DOI: 10.5061/dryad.j6q573nq6
title: SNP dataset for 27 populations of Adenocaulon himalaicum (Asteraceae)

description: 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 = 0.18, p
 = 0.03). Redundancy analysis (RDA) revealed that the
 genomic variation were significantly explained
 by mean diurnal range (bio2), precipitation of driest
 quarter (bio17) and precipitation of warmest quarter (bio18) and soil type
 (TAXNWRB). Using two genotype-environment association (GEA) methods, we
 identified 27 SNPs as candidates for
 core climate-related adaption loci and two loci of these
 were further validated by qRT-RCR experiments. Furthermore,
 predictions to spatiotemporal pattern of genomic offsets under
 different future climate
 scenarios revealed that populations near
 southeastern edge of Himalaya, Yunnan-Guizhou Plateau, northern
 Korean Peninsula, and southern Japan were regarded as the most
 vulnerable populations. Therefore, conservation priority
 is needed for these populations due
 to candidate variants and unique genetic compositions being
 useful for future breeding.
description: # 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 data, respectively. We filtered the loci according to loci with minor allele frequencies &lt;0.05, and a maximum observed heterozygosity was set at 0.5 to reduce the potential paralogs. The polymorphic loci present in at least 85% of the individuals were retained. This file shows the 34,398 SNPs identified by Stacks v2.41 for 221 individuals of  *Adenocaulon himalaicum.* ## Code/Software These files can all be opened with a standard text editor, such as Notepad. It can also be opened with Tassel as vcf files.