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Due to only a weak conflict, we combined the total datasets for the additional phylogenetic analyses.
As already mentioned in Section 2, the trends reported here are robust enough to be valid for any subset of the total datasets of orthologous sequences.
Tajima's D for the total datasets are −1.15 and 0.71 (−0.52 and 0.73 for synonymous) for C. grandiflora and C. rubella, respectively, suggesting population expansion in C. grandiflora and a population bottleneck in C. rubella.
Genetic diversity is reduced in C. rubella compared with C. grandiflora (total sites π = 0.007 and 0.005, synonymous sites π = 0.021 and 0.013, and average number of haplotypes per locus = 38.3 and 4.23 for the total datasets of C. grandiflora and C. rubella, respectively).
Two species, P. petelotii (series Aloenses) and P. lachnoglossa (series Lachnoglossae, one species in Himalaya), formed a grade, followed by the alternate-leaved clade 5. Clade 5 was strongly supported by the total datasets (1.00/8 6, but it was weakly supported using the nrITS and plastid datasets (Additional files 2, 3 and Table 2).
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The total dataset consists of 96 h of observation time.
The error rate for the total dataset was 3.16%.
PC 6 explains 1.79 % of the total dataset.
Cluster analysis was applied on the total dataset from the two seasons.
The table indicates the percentage each vulnerability represents of the total dataset.
Spatial FA/PCA for HIG, five VFs explained 100% variations in the total dataset (Table 1).
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