A Diverging Species within the (Theaceae) Complex Revealed by RAD-Seq Data.

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, and (the complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the complex and , and the latter was nested within the former. Among individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between and was relatively low (an of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that diverged from along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that is a variety of and is diverging from , providing empirical insights into the nascent speciation within a species complex.