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SNP dataset, analysis scripts, and raw phylogenetic & phylogenomic trees for the sub-Antarctic Ectemnorhinini weevils

dataset
posted on 21.04.2021, 00:07 authored by Helena BairdHelena Baird, Seunggwan Shin, Rolf G. Oberprieler, Maurice Hullé, Philippe Vernon, Katherine L. Moon, Richard H. Adams, Duane McKenna, Steven L. Chown

Data and files associated with the manuscript: Baird et al (2021) 'Fifty Million Years of Beetle Evolution Along the Antarctic Polar Front', published in PNAS.

- Full, quality-filtered dataset of 5,859 genome-wide SNPs for the sub-Antarctic weevil Palirhoeus eatoni (Coleoptera: Curculionidae), provided in vcf format

- A metadata spreadsheet (providing the collection details for every P. eatoni individual, corresponding to sample IDs in the SNP dataset)

- R script used to filter the SNP dataset and perform basic SNP-based phylogeographic analyses

- Phylogenetic trees in .newick format, both dated and undated, are provided for the sub-Antarctic Ectemnorhinini weevil tribe as inferred from concatenated COI, cytochrome b, 16S, 28S, and Elongation factor 1-alpha sequences

- R script is provided for RPANDA macroevolutionary analyses, which are based on the dated phylogenetic tree generated in BEAST.

- R script and input files (with prefix 'BGB') are provided for BioGeoBEARS biogeographic inference analysis

- Phylogenomic trees in .nexus format are provided for representatives of the sub-Antarctic Ectemnorhinini together with a worldwide sample of Entiminae weevils, based on a concatenated dataset of 515 genes (1st and 2nd codons)

Funding

This work received support from EPFL, Swiss Polar Institute and Ferring Pharmaceuticals through the Antarctic Circumnavigation Expedition (‘ACE’). Co-author D.D.M. also received funding from the U.S. National Science Foundation (DEB1355169).

History