Genome-wide analyses reveal drivers of penguin diversification

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.

The genomic basis of evolutionary differentiation among honey bees

“…Our results parallel previous analyses that indicate accelerated evolution during the diversification of species within a family (Nevado et al 2016;Tollis et al 2018;Vianna et al 2020), suggesting a common evolutionary pattern. We also find evidence for selection for sequence changes in existing protein-coding regions and evolutionary turnover of genes, similar to a genomic study of the radiation of closely related bumble bees (Sun et al 2021).…”

Fifty million years of beetle evolution along the Antarctic Polar Front

“…Indeed, diversification appears to be ongoing as indicated by significant phylogeographic structure for the widespread species P. eatoni. A similar pattern of continued or accelerated diversification over the Plio-Pleistocene has been documented in many Antarctic marine groups (36,38,48). Moreover, preliminary evidence indicates the same timing of diversification processes for other terrestrial groups, such as mites (49), mosses (50), springtails (16), and diatoms (12), with diversification ongoing in some of these groups too (51).…”

“…Significant global cooling, ice sheet growth, and oceanographic changes during the middle and late Miocene climate transitions (∼14 and ∼7 Ma ago) finalized the isolation of Antarctica and the establishment of permanent polar conditions both marine and terrestrial (43). The emergence of most Antarctic marine biodiversity around this time has been attributed to these profound environmental changes, which provided ecological opportunities (e.g., new habitat and diet niches, extinction of predators) for marine life to exploit (2,17,36). This also seems to be the case for Ectemnorhinini weevils.…”

Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle

“…Comparative genomic analyses will also be useful to examine in further detail genes controlling physiological or morphological sea turtle traits related to EPO adaptations, as has been studied in other Chelonians and seabirds associated with desert and climate adaptations, respectively (e.g. genes related to desert adaptations in the Gopherus species complex [69] and genes related to climate adaptation in penguins [70]). Our study challenges researchers to increase adaptive investigation in marine vertebrate species which inhabit this unique ecosystem in the world.…”