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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 by Helena 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 (TBA).

- 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).

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