Species Differentiation of Prunus serrulata and Prunus xueluoensis Based on Combined Analysis of SSR and cpDNA Markers

Prunus xueluoensis C. H. Nan & X. R. Wang is a new species of the Subg. Cerasus Mill., described by C. H. Nan and X. R. Wang in 2013. Since the publication of P. xueluoensis, its taxonomic status has been the subject of ongoing debate. This study focuses on wild populations of P. xueluoensis and Prunus serrulata (Lindley) London, utilizing 18 pairs of SSR molecular markers and variations in chloroplast DNA sequences (matK, trnD-E, and trnS-G) to delineate the relationship between the two species. The results showed that P. serrulate (N = 12.400, Na = 5.144, H = 0.578, I = 1.129, Ho = 0.493) and P. xueluoensis (N = 13.625, Na = 6.264, H = 0.614, I = 1.342, Ho = 0.495) populations exhibit rich genetic diversity, which may be related to their wide geographical distribution. The CpDNA genetic diversities of P. serrulata (Hd = 0.553, Pi = 0.00136) and P. xueluoensis (Hd = 0.496, Pi = 0.00180) are at a high level within the Subg. Cerasus Mill. The UPGMA clustering, along with MP and ML phylogenetic trees, show that the unique haplotypes of P. xueluoensis cluster separately as a terminal branch in the evolutionary tree with high support. The shared haplotypes and unique haplotypes of P. serrulata are predominantly located at the base of the phylogenetic tree, suggesting that the two species have diverged. In the TCS haplotype network, the central and key node haplotypes are primarily unique to P. serrulata and shared haplotypes, while the unique haplotypes of P. xueluoensis are all distributed along the network’s periphery. Both P. serrulata (Nst = 0.254, Gst = 0.103, Nst/Gst = 2.466, p < 0.05) and P. xueluoensis (Nst = 0.366, Gst = 0.268, Nst/Gst = 1.366, p < 0.05) exhibit phylogeographic structures. However, when considered as a whole, the combined entity of P. serrulata and P. xueluoensis does not show a significant phylogeographic structure (Nst = 0.317, Gst = 0.400, Nst/Gst = 0.793, p < 0.05), which supports the classification of these as two distinct species. The estimate of the average age of the latest common ancestor of P. serrulata and P. xueluoensis is 3.22 mya (PP = 1; 95% HPD: 3.07~3.46 mya). Due to environmental differences in altitude, the group of P. serrulata differentiated in the expansion into the cold and humid alpine environment and gradually formed P. xueluoensis. The findings support the classification of P. serrulata and P. xueluoensis as two distinct species.