Genetic diversity and differentiation
After quality filtering, 224,000 reads (SD = 36,000) were recovered per individual, and a mean coverage of 127 x (SD = 20 x) was obtained for the target regions. Genes that did not map to any of the nine chromosomes of the reference genome were discarded in the following analyses. A total of 489 biallelic SNPs (average 9.4 (SD = 7.4) SNP sites per gene) were recovered from the enriched genes after filtering with VCFtools (Table S6).
The genetic diversity varied between populations and species (Table S3). The species-specific H exp ranged from 0.18 to 0.3 and was highest in S. taiwanensis (0.3) and S. hsiehii(0.26). Moreover, private alleles were most abundant in the non-endemic species S. barbata, with 61 private alleles, followed by another non-endemic species, S. indica , with 16 private alleles.
In S. barbata and S. indica , the intraspeciesF ST values were larger than theF ST values between species (Fig. S3A).F IS was negative in all populations (Table S3). The PCA indicated considerable intraspecific differentiation in S. barbata , S. indica , and S. taiwanensis . S. tashiroi and S. playfairii formed distinct clusters within species in the first three axes (Fig. 1B). Strong genetic structure was observed in S. barbata , S. indica , S. taiwanensis .S. tashiroi , and S. playfairii, and the two best K values revealed substantial admixture between most species (Fig. 1A, C; Fig. S2). S. taiwanensis was grouped with some populations of S. indica and S. tashiroi . A similar phenomenon was observed inS. hsiehii , which contained genetic components from S. austrotaiwanensis and some S. indica populations (Fig. 1 C). The FH and CC populations of S. barbata contained genetic components from S. tashiroi and an unknown source. The AWD and INDWL populations of S. indica included genetic components fromS. tashiroi and S. hsiehii . The HDD population of S. indica and the PLAWLLD population of S. playfairii also contained genetic components from S. tashiroi . Conversely, the TASWLLD population of S. tashiroi included genetic components from S. playfairii . On the basis of the results of the STRUCTURE analysis, we conclude that hybridization and introgression occurred frequently between Taiwanese Scutellaria species.
Consistent with these findings, the distance-based phylogenetic network revealed a web-like and reticulated evolutionary history; not all species were well resolved as monophyletic groups (Fig. 2). S. barbata, S. indica, S. tashiroi, and S. taiwanensis each formed two distinct phylogenetic groups. Within S. tashiroi , TAS1 was resolved as a sister to PLA, whereas TAS2 was resolved as a sister to IND1 (Fig. 2). S. indica exhibited similar relationships with other species, with IND1 and IND2 resolved as sisters to TAI2 and TAS1, respectively.