The population demography and genetic divergence of Taihangia rupestris based nuclear and choloroplast DNA evidences

Background/Question/Methods

Taihangia rupestris Yu et Li is an perennial herb endemic to China. It is the most primitive diploid species (2n =l4) in the tribe Dryadeae belong to the family Rosaceae according to its morphology, and it is regarded as an ancient relic species. At present, it has a disjunct distribution and occurs sporadically across the limestone region of  the eastern edge of the Taihang Mountains. Our research focused on a) what kind of population history lead to current distribution of this species? b) whether its populations experienced recent bottleneck effect, and c) whether there is distinct genetic divergence among populations. We studied the demographic history and genetic divergence in T. rupestris using nuclear microsatellite markers and choloroplast (cp) DNA sequences.

Results/Conclusions

High genetic diversity was detected in T. rupestris, and similar genetic diversity was found among populations. Unweigted pair group method analysis clustered the 10 studied populations into two groups. Group I contained 6 populations, and all of them are belong to T.rupestrisYu et Li var.rupestris. Group II included other four populations of T. rupestris var.ciliata. Structure analysis also revealed similar phylogeographical groups: Southern and Northern populations. There was a significant positive correlation between geographical distance and genetic distance. Most of populations experienced recent bottleneck effect based two-phased model of mutation and stepwise mutation model, and significant inbreeding was detected in these populations. CpDNA Nucleotide diversity and haplotype diversity are high (π=1.37×10^-3, Hd=0.729) at level of species, while both them are low at population. Seven choloropast haplotypes clustered into three clades. Two haplotypes from North populations formed one clade, while both of other two clades included haplotypes from South and North populations. Additionally, among all of the 10 studied populations, eight populations contained only one haplotype and six of these populations come from southern region. Our results indicated that multiple refugia resulted in current population structure of T. rupestris, and then most of populations experienced recent bottleneck effect. Distinct genetic divergence of this species occurred between regions.