Population Genetics Structure And Phylogeography Of Quercus Fabri

Quercus fabri Hance,which belongs to the family Fagaceae,is a deciduous forest species endemic to China.As one of the most important tree species in the Quercus group,the genetic diversity of Quercus fabri is significant to the stability of the ecosystem because this species is main component of the arbor layer in the forest community.Till now,Molecular genetic research of Q.fabri is limited because most studies have mainly focused on morphological structure,food processing and so on.In this study,we use the maternally inherited cpDNA markers and the parents inherited ITS and SSR markers to investigate the geographical structure and genetic diversity of the Q.fabri,then we infer the historical dynamics of populations and LGM refugia of Q.fabri using ENM and BSPs method.The main results are as follows:（1）Phylogeography of Quercus fabri Three chloroplast DNA fragments（coding region ycf1 and non-coding regions psbA-trnH,rps15-ycf1）were used to analyze 293 individuals from 31 populations of Q.fabri.In total,21 haplotypes were recovered,the overall haplotype diversity（Hd）was 0.870 and the nucleotide diversity（π）was 1.60×10^-3.There were significant geographic structures in 31 populations of Q.fabri because of N_ST>G_ST（P<0.05）,Mantel test results showed that there was significant correlation between genetic and geographical distance（r ²=0.018;P=0.043<0.05）.AMOVA analysis showed that the genetic variation between populations（85.51%）was greater than within the populations（14.49%）.The Mismatch analysis showed that populations of Q.fabri have been experienced range expasion about 14.62 kyr ago.The phylogenetic tree using BEAST software and haplotype Network suggested that haplotypes of Q.fabri divided into three groups,but SAMOVA results showed that haplotype groups does not correspond to geographical distribution,the divergence between Q.fabri and outgroup occurred 12.33 million years ago according to BEAST software,the haplotypes showed a radial diversification pattern in the late Miocene and early Pleistocene and diversified occurred 2.73 million years ago.ITS was also used to analyze genetic diversity of Q.fabri in 260 individuals from 31 populations,a total of 33 ribosomal haplotypes were obtained and the haplotypes diversity of all populations（Hd）was 0.829 and the nucleotide diversity（π）was 4.26×10^-3.There was no significant geographical structure(N_ST>G_ST;P>0.05)in the populations of Q.fabri through SPADS software based on ITS,Mantel test results showed that there was no significant correlation between genetic and geographic distance（P>0.05）.AMOVA analysis showed that the genetic variation inter-populations（8.79%）was less than intra-population（91.21%）.The Mismach analysis showed a single peak distribution,which indicated that species experienced range expansion 13.22 kyr ago.The BSPs curve analysis showed that the size of the effective population of the Q.fabri expanded 21 kyr ago using the combined data.In addition,both the geographical distribution of haplotype patterns and the genetic diversity of Q.fabri suggested that the Yunnan Guizhou Plateau,Wuyi and Xuefeng mountain,Tianmu Mountain Area were potential refugia for Q.fabri.（2）Analysis of microsatellite data The analysis of microsatellite data shows that there had moderate levels of genetic diversity（Na=5.41,Ne=3.345,I=1.151,Ho=0.371,He=0.542,PPL=0.941%）in 490 individuals from 29 populations of Q.fabri using 17 pairs of microsatellite.Pearson’s correlation analysis of the genetic diversity and linear regression indicated a significant negative correlation between the observed heterozygosity and the latitude（r=-0.375;P=0.045）.The analysis based on STRUCTURE software suggested that populations of Q.fabri were divided into two major groups,the Middle East and the West,which was consistent with results of PCoA.Mantel test showed a significant correlation between geographical and genetic distance（P<0.05;r²=0.111）.The results of AMOVA showed that genetic variation within the population（83.70%）was greater than the genetic variation between populations（16.30%）;The populations were divided into two lineages according to the STRUCTURE analysis,and the genetic variation within the population（78.73%）was still higher than the groups.F statistical results showed that the genetic differentiation(F_ST)among the populations was 0.128,and the gene flow（Nm）was 2.354.Then we carried out clustering analysis of the two main lineages using STRUCTURE software,the results suggested that there were three sub-lineages in the West,and a serious mosaic phenomenon in the Middle East.BARRIER analysis showed that there is a strong barrier among different populations,BOTTLENECK analysis revealed that some populations had experienced bottlenecks.We found that the hight heterozygosity populations located in YunGui Plateau,Wuyi Moutains,Tianmu Mountains,Xuefeng mountains through IDW analysis,so these places might be a shelter for Q.fabri during the LGM period.（3）ENM,Population dynamics and glacial refugia The BSPs curves indicated that the effective population of Q.fabri began to decrease 100kyr-21 kyr ago based on chloroplast and ITS data and reached the minimum number 21 kyr ago after that the effective population expanded rapidly,which coincided with the large-scale contraction of the distribution during the LGM（21kyr）,and large-scale expansion of the distribution area of Q.fabri after glacial period.Chloroplast DNA,ITS,and nuclear microsatellite data all indicated that there were multiple refugia for Q.fabri.ENM also suggested that the Sichuan Basin,Wuyi Mountain,Xuefeng Mountain,Yungui Plateau,and Tianmu Mountain may be refugia in glacial stage.The spread of Q.fabri populations during the post-glacial period might lead to secondary contact of gene flow among the shelters,which formed the current distribution pattern.