Genome-wide analyses reveal drivers of penguin diversification ...

• Main Authors: Vianna, Juliana, Fernandes, Flávia A. N., Frugone, María José, Figueiró, Henrique V., Pertierra, Luis R., Noll, Daly, Bi, Ke, Wang-Claypool, Cynthia Y., Lowther, Andrew, Parker, Patricia, Le Bohec, Celine, Bonadonna, Francesco, Wienecke, Barbara, Pistorius, Pierre, Steinfurth, Antje, Burridge, Christopher P., Dantas, Gisele P. M., Poulin, Elie, Simison, W. Brian, Henderson, Jim, Eizirik, Eduardo, Nery, Mariana F., Bowie, Rauri C. K.
• Format: Dataset
• Language: English
• Published: Dryad 2020
• Subjects: Antarctic; Drake Passage; New Zealand; The Antarctic; Antarc*; Antarctica
• Online Access: https://dx.doi.org/10.5061/dryad.pk0p2ngj2; https://datadryad.org/stash/dataset/doi:10.5061/dryad.pk0p2ngj2

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 ... : 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: scrubReads.pl; Extracting UCE markers: extractUces.pl; Performing MSA for introns/cds and cleaning the alignment: transExonCapPhyloV3.3.8.pl; Filtering for UCE: FilterByTaxNumber.py and FilterUCE.py; RaxML_NG_Astral III: laucher.py, makeDirs.py and process_runner.py; Predicted Niche Occupancy: PNO_Rscript.txt; Introgression: CreateDfoil_input.py; Natural selection: runEte3_sitemodel_contigs.sh ...