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

Abstract

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata 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 S. gemmata 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 S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an F_st 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 F_st 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 S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.

Keywords: RAD-seq; nascent species; peripatric distribution; phylogenomic analysis; taxonomic implication.

Figure 1

Geographic distribution of studied individuals of Stewartia gemmata complex and the phylogenetic tree showing the evolutionary affinities among these plants. The distribution ranges (shadowed) of S. gemmata and S. acutisepala were drawn based on [22,25,28]. In the consensus maximum likelihood (ML) tree, ‘gem’ stands for S. gemmata (blue) and ‘acu’ stands for S. acutisepala (red). The bootstrap support value is shown for each node. The scale bar is in the unit of the number of substitutions per site. The map was retrieved from the Geospatial Data Cloud, Computer Network Information Center, Chinese Academy of Sciences (http://www.gscloud.cn/; accessed on 12 November 2023). The accession IDs are consistent with those in Table 1.

Figure 2

Genetic differentiation between S. gemmata and S. acutisepala measured using weighted Weir and Cockerham’s F_st on a windowed basis. The dashed line indicates an F_st value greater than 0.25 in each pseudo-chromosome. The red, blue, and gray genomic bins indicate F_st values > 0.50, 0.50–0.25, and ≤0.25, respectively.

Figure 3

The distribution of five S. gemmata individuals (blue dots), five S. acutisepala individuals (red dots), and one S. monadelpha individual (the black dot) along the first and the second principal components (PCs) of genetic variations. PC1 explained 1.79% of the total variation, and PC2 explained 1.53% of the total variation. The accession IDs are consistent with those in Table 1. The ellipse draws a 95% confidence level with a t-distribution.

Figure 4

The ADMIXTURE results showing the ancestries of 11 studied individuals through the K = 2 to K = 4 scenarios. Under each scenario, the individual ancestries of S. acutisepala can all be found within S. gemmata, and no genetic admixtures were found among individuals (ancestry proportion (Q) > 0.99). The accession IDs are consistent with those in Table 1.