Population Genetics And Speciation Of Sect.Parrya Mayr

Population genetic structure and evolutionary history of the current species are one of the core contents in evolutionary biology, it has important scientific significance for understanding the nature process of speciation. In this study, we focused on the three endangered conifer tree species Pinus bungeana Zucc. ex Endl.?P. gerardiana Wall, and P. squamata X. W. Li which are subordinate to Pinaceae family, Pinus genera, Strobus subgenus, Parrya section. We sequenced 10 nuclear loci, one chloroplast DNA in these three related species using Isolation-with-Migration (IM) analysis?analyses of genetic structure simulation and Ecological Niche Modeling to study phylogenetic and evolutionary history of Sect. Parrya Mayr, to understand the system relationship and speciation history of three conifer species. The results show that:1) Three species exhibited low level of nucleotide diversity, the P. squamata had the highest nucleotide diversity (?sil= 0.00976); P. bungeana had the lowest nucleotide diversity (?sil= 0.00025); P. gerardiana was somewhere in between (?sil= 0.00040). In addition, the genetic variation of three species mainly existed among species (83.15%); 2) The effective population size of three species were smaller than their ancestral effective population size, suggesting that the species in this section may experienced the range contraction based on IM analysis. Combined with Ecological Niche Modeling of P. bungeana, we speculated that P. bungeana populations may have experienced wide range contractions from Last Interglacial to Last Glacial Maximum due to geological or weather events, and then may have experienced the recent range expansions. The founder effect or bottleneck effect in this process have resulted in the low level of nucleotide polymorphism of the species; 3) The structure cluster analysis based on Bayesian theory showed obvious genetic introgression among three species, P. bungeana and P. gerardiana had relatively close genetic relationship based on phylogenetic analysis. Moreover, P. squamata located in the base of the phylogenetic tree, indicating that P. squamata was an earlier origin taxa.4) Based on the current allopatric discontinuous distribution and species tree along with the results of IM analysis of Sect. Parrya Mayr, we speculated that the species differentiation of three species occurred in 0.34-0.61 Ma, the divergence among three species may be significantly associated with the uplift events of Qing-Xizang (Tibetan) Plateau in the Middle Pleistocene.5) According to the geographical distribution patterns of nucleotide DNA haplotype and population genetic structure model of P. bungeana, we inferred that the southwest areas of Qinling-Daba Mountains and the Lvliang Mountains might be the refuges during the Quaternary glacial period. Expansion or reverse migration of the species after the glaciation may resulted in a second contact or introgression in the Qinling Mountains between the two refuges.