SNP dataset for 27 populations of Adenocaulon himalaicum (Asteraceae)

Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. It is not well understood how environmental gradients mediate local adaptation and how populations respond to changing environment of understory herbs. In this study, we conducted the population genomic analysis of Adenocaulon himalaicum (Asteraceae) in East Asia, representing a good model of dominant understory herb to unveil the adaptive evolution mechanisms of this species. Based on 34,398 single nucleotide polymorphisms (SNPs) across 27 populations, we identified three genetic lineages companied with high levels genetic differentiation between populations. Our isolation by environment results (IBE) indicated the significant effect of environmental gradients on genomic variation of A. himalaicum (r = 0...., , , # SNP dataset for 27 populations of Adenocaulon himalaicum (Asteraceae)

[https://doi.org/10.5061/dryad.j6q573nq6](https://doi.org/10.5061/dryad.j6q573nq6)

## Description of the data and file structure

A VCF (Variant Call Format) file is a text file storing genetic variation data, like SNPs or insertions/deletions.

### Files and variables

#### File: neutral_SNPs_of_A._himalaicum.vcf

The dataset is structured with individual VCF files for 27 Adenocaulon himalaicum populations from 221 individuals. Each VCF file contains meta-information lines, followed by a header line specifying eight fixed fields per sample and subsequent data lines detailing genomic positions. The fixed fields include information such as chromosome (CHROM), position (POS), identifier (ID), the reference base(s) (REF), alternate base(s) (ALT), quality (QUAL), filter status (FILTER), and additional information (INFO). Genotypes are encoded as allele values separated by '/' or 'l' to indicate unphased or phased dat...,

阐明林下草本植物的适应性演化与生存风险机制，对于生物多样性的有效保护至关重要。目前学界对于环境梯度如何介导局部适应，以及林下草本植物种群如何响应环境变化的认知仍较为匮乏。本研究以东亚地区的喜马拉雅腺头草（Adenocaulon himalaicum，菊科）为研究对象——该物种作为林下优势草本的优良模型类群，可用于揭示其适应性演化机制。基于覆盖27个种群的34398个单核苷酸多态性位点（single nucleotide polymorphisms, SNPs），本研究鉴定出三个遗传谱系，且种群间存在高水平遗传分化。本研究的环境隔离（Isolation by Environment, IBE）分析结果显示，环境梯度对喜马拉雅腺头草的基因组变异具有显著影响（r=0……）。
# 基于27个喜马拉雅腺头草（Adenocaulon himalaicum，菊科）种群的SNP数据集
数据集DOI：https://doi.org/10.5061/dryad.j6q573nq6

## 数据与文件结构说明
变异检测格式（Variant Call Format, VCF）文件是一种存储遗传变异数据（如单核苷酸多态性、插入/缺失变异）的文本文件。

### 文件与变量说明
#### 文件：neutral_SNPs_of_A._himalaicum.vcf
本数据集包含27个喜马拉雅腺头草种群（共221个个体）的独立VCF文件。每个VCF文件由若干元信息行、一行样本表头行以及后续的基因组位置详情数据行组成，其中表头行定义了8个固定字段。上述固定字段涵盖以下信息：染色体编号（CHROM）、位点位置（POS）、位点标识符（ID）、参考碱基（REF）、变异碱基（ALT）、测序质量（QUAL）、过滤状态（FILTER）以及附加信息（INFO）。基因型以等位基因值表示，等位基因间用'/'或'l'分隔，分别代表非相位化或相位化数据……