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Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai–Tibet Plateau: homoploid hybrid origin and Pleistocene expansion



Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai–Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, Plikiangensis and Pwilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and Ppurpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well-established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between Ppurpurea and Pwilsonii, while variation at the nuclear se1364 gene suggested Ppurpurea was more closely related to Plikiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that Ppurpurea originated by homoploid hybrid speciation from Pwilsonii and Plikiangensis. The ABC analysis dated the origin of Ppurpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by Plikiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from Pwilsonii such that it came to possess both mtDNA and cpDNA of Pwilsonii. The estimated parameters indicated that following its origin, Ppurpurea underwent an expansion during/after the largest Pleistocene glaciation recorded for the QTP.