The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae)

Abstract

Background: Panax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested two independent origins of the East Asia and North America disjunct distribution of this genus and multiple rounds of whole genome duplications (WGDs) might have occurred during the evolutionary process.

Results: We employed multiple chloroplast and nuclear markers to investigate the evolution and diversification of Panax. Our phylogenetic analyses confirmed previous observations of the independent origins of disjunct distribution and both ancient and recent WGDs have occurred within Panax. The estimations of divergence time implied that the ancient WGD might have occurred before the establishment of Panax. Thereafter, at least two independent recent WGD events have occurred within Panax, one of which has led to the formation of three geographically isolated tetraploid species P. ginseng, P. japonicus and P. quinquefolius. Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions.

Conclusion: Our findings based on the phylogenetic and population genetic analyses, coupled with the species distribution patterns of Panax, suggested that the two rounds of WGD along with the geographic and ecological isolations might have together contributed to the evolution and diversification of this genus.

Fig. 1

Geographic distributions and chromosome numbers of the extant diploid and tetraploid Panax species. The diploid species P. trifolius shows overlapped distribution with the tetraploid P. quinquefolius. The P. bipinnatifidus species complex covers the distribution ranges of P. notoginseng, P. stipuleanatus and P. pseudoginseng. Star, sampling locations of the species P. ginseng and P. quinquefolius in Jilin province of China; Circle, sampling location of P. bipinnatifidus species complex in Sichuan province of China; Triangle, sampling locations of P. notoginseng, P. stipuleanatus and P. bipinnatifidus species complex in Yunnan province of China. The original map was downloaded from Wikimedia Commons(https://commons.wikimedia.org/wiki/File:Map_of_the_Pacific_region.svg?uselang=zh-cn). The information of geographic distributions of Panax species was retrieved from the Natural Resources Conservation Service of USDA (www.plants.usda.gov) and Flora of China (www.efloras.org)

Fig. 2

Divergence times and topologies of Bayesian trees based on whole chloroplast genome (a) and four selected chloroplast genes (b). The values on the left and right of each node are the divergence time (one million years ago) and poster prior support, respectively. Length of each branch is not shown in the two phylogenetic trees

Fig. 3

Topologies of Bayesian trees based on nrITS and seven single copy nuclear genes. Each branch represents one haplotype and identical sequences from the same species were removed. The color of branch stands for different species. Numbers of haplotypes for each gene were shown in Additional file 2: Table S2

Fig. 4

Quantification of segregating site per gene at total a, species-specific b synonymous c and nonsynonymous d sites for the 36 genes. The numbers above the vertical bars are the exact numbers of segregating sites per gene. Detailed information of the 36 nuclear genes was shown in Additional file 4: Table S4