Population Genetic Divergence Among Four Closely Related Picea Species

Picea is the third largest genus in Pinaceae with a wide distribution in the Northern Hemisphere.The species of this genus are the important components of the conifer forests in the Northern Hemisphere.However,it is difficult to clarify speciation pattern and divergence process between the closely related species of this genus because of their long-life histories,large effective population sizes,frequent interspecific hybridizations and incomplete lineage sorting.Four morphologically similar species,Picea asperata,P.meyeri,P.koraiensis and P.obovata,were chosen as our study system.Except for P.obovata that widely occurs in Siberia,the rest species are allopatrically distributed in China.Previous studies suggested that these four species comprised a monophyletic clade on the basis of the phylogenetic analyses of the cpDNA and/or nrDNA sequence variations,howerer,the delimitation and population genetic divergence among them remains unclear.In the present study,we used population genetic data to examine the nucleotide diversity,population structure,interspecific divergence and demographic history of these four species.We sequenced 13 nuclear loci for 332 individuals from 34 natural populations throughout the natural distribution ranges of the four species in China.A total of 87 polymorphic sites were private in P.obovate while only a few private sites were found in the other three species.The average nucleotide diversity is relatively low for each of four species;the highest diversity(θ_wt=0.00410 andπ_t=0.00459)was found in P.obovata,and the lowest(θ_wt=0.00181 andπ_t=0.00245)in P.asperata.Genetic differentiations are relatively low among the four species.P.obovata was the most differentiated species from the other three species,withΦ_ST=0.28417,0.29674 and 0.30388 compered to P.asperata,P.meyeri and P.koraiensis,respectively.STRUCTURE analyses revealed that the most likely number of clusters was K=2.When K=2,the first cluster comprised all individuals of P.asperata,P.meyeri and P.koraiensis,while the other consisted only P.obovata.Furthermore,we used the concatenated nuclear sequence data obtained in this study,together with those from nine representatives of other spruce species,to reconstruct the interspecific relationships between the four species.The phylogenetic tree based on Bayesian phylogenetic analysis suggested that the four species comprised a monophyletic lineage that is well differentiated from the other Asian species.Within this lineage,P.obovata diverged firstly and comprised a monophyletic clade,while all the other three species together comprised another clade,which is consistent with the result of Principal Component Analysis（PCA）analysis.Based on these population genetic data,we further modeled and examined interspecific divergence of the four species using ABC method.The results showed that P.obovata diverged from the common ancestor of the other three species around 1.71 million years ago（Ma）followed by a divergence of P.koraiensis around 0.287 Ma,and finally,P.asperata and P.meyeri diverged around 0.204 Ma.Our further demographic estimates using IM produced the roughly consistent results.In each pairs of species,the highest gene flow was detected from P.meyeri to P.asperata and less gene flow between P.obovata and the remaining species.We also modeled the potential distributions of the four species during the Quaternary glacial ages.We found that all of the four species expanded their distributions during the Last Glacial Maximum（LGM）.The predicted distribution of P.obovata has reduced at present compared with the LGM,while the distributions of the others stayed stable.In conclusion,our results suggested that four species derived from a common ancestor and their divergence occurred recently.P.obovata diverged firstly and then P.koraiensis.At last,P.aspeata and P.meyeri diverged from each other.Gene flow occurred between them although the degrees varied greatly.Each of the four species has experienced demographic shrinks and expansions in response to the Quaternary climatic oscillations.The indistinct interspecific differentiation and the shared polymorphism among four specie are mainly attributed to incomplete lineage sorting and frequent gene flow due to the recent divergence.