Genetic Diversity And Phylogeography Of Liquidambar Formosana Hance In China

Liquidambar formosana Hance is a Tertiary relict plant which is distributed widely in subtropical region of China,and has a long evolutionary history.In recent years,relict plants have received increasing attention from the science community,becoming one of the hotspots of biodiversity conservation and research.Studies on population genetics and phylogeography of L.formosana to understand genetic structure and clarify the origin and evolution of pattern,and disscuss on geographical and its history and patterns of evolution,and geographical and historical causes for the formation of current distribution pattern are of great significance.Results from these studies would be helpful not only to protect the genetic resources but also to attain effective management and exploration of the genetic resources.This study focuses on population genetics and phylogeographic structure and population dynamics of L.formosana within the natural range using SSR molecular marker and cpDNA non-coding sequences,meanwhile,using Biomod2 models to reconstruct geography distribution of different periods based on the existing data of geographical distribution and climate data.The main results are as the followings:(1)A total of 10 645 potential SSR loci were identified in 80 482 unigenes.The average frequency was one SSR per 5.12 kb,with an occurrence rate of 13.22%,and the dinucleotide unit was the most abundant motif.Fourteen polymorphism primer pairs were mined from transcriptome data.Subsequently,these primers were used to study population sampling strategy.These results indicated the optimum sampling number should be 17-26 individuals within a population,the sampled individuals should be kept more than 50 m apart.(2)A total of 691 individual trees from 25 populations across nearly the entire natural range of L.formosana in China were analyzed by 11 SSR loci which were further selected from 14 loci.A total of 67 alleles were found,with a mean number of alleles(Na)of 6.091 and an average effective number of alleles(Ne)of 1.9266.The Shannon's Information Index(I)had an average of 0.8178,and the mean observed heterozygosity(Ho)and expected heterozygosity(He)was 0.4090 and 0.4322,respectively.Compared with the average expected heterozygosity value(He =0.650)of outcrossing plants using SSR markers,L.formosana exhibited a relatively moderate level of genetic diversity(He=0.399),with the highest was found in population XY(He=0.469).Compared with the genetic diversity at the region level,the southwestern region displayed the highest genetic diversity(He =0.435),followed by the Dabie Mountains and Foothills and Coastal regions,whereas the Central region showed the lowest genetic diversity and deficit of heterozygosity.These results indicated that Southwestern China may be the genetic diversity hot spot of L.formosana,and the lower genetic diversity of the marginal population could be the result of geographic isolation or the founder effect.The coefficient of genetic differentiation(Fst)for L.formosana was 0.0757,which stands for a moderate level of population differentiation.Furthermore,the Mantel test displayed a lack of correlation between genetic variation and geographic isolation in the sampled populations(P>0.05).These results suggested that geographic isolation was not the primary factor leading to moderate genetic differentiation of L.formosana.As most of the genetic diversity of L.formosana exists among individuals within a population,individual plant selection would be an effective way to use natural variation in genetic improvement programs.The UPGMA dendrogram showed that these 25 populations were grouped into three clusters,which were essentially identical to those determined by PCoA and Structure analysis.(3)Four cpDNA intergenic spacer regions were amplified and sequenced for the 251 individuals from 25 populations.The total alignment length of these four cpDNA fragments was 2 732 bp.Based on the concatenated sequences,20 polymorphic sites were detected and 20 haplotypes(H1-H20)were recovered from 25 populations.Among these 25 populations,18 exhibited more than one haplotype,and among these 20 haplotypes,10 haplotypes were private to a single population.The species had high level of chloroplast genetic variation(Ht=0.909±0.0192),whereas the low level of genetic variation whin populations was only Hs=0.323±0.0553.The variation of haplotype mainly occurs among populations(Fst= 0.73012),the low genetic diversity within populations may be attributed to the restricted gene flow(Nm=0.18).The total haplotype diversity(Hd)and nucleotide diversity(?)were 0.88762 and 0.00144,respectively.The highest haplotype diversity was found in population PX(Hd =0.75556),which had five haplotypes;JO had the highest nucleotide diversity(?=0.00120).The coefficient of population genetic differentiation(Nst(0.730)>Gst(0.645),P<0.05),indicating significant phylogeographic structure across the species' distribution range.The result of analysis of molecular variance(AMOVA)indicated that the chloroplast genetic variation mainly occurred within populations,accounting for 75.34% of the total variation,whereas the genetic variation among populations was only 24.66%.Mantel test indicated a lack of correlation between genetic variation and geographic isolation in the sampled populations(P>0.05),neutrality test and the mismatch distribution analysis showed L.formosana experienced expansion event in history.The most frequent haplotype was found in H4(50/251),followed by H1(42/251)and H5(32/251),comprising 49.4%(124/251)by pooling them together.H4 and H1 were the most widespread haplotypes,H5 was an ancestral haplotype because it was located a center position in the network.According to the results of population genetics and haplotype analysis,we speculated that there were several refugia,such as southwestern region(PX and XY)and eastern region(HSAH and JO)may be the important refugia for L.formosana.Using the uncorrelated log-normal relaxed-clock model,we calculated the time of the most recent common ancestor for L.formosana was 10.30 MYA(95%HPD: 9.74-15.28),belonging to the middle and late Tertiary period.The results indicated that the earliest lead to genetic differentiation was due to the Tertiary geology and climate events.(4)Biomod2 species distribution models was used to reconstruct geographic distribution patterns of L.formosana in different historical periods.These results showed that the optimum distribution was consistent with their existing distribution,which indicated the distribution has reached its maximum range.Reconstruction of the potential geographic distribution for past historical period,the phenomenon of glacial expansion and interglacial contraction was found.We found in the next 80 years,climate change has no significant effect on distribution of L.formosana,according to compared with species distribution area changes.Mean diurnal range and mean temperature of coldest quarter were the most important environmental factors affecting distribution for L.formosana,the result showed that temperature was the dominant climatic factors for northward expansion.