Tertiary origin and pleistocene diversification of dragon blood tree (Dracaena cambodiana-Asparagaceae) populations in the Asian tropical forests

Abstract

Background: The origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests.

Methods: WE ANALYZED NUCLEOTIDE SEQUENCE DATA OF TWO CHLOROPLAST DNA (CPDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs.

Results: A significant phylogeographic structure (N ST = 0.876, G ST = 0.796, F ST-SSR = 0.329, R ST = 0.449; N ST>G ST, R ST>F ST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period.

Conclusions: The results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana.

Figure 1. Geographic distribution and evolutionary relationships of 18 cpDNA haplotypes in Dracaena cambodiana.

a: Different colors in pies charts represent haplotypes. The dashed lines indicate the division of fifteen populations into four groups based upon their geographic location. Black triangles represent main geographical barriers originated during the Tertiary era (modified from Lacassin et al., 1993; Huchon et al.,1994; Searle, 2006). b: Colorsrepresent populations. The black dots are the missing haplotypes or missing samples. The numbers on the branches represent number of mutations between two connected haplotypes. The gray connected lines among haplotypes were resolved based on the methods of Crandall & Templeton (1993). Segmented-elliptic-dashed lines represent the cluster of S-I populations. Straight-dashed line is the connection to outgroups. The detailed connections of outgroups is given in Figure S2. c: general position of map A in Southeast Asia. d: The trend of altitudes shifting along latitudes.

Figure 2. Results of Bayesian model based clustering of individuals using the STRUCTURE program.

a) Distribution of likelihood value LnP(D) and the distribution of model parameter DeltaK (ΔK). All estimated values are based on 20 replicates and values of LnP(D)(±SD) and ΔK are plotted against its corresponding K. b) Barplots showing the results of the Bayesian cluster analysis. The colour in each barplot represents the probability of each individual to belong to an admixture group. Populations are ordered based on their population IDs as given in Table1.

Figure 3. The Phylogenetic tree representing evolutionary relationships of four geographically based groups of Dracaena cambodiana populations.

The coalescent times of the most recent common ancestor (T _TMRCA) for overall populations and each group (A, B, C, D) based on IMa2 (★)and BEAST (♦) analyses. The divergence times among the four geographic groups are T0 T1 and T2. Dashed lines corresponds to T _TMRCA. The 95% highest posterior density intervals (95%HPD) are given in parentheses. The unit time is in million years ago (Ma).

Figure 4. Population demographics of Dracaena cambodiana.

a: mismatch distribution. dashed lines are observed and black lines are expected values. b (change in population size over time) and c (divergence of lineages): x-axis is the median time in millions years ago (Ma); black lines represent median estimate and gray lines represent 95% confidence intervals.