Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect

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1 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan province, China
2 University of Chinese Academy of Sciences, Beijing, China
DOI
10.7287/peerj.preprints.27265v1
Published
Accepted
Subject Areas
Biodiversity, Conservation Biology, Genetics, Plant Science, Population Biology
Keywords
Cycas panzhihuaensis, Conservation, Genetic diversity, Phylogeography, Chloroplast and nuclear DNA, Microsatellite, Effective population size
Copyright
© 2018 Xiao et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Xiao S, Ji Y, Liu J, Gong X. 2018. Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect. PeerJ Preprints 6:e27265v1

Abstract

Background

Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic in the dry-hot valley of Jinsha River basin from southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected, other known populations that fall outside the natural reserve may preserve specific genetic resources while face with larger extinction risk because of lacking essential monitoring.

Methods

In this study, we analyzed the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from seven known locations so far by sequencing three chloroplastic DNA regions (psbA-trnH, psbM-trnD, and trnS-trnG), four single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, and eleven microsatellite loci (SSR) from 102 individuals.

Results and Discussion

We found relative high genetic diversity within populations and high genetic differentiation among the populations of C. panzhihuaensis, which is similar with the other Asian inland cycads. Despite no significant phylogeographical structure was detected, small and unprotected populations possess higher genetic diversity and more unique haplotypes, which deserve due attention. Results of demographic dynamics suggest that human activity is the key factor that leads C. panzhihuaensis to endangered status. Basing on the genetic characterization of C. panzhihuaensis, we proposed several practical guidelines for the conservation of this species, especially for its small populations.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Cycas panzhihuaensis psbA-trnH haplotype and outgroup intergenic spacer region, partial sequence, chloroplast

DOI: 10.7287/peerj.preprints.27265v1/supp-1

Cycas panzhihuaensis psbM-trnD haplotype and outgroup intergenic spacer region, partial sequence, chloroplast

DOI: 10.7287/peerj.preprints.27265v1/supp-2

Cycas panzhihuaensis trnS-trnG haplotype and outgroup intergenic spacer region, partial sequence, chloroplast

DOI: 10.7287/peerj.preprints.27265v1/supp-3

Cycas panzhihuaensis haplotype and outgroup phytochrome P gene (PHYP), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-4

Cycas panzhihuaensis haplotype and outgroup actin 5 gene (AC5), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-5

Cycas panzhihuaensis haplotype and outgroup heat shock protein 70 kDa gene (HSP70), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-6

Cycas panzhihuaensis haplotype and outgroup aspartate aminotransferase gene (AAT), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-7

Microsatellite raw data (11 SSR markers) of Cycas panzhihuaensis from 102 individuals from 7 populations

DOI: 10.7287/peerj.preprints.27265v1/supp-8

Information of cpDNA and nDNA fragments and primers sequences used in this study

DOI: 10.7287/peerj.preprints.27265v1/supp-9

Information of SSR marker primers used in this study

DOI: 10.7287/peerj.preprints.27265v1/supp-10

Sample locations, sample sizes (n), the composition of haplotypes, haplotype diversity (Hd) and nucleotide diversity (π) surveyed for cpDNA and nDNA of C. panzhihuaensis investigated in this study

Hd: Haplotype (gene) diversity; π: Nucleotide diversity

DOI: 10.7287/peerj.preprints.27265v1/supp-11

Figure plot of geographical distance (X axial) against genetic distance (FST, Y axial) for seven populations C. panzhihuaensis based on different DNA datasets

(a) cpDNA; (b) PHYP; (c) N3.

DOI: 10.7287/peerj.preprints.27265v1/supp-12

Principal coordinate analysis and STRUCTURE analyses of 102 individuals from seven populations of C. panzhihuaensis based on phenotypes of 11 microsatellite markers

(a) Principal coordinate analysis (PCoA). (b) Estimated genetic clustering obtained by STRUCTURE analyses using Bayesian approach (K= 5).

DOI: 10.7287/peerj.preprints.27265v1/supp-13

Mismatch distribution plot of C. panzhihuaensis based on different datasets

(a) cpDNA; (b) PHYP; (c) N3.

DOI: 10.7287/peerj.preprints.27265v1/supp-14