Genomic clustering and admixture analyses
The quality filtered and trimmed reads were mapped to the M.
longifolia reference genome (GCA_001642375.1_Mlong1.0; Vining et al.,
2017) using bowtie2 with default settings. Mapped reads were quality
filtered as outlined above and reads previously identified to map to the
plastome were removed. The quality filtered mapping files were used to
call single nucleotide polymorphisms (SNPs) in angsd v.0.931
(Korneliussen, Albrechtsen, & Nielsen, 2014). Only SNPs with less than
50% missing data across all individuals were retained and maximum depth
to call a SNP within an individual was set to 50. SNPs were called using
the SAMtools option and only genotypes with a posterior probability
above 0.95 were used in downstream analyses. Genomic clusters were
evaluated from the nuclear SNPs in PCangsd v.0.95 (Meisner &
Albrechtsen, 2018) with default settings. The resulting covariance
matrices were converted to eigen-values and visualized in R. Genomic
admixture was evaluated using the nuclear SNPs in NGSadmix v3.2 (Skotte,
Korneliussen, & Albrechtsen, 2013) with K increasing from 1 to
10. The best fit K was evaluated using the method of Evanno,
Regnaut, and Goudet (2005) implemented in CLUMPAK (Kopelman et al.,
2015) using ten independent runs of NGSasmix for each K .