The evolution of fungus farming in ship-timber beetles (Coleoptera: Lymexyloidea)

This dataset contains files associated with the three different phylogenetic analyses:

The *_scaffolds.fasta files contain the cleaned genome assemblies of the five lymexyloid species that were used for this study.

The contig_filter.txt and contig_sorter.py files contain the instructions and scripts we used to remove bacterial scaffolds from the genome assemblies.

Lym_SUPERMATRIX: this the concatenated alignment of 827 amino acid sequences that were used in the phylogenomic analysis. The 827 gene partitions are included in the partition file.

Lym_busco: output files from IQ-tree of the phylogenomic analysis (log file and tree file).

Lym_827_genetrees.treefile: contains the 827 gene trees from each busco locus used for the ASTRAL analysis.

Lym_constraint_tree: the treefile containing the constraint tree that was used for the maximum likelihood analysis.

Lym_mt_concatenated.fa: concatenated alignment of mitochondrial genes. The Lym_ML_partitions.txt file contains the partitions.

Lym_ML: output files from IQ-tree of the phylogenetic analysis using mitochondrial genome data (log file and tree file).

Lym_Bayes: the input file, log file and tree file resulting from the Bayesian analysis using mitochondrial genome data.

Lym_ASTRAL: the resulting phylogenetic tree and log file of the ASTRAL analysis.