RAD-seq data of Ligidium and Ligia
We applied genome-wide analysis (RAD-seq; Restriction Site Associated DNA Sequence) to examine the regional distribution of genetic diversity of Ligidium throughout Japan. To search for single nucleotide polymorphisms (SNPs), we performed RAD-seq for the following individuals: from Niigata and Hokkaido obtained in previous studies, two regions in northern Japan (Aomori and Sendai), and two regions in western Japan (Shizuoka and Sendai). Genomic DNA was isolated from almost whole body tissues with a DNA Mini kit (Qiagen, USA). Libraries for RAD-seq were prepared with EcoRI and BglII restriction enzymes. The library was sequenced with 150 + 150 bp paired-end reads in one lane of Illumina HiSeqX (Illumina, San Diego, CA, USA) by Macrogen (Seoul, South Korea). The Illumina HiSeq X generates raw images and base calling through an integrated primary analysis software called RTA 2(Real Time Analysis 2). The BCL (base calls) binary is converted into FASTQ using illumina package bcl2fastq2-v2.20.0. The demultiplexing option (--barcode-mismatches) was set to default (value : 0). Adapters are not trimmed away from the reads.