Chloroplast alignment and phylogenetics
Quality filtered and trimmed reads were mapped to the Mentha longifolia plastome (GenBank NC_032054, masking one of the inverted repeats) using bowtie2 v.2.3.4.3 (Langmead & Salzberg, 2012; Langmead, Wilks Antonescu, & Charles, 2019) with default settings. Mapped reads were quality filtered using SAMtools v.1.9 (Danecek et al., 2021) removing all reads mapping with a mapping quality score below 20 and PCR duplicated reads were removed using PicardTools v.2.25.2 (https://github.com/broadinstitute/picard). For each sample a consensus sequence was extracted using BCFtools v.1.9 (Danecek et al., 2021) and all ambiguous bases were recorded as N. Plastomes were aligned in mafft v.7.392 (Katoh & Standley, 2013) with default settings and a bootstrapped maximum-likelihood phylogenetic tree was inferred in RaxML v.8.2.11 (Stamatakis, 2014) with a GTR+G+I mutation model usingSalvia an outgroup (Li et al., 2016; NCBI Genebank accessions: NC_050898, MN520020, MN520021, NC_038165, MG772529, MN520019, NC_050897, MN520023, and NC_050900).