Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Abstract

Historical geology, climatic oscillations, and seed dispersal capabilities are thought to influence the population dynamics and genetics of plants, especially for distribution-restricted and threatened species. Investigating the genetic resources within and among taxa is a prerequisite for conservation management. The Cycas taiwaniana complex consists of six endangered species that are endemic to South China. In this study, we investigated the relationship between phylogeographic history and the genetic structure of the C. taiwaniana complex. To estimate the phylogeographic history of the complex, we assessed the genetic structure and divergence time, and performed phylogenetic and demographic historical analyses. Two chloroplast DNA intergenic regions (cpDNA), two single-copy nuclear genes (SCNGs), and six microsatellite loci (SSR) were sequenced for 18 populations. The SCNG data indicated a high genetic diversity within populations, a low genetic diversity among populations, and significant genetic differentiation among populations. Significant phylogeographical structure was detected. Structure and phylogenetic analyses both revealed that the 18 populations of the C. taiwaniana complex have two main lineages, which were estimated to diverge in the Middle Pleistocene. We propose that Cycas fairylakea was incorporated into Cycas szechuanensis and that the other populations, which are mainly located on Hainan Island, merged into one lineage. Bayesian skyline plot analyses revealed that the C. taiwaniana complex experienced a recent decline, suggesting that the complex probably experienced a bottleneck event. We infer that the genetic structure of the C. taiwaniana complex has been affected by Pleistocene climate shifts, sea-level oscillations, and human activities. In addition to providing new insights into the evolutionary legacy of the genus, the genetic characterizations will be useful for the conservation of Cycas species.

Geographic factors and climatic fluctuation drive the genetic structure and demographic history of Cycas taiwaniana (Cycadaceae), an endemic endangered species to Hainan Island in China

“…The AMOVA results were consistent with those of other studies, which showed that the genetic differentiations of many Cycas species were distributed among populations based on the cpDNA data (Feng et al, 2014(Feng et al, , 2017Feng, Zheng, & Gong, 2016;Wang et al, 2019;Xiao et al, 2020;Yang et al, 2017;Zheng et al, 2016). Moreover, nuclear genes explored the opposite results (Feng et al, 2014;Feng, Zheng, & Gong, 2016;Wang et al, 2019;Xiao et al, 2020;Yang et al, 2017), genetic variations were mainly distributed within populations with the species C. dolichophylla as an exception, whose genetic variations among populations was greater than that within populations (Zheng et al, 2016). In Cycas, the chloroplast DNAs are maternal inheritance (Zhong et al, 2011), and genetic materials are transmitted by seeds.…”

“…Climate fluctuation during the Quaternary period had effects on the population historical dynamics of Cycas species, and different species had different responses to glacial and interglacial influences (Wang et al, 2019 ). The mismatch distribution analysis of nuclear genes AC 5, PPRC , and AAT showed a unimodal curve, which were consistent with the BSP results, indicating that C. taiwaniana experienced an expansion event.…”

“…It provides the maximum and accurate conservation strategy by using DNA data to study the genetic structure and the factors causing the genetic change in populations. Population genetics is becoming more and more popular in animals and plants conservation (Qiao et al, 2021 ; Sanal Demirci et al, 2021 ; Shan & Diao, 2011 ; Wang et al, 2021 ) and is also widely used in cycads (Feng et al, 2017 ; Wang et al, 2019 ; Xiao et al, 2020 ).…”

Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

“…The identification of conservation units (CUs) is important for the conservation and management of threatened species, providing managers and policy‐makers with a clear understanding of the boundaries of population units (Funk et al, 2012; Li, Milne, et al, 2020; Li, Wang, et al, 2020). A comprehensive understanding of population structure, genetic differentiation and demographic history is crucial for an understanding of the evolutionary history of a species, and the implications of these issues for the conservation of the organisms (Wang et al, 2019). Genetic markers such as microsatellite loci, chloroplast DNA and mitochondrial DNA may be inadequate for determining the population genetic structure of species with complex demographic histories.…”

“…A comprehensive understanding of population structure, genetic differentiation and demographic history is crucial for an understanding of the evolutionary history of a species, and the implications of these issues for the conservation of the organisms (Wang et al, 2019). Genetic markers such as microsatellite loci, chloroplast DNA and mitochondrial DNA may be inadequate for determining the population genetic structure of species with complex demographic histories.…”