Genetic diversity, genetic structure and demographic history of Cycas simplicipinna(Cycadaceae) assessed by DNA sequences and SSR markers

Abstract

BackgroundCycas simplicipinna (T. Smitinand) K. Hill. (Cycadaceae) is an endangered species in China. There were seven populations and 118 individuals that we could collect were genotyped in this study. Here, we assessed the genetic diversity, genetic structure and demographic history of this species.ResultsAnalyses of data of DNA sequences (two maternally inherited intergenic spacers of chloroplast, cpDNA and one biparentally inherited internal transcribed spacer region ITS4-ITS5, nrDNA) and sixteen microsatellite loci (SSR) were conducted in the species. Of the 118 samples, 86 individuals from the seven populations were used for DNA sequencing and 115 individuals from six populations were used for the microsatellite study. We found high genetic diversity at the species level, low genetic diversity within each of the seven populations and high genetic differentiation among the populations. There was a clear genetic structure within populations of C. simplicipinna. A demographic history inferred from DNA sequencing data indicates that C. simplicipinna experienced a recent population contraction without retreating to a common refugium during the last glacial period. The results derived from SSR data also showed that C. simplicipinna underwent past effective population contraction, likely during the Pleistocene.ConclusionsSome genetic features of C. simplicipinna such as having high genetic differentiation among the populations, a clear genetic structure and a recent population contraction could provide guidelines for protecting this endangered species from extinction. Furthermore, the genetic features with population dynamics of the species in our study would help provide insights and guidelines for protecting other endangered species effectively.

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

“…PCR amplification procedures were the same as those used in C. simplicipinna (Feng et al, 2014). The PCR products were sequenced on an ABI 3770 automated sequencer at Shanghai Major Biological Medicine and Technology Co Ltd in both directions.…”

“…PCR amplification and microsatellite genotyping were conducted with the same protocol as used in C. simplicipinna (Feng et al, 2014). Finally, we chose 12 polymorphic microsatellite loci, the same used in our study on species delimitation of the C. segmentifida complex (Feng et al, 2016a), for C. segmentifida .…”

The distribution, diversity, and conservation status of Cycas in China

“…As a recently radiated lineage, some Cycas species in southwest China exhibit high genetic diversity at the species level, low genetic diversity within populations, and significant genetic differentiation among populations (Feng, Wang, & Gong, ; Gong et al., ; Liu, Zhou, & Gong, ; Zheng, Liu, & Gong, ). However, specific comparison concerning genetic variations of all the Cycas species in China has rarely been performed.…”

Genetic relationships and polyploid origins in the Lippia alba complex

“…The comparison of gene sequences and SSR data has contributed to a better evolutionary understanding of the Lippia alba complex. Whereas polyploid complexes from the temperate zone have been comparatively analyzed (Garcia‐Mas et al., ; Yang et al., ; Feng et al., ; Ferradini et al., ), this natural tropical polyploid complex is the first to be studied in this manner. SSR analysis showed patterns of similarity among ploidal levels, and the DNA sequence analysis adds further information about polyploid origins.…”