Phylogeographic Studies On Pseudotaxus Chienii(Taxaceae),an Endemic Gymnosperm In China

The geological history of the Late Tertiary and the Quaternary climate oscillations have profoundly affected the geographical distribution and genetic differentiation of relict plants.By means of phylogeographic inference,the knowledge concerning the distribution shift of plants in response to the historical events in subtropical China,a place that is rich in tertiary relics,has advanced during the past decade.However,most of these phylogeographic studies made their inference relying heavily on chloroplast genomic markers,nuclear genomic loci(particularly nuclear sequences)have not been fully utilized in such studies.For this reason,population divergence and demography have always been represented by a single chloroplast loci,which is prone to incomplete sorting thus underestimate population divergence time.In addition,because the limit of informative site in chloroplast sequences,rigorous tests of different evolutionary hypotheses using statistical phylogeography have rarely been applied previously.In this study,I investigated the phylogeographic structure and demographic history of a Tertiary relict plant,Pseudotaxus chienii,in subtropical China.Using the method of statistical phylogeography based on two chloroplast DNA(cpDNA)fragments and 14 nuclear loci.The main findings are as follows:(1)Phylogeographic pattern of cpDNAAcross 134 individuals of 12 populations in Pseudotaxus chienii,seven haplotypes were identified from two cpDNA fragments(rpl16 and psbA-trnH).The genetic diversity(Ht)was 0.547,the nucleotide diversity(?)was 0.00097;AMOVA analysis of molecular variance showed that the genetic variation between populations was 54.66%,the intra-population variation was 45.34%;the genetic differentiation(Fst)between populations was 0.55,and the gene flow between populations was low with Nm=0.14.In addition,the difference between Nst(0.6)and Gst(0.52)was not significant(P>0.05),indicating that Pseudotaxus chienii did not have obvious phylogeographic structure.The mismatch analysis showed that this species did not experienced range expansion.(2)Phylogeographic structure and demographic history based on 14 nuclear lociAt 14 nuclear loci,the average nucleotide diversity of Pseudotaxus chienii was ?t = 0.00265,Watterson's parameter ?wt was 0.00293,and the average haplotype diversity Hd was 0.54.The parameters of neutral tests(Tajima's D,Tajima's D* and F*,Fu and Li's F*)were all positive,but not significant,indicating that the 14 nuclear loci did not reject the neutral hypothesis.Structure analysis showed that all Pseudotaxus chienii populations can be clustered into three groups,namely Eastern(E),Middle(C)and Western(W)groups.Using approximate Bayesian computation(ABC)to simulate the differentiation history of three groups,the eastern,middle,and western populations differentiated simultaneously.The divergence time of three groups was at the early Pleistocene(2.28Ma).The results of this study clarified the evolutionary history of Pseudotaxus chienii since the late Tertiary and have important implications for the conservation of this ancient plant.This study also provides a profound insight into the evolutionary history of plants in subtropical China...