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. https://doi.org/10.5061/dryad.pk0p2ngj2
Abstract
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: 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
Funding
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