Evolutionary mechanisms of varying chromosome numbers in the radiation of Erebia butterflies

This is the dataset for the study with the same title published at MDPI Genes (please see the paper for all details).

To test for a phylogenetic signal of varying chromosome numbers in Erebia butterflies (Lucek submitted), I reconstructed a phylogeny using a subset of Peña et al. Biol J Linn Soc 2016 for which chromosome numbers were available. Data for an additional 5 species was taken from GenBank. Chromosome numbers used are included.
The final alignment comprised sequence data for four genes: 620 bp of the mitochondrial cytochrome oxidase subunit I (COI), 598 bp of the nuclear glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 565 bp of the nuclear ribosomal protein S5 (RpS5) and 343 bp of the nuclear wingless gene.

I used PartitionFinder 2 (Lanfear et al. Mol Biol Evol 2017) to infer the best partition scheme and associated substitution model for each codon position and gene. The output of PartitionFinder is provided in the data file. The resulting best partitioning scheme for the Bayesian inference is given in each nexus file. For the maximum likelihood (ML) based phylogeny I used the GTR model with invariant sites and gamma correction (GTR+I+G) in RAXML 8.2.8 (Stamatakis, Bioinformatics 2014) with the corresponding partition scheme from PartitionFinder. I further used 1000 bootstrap replicates to assess significance. I ran RAXML for the dataset comprising either all four genes, the mitochondrial COI gene only or the three nuclear genes. In the latter case, data was only available for 35 taxa. I conducted the Bayesian analysis in MrBayes 3.2.2 (Ronquist et al. Syst Biol 2012) for either dataset using in each case, 5’000’000 generations with four chains – three heated and one cold. Trees were sampled every 1’000 generations.
Provided are the input and output files of MrBayes and RAXML for all genes combined (subfolder all), the mitochondrial COI gene only (subfolder mtdna) or the three nuclear genes (subfolder nuclear).