Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae) Endemic to Southwest China by Multiple Molecular Markers.

Xiuyan Feng,Yu-Chung Chiang,Xun Gong,Jian Liu

doi:10.3389/fpls.2017.00839

Abstract

Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs), three nuclear genes (nDNAs) and 12 nuclear microsatellites (SSRs), we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD) in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida.

Highlights

Southwest China is seen as one of the world’s biodiversity hotspots because of its complicated terrain, diversified climates and habitats (Myers et al, 2000)
We aimed to address the following questions: (1) What is the genetic diversity level of C. segmentifida? (2) Are the 14 populations of this species divided into two groups according to the sand and karst habitats? (3) When did the haplotpes of C. segmentifida began to diverge, and how did the population dynamics respond to climate fluctuations during historical period?
Detection of recombination in nuclear genes showed that no recombination occurred in GTP

Summary

Introduction

Southwest China is seen as one of the world’s biodiversity hotspots because of its complicated terrain, diversified climates and habitats (Myers et al, 2000). Climatic oscillations in the Pleistocene led to drastic environmental changes repeatedly, which substantially influenced the species’ distribution and evolution, even extinction (Hewitt, 1996, 2000, 2004; Comes and Kadereit, 1998). Climatic oscillations during the Pleistocene have had severe effects on the divergence and population dynamics of many extant species (Hewitt, 1996, 2000, 2004; Avise, 2000). There has been an increasing body of literature on the effect of climatic oscillations on species’ divergence and population dynamics (Zhan et al, 2011; Liu et al, 2013; Feng et al, 2014, 2016b; Gong et al, 2015)

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