Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola.

BACKGROUND AND AIMS: Many plant taxa in the Qinghai-Tibetan Plateau (QTP) and the Hengduan Mountains (HM) radiated rapidly during the Quaternary but with frequent secondary contact between diverging populations. Incomplete lineage sorting and introgressive hybridization might be involved during the rapid radiation, but their effects on phylogeography have not been fully determined. METHODS: We investigated the chloroplast DNA (cpDNA)/internal transcribed spacer (ITS) sequence variations of 611 samples of Rhodiola bupleuroides, R. discolor, R. fastigiata and R. chrysanthemifolia from the QTP and HM to compare the phylogeographic patterns between the four species with different evolutionary histories, geographic ranges and reproductive modes. KEY RESULTS: The divergence times of these species were consistent with the last peak of in situ speciation in the HM. While closely related species exhibited different phylogeographic patterns, they shared several ribotypes and haplotypes in sympatric populations, suggesting introgressive hybridization. A significant phylogenetic discordance between ribotypes and haplotypes was detected in three species, implying incomplete lineage sorting. Rhodiola discolor houses an extraordinary richness of cpDNA haplotypes, and this finding may be attributed to adaptive radiation. CONCLUSION: In addition to geographic isolation and climate oscillations during the Quaternary, both introgressive hybridization and incomplete lineage sorting play important roles in species that experienced rapid diversification in the QTP and HM.

Compensation of Wild Plants Weakens the Effects of Crop-Wild Gene Flow on Wild Rice Populations.

Crop-wild gene flow may alter the fitness of the recipient i.e., crop-wild hybrids, then potentially impact wild populations, especially for the gene flow carrying selective advantageous crop alleles, such as transgenes conferring insect resistance. Given the continuous crop-wild gene flow since crop domestication and the occasionally stressful environments, the extant wild populations of most crops are still "wild." One interpretation for this phenomenon is that wild populations have the mechanism buffered for the effects of crop alleles. However, solid evidence for this has been scarce. We used wild rice (Oryza rufipogon) and transgenic (Bt/CpTI) rice (O. sativa) as a crop-wild gene flow model and established cultivated, wild, and F7 hybrid rice populations under four levels of insect (Chilo suppressalis) pressure. Then, we measured the trait performance of the plants and estimated fitness to test the compensatory response of relatively high fitness compared to the level of insect damage. The performance of all plants varied with the insect pressure level; wild plants had higher insect-tolerance that was expressed as over- or equal-compensatory responses to insect damage, whereas crop and hybrids exhibited under-compensatory responses. The higher compensation resulted in a better performance of wild rice under insect pressure where transgenes conferring insect resistance had a somewhat beneficial effect. Remarkable hybrid vigour and the benefit effect of transgenes increased the fitness of hybrids together, but this joint effect was weakened by the compensation of wild plants. These results suggest that compensation to environmental stress may reduce the potential impacts of crop alleles on wild plants, thereby it is a mechanism maintaining the "wild" characteristics of wild populations under the scenario of continuous crop-wild gene flow.

The Tanggula Mountains enhance population divergence in Carex moorcroftii: a dominant sedge on the Qinghai-Tibetan Plateau.

High-altitude mountains are often geographic barriers to gene flow and play important roles in shaping population divergence. The central Qinghai-Tibetan Plateau (QTP) stands the location of the Tanggula Mountains (TM). We use the TM as a case, using Carex moorcroftii, a dominant species on the QTP to test the effects of geographic barriers on plant population divergence. We sampled 18 C. moorcroftii populations along a north-south transect crossing the TM to investigate the correlations of genetic variation and morphological traits with climate variables. The results showed this species holds high genetic diversity (He = 0.58) and the surveyed populations can be genetically clustered into two groups: populations from the north face of TM, and the other from the south. Gene flow between populations within groups is higher than those between groups. The traits, number and mass of seeds, mass of root and infructescence significantly varied among populations. Mantel-tests detected a weak but significantly positive correlation between genetic and geographic (R2 = 0.107, p = 0.032) and climatic distance (R2 = 0.162, p = 0.005), indicating both isolation by distance and isolation by environment. These findings together suggest high-altitude mountains of TM interrupt habitat continuity, result in distinct climatic conditions on both sides, increasing population divergence of plant species.

Response to climate change of montane herbaceous plants in the genus Rhodiola predicted by ecological niche modelling.

Climate change profoundly influences species distributions. These effects are evident in poleward latitudinal range shifts for many taxa, and upward altitudinal range shifts for alpine species, that resulted from increased annual global temperatures since the Last Glacial Maximum (LGM, ca. 22,000 BP). For the latter, the ultimate consequence of upward shifts may be extinction as species in the highest alpine ecosystems can migrate no further, a phenomenon often characterized as "nowhere to go". To predict responses to climate change of the alpine plants on the Qinghai-Tibetan Plateau (QTP), we used ecological niche modelling (ENM) to estimate the range shifts of 14 Rhodiola species, beginning with the Last Interglacial (ca. 120,000-140,000 BP) through to 2050. Distributions of Rhodiola species appear to be shaped by temperature-related variables. The southeastern QTP, and especially the Hengduan Mountains, were the origin and center of distribution for Rhodiola, and also served as refugia during the LGM. Under future climate scenario in 2050, Rhodiola species might have to migrate upward and northward, but many species would expand their ranges contra the prediction of the "nowhere to go" hypothesis, caused by the appearance of additional potential habitat concomitant with the reduction of permafrost with climate warming.

Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata.

Rhodiola crenulata, a well-known medicinal Tibetan herb, is mainly grown in high-altitude regions of the Tibet, Yunnan, and Sichuan provinces in China. In the past few years, increasing numbers of studies have been published on the potential pharmacological activities of R. crenulata, strengthening our understanding into its putitive active ingredient composition, pharmacological activity, and mechanism of action. These findings also provide strong evidence supporting the important medicinal and economical value of R. crenulata. Consequently, some Rhodiola species are becoming endangered because of overexploitation and environmental destruction. However, little is known about the genetic and genomic information of any Rhodiola species. Here we report the first draft assembly ofthe R. crenulata genome, which was 344.5 Mb (25.7 Mb Ns), accounting for 82% of the estimated genome size, with a scaffold N50 length of 144.7 kb and a contig N50 length of 25.4 kb. The R. crenulata genome is not only highly heterozygous but also highly repetitive, with ratios of 1.12% and 66.15%, respectively, based on the k-mer analysis. Furthermore, 226.6 Mb of transposable elements were detected, of which 77.03% were long terminal repeats. In total, 31 517 protein-coding genes were identified, capturing 86.72% of expected plant genes in BUSCO. Additionally, 79.73% of protein-coding genes were functionally annotated. R. crenulata is an important medicinal plant and also a potentially interesting model species for studying the adaptability of Rhodiola species to extreme environments. The genomic sequences of R. crenulata will be useful for understanding the evolutionary mechanism of the stress resistance gene and the biosynthesis pathways of the different medicinal ingredients, for example, salidroside in R. crenulata.

Morphological and Genetic Variation along a North-to-South Transect in Stipa purpurea, a Dominant Grass on the Qinghai-Tibetan Plateau: Implications for Response to Climate Change.

Estimating the potential of species to cope with rapid environmental climatic modifications is of vital importance for determining their future viability and conservation. The variation between existing populations along a climatic gradient may predict how a species will respond to future climate change. Stipa purpurea is a dominant grass species in the alpine steppe and meadow of the Qinghai-Tibetan Plateau (QTP). Ecological niche modelling was applied to S. purpurea, and its distribution was found to be most strongly correlated with the annual precipitation and the mean temperature of the warmest quarter. We established a north-to-south transect over 2000 km long on the QTP reflecting the gradients of temperature and precipitation, and then we estimated the morphological by sampling fruited tussocks and genetic divergence by using 11 microsatellite markers between 20 populations along the transect. Reproductive traits (the number of seeds and reproductive shoots), the reproductive-vegetative growth ratio and the length of roots in the S. purpurea populations varied significantly with climate variables. S. purpurea has high genetic diversity (He = 0.585), a large effective population size (Ne >1,000), and a considerable level of gene flow between populations. The S. purpurea populations have a mosaic genetic structure: some distant populations (over 1000 km apart) clustered genetically, whereas closer populations (< 100 km apart) had diverged significantly, suggesting local adaptation. Asymmetrical long-distance inter-population gene flow occurs along the sampling transect and might be mediated by seed dispersal via migratory herbivores, such as the chiru (Pantholops hodgsonii). These findings suggest that population performance variation and gene flow both facilitate the response of S. purpurea to climate change.

Microsatellite markers in Rhodiola (Crassulaceae), a medicinal herb genus widely used in traditional Chinese medicine.

PREMISE OF THE STUDY: Microsatellite loci are described for Rhodiola, a medicinal herb genus widely used in traditional Chinese medicine. • METHODS AND RESULTS: A total of 17 polymorphic microsatellite primer pairs were developed using the combined biotin capture method. The number of alleles per locus ranged from one to 12 across 192 individuals from R. bupleuroides, R. crenulata, R. fastigiata, and R. sacra, and the mean observed and expected heterozygosities ranged from 0.177 to 0.412 and from 0.363 to 0.578, respectively. • CONCLUSIONS: The results demonstrate the potential use of this new set of microsatellite markers for genotyping individuals and estimating genetic diversity in Rhodiola.