Inferring Genetic Variation and Demographic History of Michelia yunnanensis Franch. (Magnoliaceae) from Chloroplast DNA Sequences and Microsatellite Markers

Abstract

Michelia yunnanensis Franch., is a traditional ornamental, aromatic, and medicinal shrub that endemic to Yunnan Province in southwest China. Although the species has a large distribution pattern and is abundant in Yunnan Province, the populations are dramatically declining because of overexploitation and habitat destruction. Studies on the genetic variation and demography of endemic species are necessary to develop effective conservation and management strategies. To generate such knowledge, we used 3 pairs of universal cpDNA markers and 10 pairs of microsatellite markers to assess the genetic diversity, genetic structure, and demographic history of 7 M. yunnanensis populations. We calculated a total of 88 alleles for 10 polymorphic loci and 10 haplotypes for a combined 2,089 bp of cpDNA. M. yunnanensis populations showed high genetic diversity (Ho = 0.551 for nuclear markers and Hd = 0.471 for cpDNA markers) and low genetic differentiation (FST = 0.058). Geographical structure was not found among M. yunnanensis populations. Genetic distance and geographic distance were not correlated (P > 0.05), which indicated that geographic isolation is not the primary cause of the low genetic differentiation of M. yunnanensis. Additionally, M. yunnanensis populations contracted ~20,000–30,000 years ago, and no recent expansion occurred in current populations. Results indicated that the high genetic diversity of the species and within its populations holds promise for effective genetic resource management and sustainable utilization. Thus, we suggest that the conservation and management of M. yunnanensis should address exotic overexploitation and habitat destruction.

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

“…rex using STRUCTURE ver. 2.2 was also explored [22,45]. K-values in the model ranged from two to 15 with 20 independent variables for each set with a burn-in of 1 × 10 5 iterations and 1 × 10 5 subsequent Markov chain Monte Carlo steps [45].…”

“…We used SeqMan II [50] and Bioedit ver. 7.0.4.1 [51] to treat the raw sequencing data and manually edited and assembled these sequences [22]. Three cpDNA intergenic spacers of R. rex subsp.…”

“…In addition, we calculated H T and within-population gene diversity (H S ) with Permut ver. 1.0 [22]. The two values of population differentiation G ST and N ST were computed in accordance with the methods described by Pons and Petit [54] and with the same software.…”

“…rex possesses a relatively moderate genetic diversity compared with the other species in Rhododendron. In general, life span, reproductive mode, and breeding system are the important factors in genetic diversity [6,22,69]. As in other outcrossing and long-lived species in Rhododendron, high historical gene flow among ancestral population mitigates the loss of genetic diversity and further results in a moderate or high genetic diversity in remnant populations [69,73].…”

“…cpDNA can reveal a more highly geographical structure than a nuclear genome [17] and is generally used in the detection of phylogeographical patterns in plant species [18,19]. Thus, nSSRs and cpDNA were extensively and successfully documented to study the genetic diversity, variation, and population demographic of plant species [17,[20][21][22].Habitat loss and destruction are global problems that continue to threaten global biodiversity [23,24]. Firstly, habitat destruction and loss can cause a decline in the distribution range and population and limit the natural regeneration of a species.…”