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

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.

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

“…The Cycas species, with similar life history and reproductive characteristics, are thought to have a high level of genetic variation within populations and significant genetic differentiation among populations (Liu et al, 2015). The significant genetic differentiation and clear genetic structure observed in the C. taiwaniana complex may be explained by limited gene flow (Feng et al, 2014;James et al, 2018), which had also been reported for other Cycas species (Zhao and Gong, 2015;Feng et al, 2017). The effective propagation distance of Cycas species is 2-7 km (Yang and Meerow, 1996).…”

“…We selected the F81 model with a relaxed uncorrelated molecular clock for combined cpDNAs and an HKY+I model with a strict molecular clock for joint nDNAs. Because an accurate evolutionary rate for Cycas was unavailable, we applied the evolutionary rates for seed plants of 1.01 × 10 −9 substitutions per site per year for synonymous sites for cpDNA and 6.1 × 10 −9 (5.1-7.1 × 10 −9 ) substitutions per site per year for synonymous sites for SCNGs (Graur and Li, 2000;Feng et al, 2017). The MCMC analyses were run for 10 8 generations and was sampled every 10,000 steps.…”

“…However, molecular phylogenetic analyses indicated that the extant cycads underwent a synchronous global re-diversification and are not much more than 12 million years old (Nagalingum et al, 2011). In recent years, researchers have studied cycad phylogeny Wei et al, 2015), conservation (Feng et al, 2014;Feng et al, 2016;Feng et al, 2017;Gregory and Lopez-Gallego, 2018;Tang et al, 2018a;Zheng et al, 2017), biogeography (Gutiérrez-Ortega et al, 2017Meerow et al, 2018;Cabrera-Toledo et al, 2019), pollination biology (Tang et al, 2018b;Santiago-Jimnez et al, 2019), and physiology (Vovides and Galicia, 2016). Cycads comprise two families (Cycadaceae and Zamiaceae), with 10 genera and 355 accepted species (Calonje et al, 2019).…”

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

“…Estimates of genetic diversity based on cpDNA sequences can be used to provide inferences on the evolutionary history of plant species, including possible recolonization routes, diversification events, and gene flow [18][19][20]. This approach has been used not only to analyze ecologically important species, such as those with a high degree of endemism [21], but also medicinal plants [22], and those with commercial potential [23].…”

Species delimitation with distinct methods based on molecular data to elucidate species boundaries in the Cycas taiwaniana complex (Cycadaceae)

“…A modified CTAB method was used to extract genomic DNA from silica‐gel dried leaf tissue (Doyle, 1991). Four cpDNA intergenic spacers, atpB‐rbcL (Sang & al., 1997), psbA‐trnH (Chiang & Peng, 1998), psbM‐trnD (Shaw & al., 2005), and trnS‐trnG (Shaw & al., 2005) and four nuclear genes, AC5 (actin 5 gene), PHYP (phytochrome P gene) (Feng & al., 2016a), PPRC (pentatricopeptide repeat‐containing protein gene) (Feng & al., 2017) and AAT (aspartate aminotransferase gene) were chosen for complete analysis. Primers are provided in Table 2.…”