Investigation of phylogenetic relationships within Saxifraga diversifolia complex (Saxifragaceae) based on restriction-site associated DNA sequence markers

Abstract

Subsect. Hirculoideae Engl. & Irmsch., belonging to Saxifraga sect. Ciliatae Haw., has high species richness. It can be divided into S. diversifolia, S. pseudohirculus, and S. sinomontana complexes based on morphological characteristics. The species with prominent leaf veins on the posterior leaf edge were placed in the S. diversifolia complex, which is mainly distributed on the eastern and southern margins of the Qinghai-Tibetan Plateau. In this study, 53 samples, representing 15 of the 33 described species in the S. diversifolia complex, were sequenced using the Restriction-site Associated DNA Sequence (RAD-seq) technique. A total of 111,938 high-quality SNP loci were screened to investigate the phylogenetic relationships within the S. diversifolia complex. The result of the neighbor-joining (NJ) tree shows that the S. diversifolia complex is a paraphyletic group. Despite of some inconsistencies as revealed by genetic structural analysis, clustering results of representative species reconstructed by both NJ and principal component analysis analyses support previous biogeographic and morphological evidences. In addition, long-distance gene flow events for 11 taxa were detected in the S. diversifolia complex, respectively from S. implicans 1 to S. implicans 2, S. diversifolia and S. maxionggouensis, and from S. maxionggouensis to S. nigroglandulifera. These findings may improve our comprehension of the phylogeny, classification, and evolution of the S. diversifolia complex.

Keywords: RAD‐seq; S. diversifolia complex; SNP loci; Saxifraga; phylogeny.

FIGURE 1

The illustration from S. egregia. (a) Herbs perennial, 9–32 cm tall. (b) Sepals yellow with callose, elliptic to ovate, apex obtuse or subacute, base clawed. (c) Cauline leaves cordate‐ovate to cordate, marginally brown villous, base petiolate. (d) Stamens 10; styles 2; ovary subsuperior; sepals reflexed.

FIGURE 2

Phylogenetic tree reconstructed based on the SNP data of high quality using unrooted neighbor‐joining (NJ) methods. Taxa includes 53 samples representing 28 species of Saxifraga, including 15 of the 33 described in the S. diversifolia complex.

FIGURE 3

Phylogenetic tree reconstructed based on the SNP data of high quality using rooted neighbor‐joining (NJ) methods. Taxa includes 53 samples representing unique 28 species of Saxifraga, including 15 of the 33 described in the S. diversifolia complex. Numbers at the nodes represent bootstrap values of the support rate. Different colors represent different groups, meaning that green indicates outgroups and blue denotes S. diversifolia complex. The taxonomic information in previous studies and important morphological characteristics of the S. diversifolia complex are arranged in columns.

FIGURE 4

Results of principal component (PCA) and genetic structure analysis. Display the clustering results of PCA in two‐dimensional (a) and three‐dimensional (b). Different colors represent different taxa, where 27 samples lineage stand for 10 taxa, namely S. insolens, S. subaequifoliata, S. implicans, S. egregia, S. pardanthina, S. diversifolia, S. cardiophylla, S. maxionggouensis, S. pratensis, S. erectisepala. (c) Different k values correspond to the CV error value. The result shows that the CV error value is the minimum when K equals three, which is the optimal number of clusters. (d) The clustering results of genetic structure in 53 samples when k is equal to two to five.

FIGURE 5

The result of gene flow evaluation. (a) The different migration edges correspond to the change rate of likelihood value (Δm). When the number of gene exchanges is four, it is the relatively optimal migration edge. (b) The direction and weight of four gene flow events. The arrows indicate the direction of gene flow and the legend represents the weights. Each branch represents a taxon and its length refers to the proportion of genetic drift.