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Genetic diversity of Horsfieldia tetratepala (Myristicaceae), an endangered plant species with extremely small populations to China: implications for its conservation

Citation

Cai, Chaonan (2022), Genetic diversity of Horsfieldia tetratepala (Myristicaceae), an endangered plant species with extremely small populations to China: implications for its conservation, Dryad, Dataset, https://doi.org/10.5061/dryad.x95x69ph1

Abstract

Genetic variation determines the evolutionary potential of a species and is vital for fully understanding the evolution of a species, as well as for developing optimal conservation strategies. Horsfieldia tetratepala is an economically important rainforest tree which has declined steadily, mainly though habitat destruction, and an endangered, narrow endemic in China where it is also classified as a Plant Species with Extremely Small Populations (PSESP). Effective conservation strategies for H. tetratepala are required urgently, but limited information about its genome is available. Accordingly, restriction site-associated DNA sequencing (RAD_seq) was used to sequence sixty-three H. tetratepala trees covering ten isolated populations to assess genome-level diversity and population structure, generating 8,103 high-quality SNPs. Low genetic diversity and moderate genetic differentiation was observed among populations, but Bayesian clustering divided the sampled H. tetratepala populations into two genetic clusters, though with some populations from Guangxi and Yunnan intermixed. Because of increasing of habitat fragmentation and human disturbance, conservation priority should be placed on populations with higher genetic variation (e.g., BB, TKH, DWS, and GLQ). Overall, our study provides valuable genomic resources for H. tetratepala that will significantly advance the formulation of effective conservation strategies.

Usage Notes

The file pop.str includes 8103 SNPs is the input file for "Structure" software.

The pop.str file can be transformed to others formats (.arp) by PGDspider. And the PCA input file (plink.ped and plink.map) is the Stacks v 2.2 output file from "Population" model.

The IBD analyses input file (Fst values) is the  Stacks v 2.2 output file (populations.Fst.tsv) from "Population" model.

The popmap.txt file refers to the information of  samples collection and populations code. 

The p1r0.75populations.snps.vcf file: species level; the p5r0.75populations.snps.vcf :population level.

catalog.tags.tsv.gz, catalog.snps.tsv.gz and catalog.alleles.tsv.gz is the Stacks v 2.2 output file from "Cstacks" model.