Phylogenomic alignments, maximum-likelihood trees, and monoterpene presence–absence figures for 28 Menthinae taxa

This dataset contains the phylogenetic data and publication figures for 28 taxa (24 Menthinae ingroup species and 4 outgroups) in Lamiaceae. It includes concatenated alignments and maximum-likelihood trees from two genomic sources: 520 low-copy nuclear loci (682,944 positions) and 80 plastid protein-coding genes (69,616 positions). Both matrices were analysed in IQ-TREE 2. Node labels on the treefiles are SH-aLRT / ultrafast bootstrap support. A checked matrix records the presence (1) or absence (0) of 10 monoterpene or monoterpenoid compounds across the 28 taxa. Contents phylogenetic_data/Menthinae_LCNG_520genes_28taxa_alignment.fasta — concatenated nuclear alignment phylogenetic_data/Menthinae_LCNG_520genes_28taxa_partitions.txt — locus partitions for the nuclear supermatrix phylogenetic_data/Menthinae_LCNG_520genes_28taxa_ML.treefile — nuclear maximum-likelihood tree phylogenetic_data/LCNG520_ML_bootstrap_reordered.nex — rooted nuclear tree used for the figure phylogenetic_data/Menthinae_Plastome_80genes_28taxa_alignment.fasta — concatenated plastome alignment phylogenetic_data/Menthinae_Plastome_80genes_28taxa_ML.treefile — plastome maximum-likelihood tree phylogenetic_data/Plastome_ML_bootstrap_reordered.nex — rooted plastome tree used for the figure phylogenetic_data/Chapter2_presence_absence_checked.xlsx — presence/absence of 10 compounds figures/LCNG_phylogeny_compound_matrix.pdf (also .svg, .tiff, .png) — nuclear tree beside the compound matrix figures/Plastome_phylogeny_compound_matrix.pdf (also .svg, .png, .tiff) — plastome tree beside the compound matrix figures/Figure_preparation_methods.md and figures/Figure_preparation_methods.txt — how the figures were drawn In each figure, matrix rows are aligned to the tree tips. Filled cells indicate presence and white cells indicate absence. Background shading marks Clade 1 (Micromeria), Clade 2 (Clinopodium), and the outgroups. Raster images are 600 dpi.