Abstract
Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Ne ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased Ne between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.
Highlights
Few organisms have been as successful at colonizing the globe as seabirds, a large ecological assemblage of oceanic and nearshore species that undergo some of the most remarkable foraging and migratory journeys on Earth [1, 2]
The phylogeny based on mitogenomes was similar to that retrieved from the genomic datasets, with a few minor differences in Eudyptes penguins that are likely explained by genome-wide introgression among closely related species (Figs. 2, S7, S9, Table S7) as we found evidence that some species may had hybridized during the course of their diversification
Phylogenetic reconstructions recovered by this study show that the large emperor and king penguins (i.e., Aptenodytes) are sister to all other extant penguins, refuting the hypothesis that Aptenodytes and Pygoscelis are sister-taxa [4, 8, 9]
Summary
Few organisms have been as successful at colonizing the globe as seabirds, a large ecological assemblage of oceanic and nearshore species that undergo some of the most remarkable foraging and migratory journeys on Earth [1, 2] Despite their ubiquitous presence, surprisingly little is known about the mechanisms that spurred their diversification and allowed for their adaptation to diverse and often dynamic oceanic habitats. Our understanding of penguin diversification and adaptation is hampered by disagreements about their phylogenetic relationships [4,5,6,7,8,9,10] and the chronology of their radiation When these estimations are made using few genetic markers from different sections of the genome, discordant results are to be expected as genomic regions vary in their mutation rates and evolutionary history, including unknown patterns of gene introgression when different species hybridize [11]. The earliest crowngroup fossil dates to the late Miocene [12]
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