DOI: 10.5061/dryad.69p8cz9b2
title: Raw data of samples of the Korean endemic shrub Abeliophyllum distichum in fastq format

description: White forsythia or Abeliophyllum distichum Nakai (Oleaceae) is the only
 member in its genus and is an endangered shrub endemic, with limited and
 fragmented distribution, to the Korean Peninsula. Due to its endemicity
 and distribution status, several populations of the species have been
 designated as Korean natural monuments, an IUCN Category III protected
 area. More recently, the species’ genomic variation and structure, and the
 demographic history of divergence of its genetic groups were investigated.
 In our current work, we look into the species’ genetic-landscape pattern,
 interpopulation connectivity, individual genetic group population size
 change history, and the species’ future distribution using SNPs and RAD
 loci datasets. Here, we provide the raw genomic data derived from high
 throughput sequencing of reduced representation libraries of
 135 A. distichum individuals across nine natural populations (15
 samples per population, including those from five natural monuments
 habitats) of the species. The libraries were prepared using the GBS
 protocol and demultiplexed using the Stacks 2 software to generate a
 dataset of fastq files for each sample. These datasets have been employed
 in our current study with the running title “Population connectivity and
 size reductions in the Anthropocene: the consequence of landscapes and
 historical bottlenecks in white forsythia fragmented habitats” submitted
 to the BMC Journal of Ecology and Evolution. 
description: We provide the raw genomic data derived from high throughput
 sequencing of reduced representation libraries of 135 <em>A.
 distichum</em> individuals across nine natural populations (15
 samples per population, including those from five natural monuments
 habitats) of the species. The libraries were prepared using the GBS
 protocol and demultiplexed using the Stacks 2 software to generate a
 dataset of fastq files for each sample. The files are
 the output of the ‘process_radtags’ program (in Stacks 2) after processing
 paired-end reads output from Illumina sequencing. Each sample is a set of
 four files: two for the single-end read and two for the pair-end read.
 Reads with low-quality scores (-q 10) had been discarded. According to
 Stacks 2 manual (Rochette et al., 2019) and protocol (Rivera-Colon and
 Catchen, 2022), the ‘process_radtags’ program keeps the reads in phase,
 hence, the first read in the sample_XXX.1.fq file is the mate of the first
 read in the sample_XXX.2.fq file. When one read in a pair is discarded due
 to low quality or a missing restriction enzyme cut site, the remaining
 read is considered a remainder read and is output into the
 sample_XXX.rem.1.fq file if the paired-end was discarded, or the
 sample_XXX.rem.2.fq file if the single-end was discarded (Rochette et al.,
 2019).
description: # Raw data of samples of the Korean endemic shrub *Abeliophyllum
 distichum* in fastq format DOI: 10.5061/dryad.69p8cz9b2 This README file
 explains the dataset. This folder contains demultiplexed fastq files of
 **135** *Abeliophyllum distichum* samples **across nine natural
 populations (15 per population)**. The files are the output of the
 ‘process_radtags’ program (in Stacks 2) on Illumina-sequenced paired-end
 reads, discarding those with low-quality scores (-q 10). Each sample has a
 **set of four fastq** files: **sample_XXX.1.fq** and **sample_XXX.2.fq**
 files being those used in further analyses, and the
 "sample_XXX.rem.1.fq" and "sample_XXX.rem.2.fq" being
 the **remainder files** which were discarded after a quality check. Each
 sample starts with a **population code (two capital letters)**, but also
 with additional information for populations with **natural monument status
 (NM identification)**, before the **final sample information (numbers)**.
 Please see Ong et al. (2023) (DOI: 10.1002/ece3.10792) for more precise
 population information.