Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing

Abstract

Background: Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. Results: In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. Conclusions: This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

Chloroplast and Nuclear Genetic Diversity Explain the Limited Distribution of Endangered and Endemic Thuja sutchuenensis in China

“…This might result from the low population size of T. sutchuenensis (∼10,000 wild individuals in the nature). It is consistent with other narrow-ranged species, for example, the Cupressaceae species Platycladus orientalis ( F ST = 0.024–0.386) ( Chang et al, 2019 ), endangered Camellia huana (FST = 0.2159 for cpSSR) ( Li et al, 2020 ), threatened Rhododendron cyanocarpum ( F ST = 0.0314–0.0452) ( Liu et al, 2020 ), and Tetraena mongolica ( F ST = 0.010–0.026) ( Cheng et al, 2020 ). The genetic differentiation between populations was strongly influenced by genetic drift, gene flow, long-term evolution, mating systems, selection, and mutation ( Hamrick and Godt, 1996 ).…”

“…However, the nucleotide genetic diversity ( pi = 0.082–0.091 for variant positions, pi = 0.0053–0.0062 for all positions) of T. sutchuenensis in this study is relatively low compared with other narrow-ranged species, such as Tetraena mongolica ( He = 0.337–0.341; pi = 0.349–0.354) based on nRAD-seq ( Cheng et al, 2020 ), or widespread species, such as Amorphophallus paeoniifolius ( pi = 0.072–0.285) ( Gao et al, 2017 ). Nuclear genetic diversity of T. sutchuenensis in our study was higher than six single-copy nuclear loci ( pi = 0.00219) ( Qin et al, 2020 ).…”

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

“…Pi and Tajima’s D of each inferred population and Fst of the pairwise inferred populations were computed using VCFtools [ 67 ]. Nm was calculated using formula Nm = (1-Fst) / 4Fst [ 73 ]. MEGA v. 10.2.4 was used to compute GD for the pairwise inferred populations.…”

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

“…This result corresponded with AMOVA results, where 27% of the total variation was accounted for among subpopulations. Cheng et al (2020) discussed three grades of Nm value and their biological signi cances. If the Nm (haploid) value is equal to or greater than one, high gene ow; if it is between 0.250-0.99, moderate gene ow; and between 0.0-0.249 signi es limited gene exchange between subpopulations.…”