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.
Project description:<i>Pinus</i> plants are the largest existing group of gymnosperms and one of the most highly differentiated taxa. Due to its huge ecological, economic, and scientific value, the genetic diversity and the relationship between the intraspecific evolution of <i>Pinus</i> plants have gained wide attention. In this study, the chloroplast genomes of several common pine trees in southwest and south China, including <i>P. massoniana</i> (masson pine), <i>P. yunnanensis</i> (yunnan pine), <i>P. latteri</i> (south asia pine), <i>P. crassicorticea</i> (la ya pine), and <i>P. elliottii</i> (slash pine), and entire cpDNA sequences were obtained. Characteristics including the structure, repeated sequence, and codon bias of the cpDNA for these five pine tree species were analyzed.
Project description:Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species.
Project description:The first complete chloroplast genome (cpDNA) sequence of <i>Michelia floribunda</i> was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,049?bp in length, contains a large single-copy region (LSC) of 88,140?bp and a small single-copy region (SSC) of 18,773?bp, which were separated by a pair of inverted repeats (IR) regions of 26,568?bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that <i>M. floribunda</i> was closely related to <i>Michelia yunnanensis</i> in Michelieae tribe.
Project description:Paris polyphylla var. yunnanensis is one of the original plants used to make the traditional medicine Paridis Rhizoma. Wild individuals have been excessively collected in recent decades, and thus, it has become increasingly endangered. Cultivation is a major method for the conservation and sustainable utilization of its wild resources. In this study, amplified fragment length polymorphism markers were used in the genetic analysis of 15 wild and 17 cultivated populations of P. polyphylla var. yunnanensis. This study revealed that cultivated populations possessed higher genetic diversity than wild ones at the species level (H = 0.2636 vs. 0.2616, respectively). However, most of the genetic variation was found within populations for both of these groups (?ST = 18.83% vs. 19.39%). In the dendrogram produced using UPGMA, the 32 populations were divided into three groups (I, II, and III). In group II, both wild and cultivated populations were included, but remained in distinct clusters within this group, which showed the significant separation between the cultivated and wild populations. Furthermore, wild populations were also clustered into three subgroups (W-I, W-II, and W-III), with an obvious geographic structure. In contrast, although cultivated populations were similarly placed in three subgroups (C-I, C-II, and C-III), the latter two of these were not separated based on geography. Finally, the wild populations in Guizhou, China (W-I), possessed higher genetic diversity than those in Yunnan (W-II and W-III). As P. polyphylla var. yunnanensis is an endangered medicinal plant, the fact that it showed richer genetic diversity in its wild populations in Guizhou means that these should be regarded as priority areas for protection and used for provenance selection. Moreover, cultivated populations also showed high genetic variation, which might be attributed to them having originated from mixed provenances, indicating that screening for superior provenances should be carried out as soon as possible.
Project description:<i>Pellacalyx yunnanensis</i> is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of <i>P. yunnanensis</i> was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743?bp in length, contains a large single-copy region (LSC) of 91,075?bp and a small single-copy region (SSC) of 18,668?bp, which were separated by a pair of inverted repeats (IR) regions of 27,000?bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that <i>P. yunnanensis</i> clustered in a unique clade in family <i>Rhizophoraceae</i>.
Project description:The Yunnan shoot borer, Tomicus yunnanensis, is a recently-discovered, aggressive pest of the Yunnan pine stands in southwestern China. Despite many bionomics studies and massive controlling efforts, research on its population genetics is extremely limited. The present study, aimed at investigating the origin and dispersal of this important forestry pest, analyzed the population genetic structure and demographic history using a mitochondrial cox1 gene fragment. Our results showed that T. yunnanensis most likely originated from the Central-Yunnan Altiplano, and the divergence time analysis placed the origin approximately 0.72 million-years ago. Host separation and specialization might have caused the speciation of T. yunnanensis. Genetic structure analyses identified two population groups, with six populations near the origin area forming one group and the remaining six populations from western and eastern Yunnan and southwestern Sichuan comprising the other. Divergence time analysis placed the split of the two groups at approximately 0.60 million-years ago, and haplotype phylogenetic tree, network, as well as migration rate suggested that populations of the latter group were established via a small number of individuals from the former one. Migration analysis also showed a certain degree of recent expansion from southwestern Sichuan to eastern Yunnan. Our findings implied that T. yunnanensis underwent both historical expansion and recent dispersal. The historical expansion may relate to the oscillation of regional climate due to glacial and interglacial periods in the Pleistocene, while human-mediated transportation of pine-wood material might have assisted the relocation and establishment of this pest in novel habitats.
Project description:Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.
Project description:Background:Isoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics of I. yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection. Methods:Expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure of I. yunguiensis, and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter of I. yunguiensis. A maximum entropy model was used to predict the past, present, and future distribution patterns of I. yunguiensis. Results:Analysis with EST-SSR markers revealed that I. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area of I. yunguiensis distribution (NST = 0.344 > GST = 0.183, p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed that I. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area of I. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes.
Project description:Premise of the Study:Psammosilene tunicoides (Caryophyllaceae) is a narrowly distributed and endemic plant species in southwestern China. The overexploitation of natural P. tunicoides has led to the destruction of many populations. Population and genetic studies will provide crucial data for the protection and management of P. tunicoides. In this study, we develop simple sequence repeat markers of P. tunicoides to analyze population diversity. Methods and Results:Microsatellite loci of P. tunicoides were isolated with FIASCO. Eleven polymorphic and 10 monomorphic primers were developed. The 11 polymorphic primers were tested in three P. tunicoides populations, yielding two to nine alleles per locus. Levels of observed heterozygosity varied from 0.000 to 1.000, and levels of expected heterozygosity ranged from 0.000 to 0.615. In addition, three of these loci were successfully amplified, and showed polymorphism, in three Silene species. Conclusions:These microsatellite markers can be valuable tools to investigate the genetic diversity and population structure of P. tunicoides.
Project description:Aim:With the late Cenozoic uplift of the Qinghai-Tibetan Plateau (QTP), drainage of the southeastern edge of the QTP changed significantly. However, the impact of this dramatic change on the geographical distribution and genetic diversity of endemic organisms is still poorly understood. Here, we examined the geographical patterns of genetic variation in the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Microhylidae), and two alternative hypotheses were tested: That is, the geographical distribution of genetic variation was determined by either the contemporary drainage basin or historical drainage basins. Location:The Mountains of southwest China. Materials and methods:Analyses were based on 417 specimens collected from across the distribution of the species. We reconstructed the genealogy (Bayesian and maximum parsimony methods) and assessed demographic history based on DNA sequencing data from mitochondrial and nuclear markers. We also mapped the genetic diversity and estimated the divergence times by a relaxed clock model. Results:The species has maintained a relatively stable population size without recent population expansion. Four major maternal lineages were identified with good support, one representing a possible cryptic species and the other three showing further subdivision. The distribution of these deeply differentiated lineages/sublineages corresponded well to geographical regions. The secondary contact zones and phylogeographic breaks in distinct lineages of G. yunnanensis were almost concordant with those of Nanorana yunnanensis. Main conclusions:Lineage division conformed to the hypothesis of drainage system evolution, that is, the phylogeographic pattern of G. yunnanensis was shaped by historical drainage patterns. Concordance in phylogeographic patterns may suggest a shared response to common hydrogeological history and also might indicate that there was more contribution of the drainage history than ecological or life-history traits in structuring genetic variation between these two disparate codistributed taxa G. yunnanensis and N. yunnanensis.