a lack of genomic data results in uncertainties of their evolutionary origin, phylogenetic relationships and the past environmental drivers of speciation and demographic fluctuations. Here, we analyse whole nuclear and mitochondrial genomes to better understand the evolutionary and demographic history of Berardius spp. Genome-wide comparisons support an initial divergence of B. minimus from the B. bairdii-B. arnuxii common ancestor ~4 million years ago (mya), and a divergence between B. bairdii and B. arnuxii ~1.5 mya. Despite these deep divergence times, gene flow was detected between species pairs for at least 75% of their post-divergence branch lengths. Strong levels of introgression (~8%) were detected between the non-sister but geographically overlapping B. bairdii and B. minimus species, despite their significant differences in body size. Our results show that the Berardius speciation process goes beyond simple bifurcating divergences. We hypothesize that resource specialization and an increased body size in the B. bairdii-B. arnuxii ancestor may have been an incipient driver of speciation and further that climate cycles during the late Pleistocene, coupled with ranging movements to the tropics, could have permitted repeated opportunities for gene flow between species.