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Genome-wide analyses reveal drivers of penguin diversification

Cite this dataset

Vianna, Juliana et al. (2020). Genome-wide analyses reveal drivers of penguin diversification [Dataset]. Dryad.


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 thatAptenodytesis 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 increasedNebetween 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.

Usage notes

Submission of all the information related to the manuscript of the penguins phylogenome:

- Genomic data: Intron, CDS, UCE, and Mitogenome alignment files for phylogenetic reconstruction and species tree for all data set and without the yellow-eyed penguin genome; and the final dated phylogeny and the BEAST files for UCE and Mitogenome.

- Scripts: Cleaning raw reads:; Extracting UCE markers:;  Performing MSA for introns/cds and cleaning the alignment:; Filtering for UCE: and; RaxML_NG_Astral III: and; Predicted Niche Occupancy: PNO_Rscript.txt; Introgression:; Natural selection:


Agencia Nacional de Investigación y Desarrollo, Award: GAB PIA ACT172065

Agencia Nacional de Investigación y Desarrollo, Award: Fondecyt 1150517

National Science Board, Award: NSF DEB-1441652

Instituto Antartico Chileno, Award: INACH RT_12-14

French Polar Institute Paul-Emile Victor, Award: IPEV

French Polar Institute Paul-Emile Victor, Award: Progs. 137 and 354

California Academy of Sciences, Award: Lakeside grant