SNP sets of Bolivian Parajubaea species

Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species’ conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus’ origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia, and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species, and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3,753 bp) challenged the hypothesis that P. c..., DNA was extracted from silica-dried leaf fragments. Raw reads were generated by Genotyping-by-Sequencing. SNP sets were produced with Stacks under different filtering parameters of the populations module., , # SNP sets of Bolivian Parajubaea species

[https://doi.org/10.5061/dryad.k0p2ngfgx](https://doi.org/10.5061/dryad.k0p2ngfgx)

## Data files accompanying the article: Peñafiel Loaiza, N., Chafe, A.H., Moraes, R.M., Oleas, N.H., Roncal, J. (2024) Genotyping by sequencing informs conservation of Andean palms sources of non-timber forest products

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## This folder contains thirteen SNP sets.

### 1. Peñafiel\_Loaiza-et-al\_2024\_Conservation-genomics-of-Andean-palms\_denovo\_ALL-SNPs.str

SNP set created through a *de novo* pipeline in *Stacks* (*populations* parameters: -p 2 -r 0.5) for the analysis of genetic structure among individuals of nine collection sites of *Parajubaea* palms in Bolivia (1=Mataralcito[Mat], 2=UAGRM, 3=Quebrada honda[Qh], 4=El Palmar[EP], 5=Ruditayoj[Ru], 6=Lajas[La], 7=Sauce Mayo[SM], 8=Palmarcito[Pal], 9=Sucre[Su]).

The file contains information on **15134** SNPs scored for 48 individuals of three collection sites of *Parajubaea sunkha* and 146 individuals of...

当前全球生物多样性丧失的背景下，对提供非木材林产品的物种类群开展保护与可持续管理至关重要。然而，多数非木材林物种缺乏能够阐明其种内变异与进化历史的基因组学研究——而这些信息恰恰可为物种保护实践提供依据。与安第斯生物多样性热点区域内诸多表现出高度分化的类群不同，*Parajubaea*属（棕榈科Arecaceae）尽管起源于2200万年前，目前仅包含3个物种。其中两个棕榈物种：托拉利椰子椰（P. torallyi）和孙克哈椰子椰（P. sunkha），是玻利维亚安第斯地区特有的非木材林物种，且被国际自然保护联盟（IUCN）列为濒危物种。第三个物种科科依德斯椰子椰（P. cocoides）为易危物种，其野生种群状况尚不明确。本研究探究了*Parajubaea*属物种的进化关系，以及玻利维亚野生种群的遗传多样性与遗传结构。研究对5个低拷贝核基因（总长3753 bp）进行测序，这一结果对“P. c...”这一假说提出了挑战。实验中，我们从硅胶干燥的叶片碎片中提取DNA，通过基因型测序（Genotyping-by-Sequencing, GBS）获得原始测序读段，并借助Stacks软件的种群模块（populations）在不同过滤参数下构建单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集。

# 玻利维亚*Parajubaea*属物种的SNP数据集
[https://doi.org/10.5061/dryad.k0p2ngfgx](https://doi.org/10.5061/dryad.k0p2ngfgx)

本文附带的数据文件：Peñafiel Loaiza, N.、Chafe, A.H.、Moraes, R.M.、Oleas, N.H.、Roncal, J.（2024）《基因型测序可为非木材林产品来源的安第斯棕榈保护提供依据》

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本文件夹包含13组SNP数据集。

### 1. Peñafiel_Loaiza-et-al_2024_Conservation-genomics-of-Andean-palms_denovo_ALL-SNPs.str
该SNP数据集通过Stacks软件的*de novo*流程构建（种群模块参数：-p 2 -r 0.5），用于分析玻利维亚9个采样点的*Parajubaea*属棕榈个体间的遗传结构：1=Mataralcito[Mat]、2=UAGRM、3=Quebrada honda[Qh]、4=El Palmar[EP]、5=Ruditayoj[Ru]、6=Lajas[La]、7=Sauce Mayo[SM]、8=Palmarcito[Pal]、9=Sucre[Su]。本文件包含了48个孙克哈椰子椰（P. sunkha）个体（来自3个采样点）以及146个个体的……（原文未完成）的15134个SNP位点分型信息。