Dual expansion routes likely underlie the present-day population structure in a Parnassius butterfly across the Japanese Archipelago

The Japanese Archipelago consists of a series of isolated yet interconnected islands off the Eurasian continent. The linear topography of the archipelago presents a unique biogeographic context for the dispersal of organisms from the continent. In this study, mitochondrial DNA (mtDNA) and single-nucleotide polymorphism (SNP) variation were employed to elucidate the dispersal history of the Japanese clouded butterfly (Parnassius glacialis) across the Japanese Archipelago, including the northern island (Hokkaido), the main island (Honshu), and Shikoku Island. Network analysis of 1192 bp of mtDNA (cytochrome oxidase I and II) regions revealed 49 haplotypes and three distinct haplotype groups, which correspond geographically to Eastern Japan, Western Japan, and Chugoku–Shikoku. The Chugoku–Shikoku group is the most ancient lineage. Divergence time estimates using whole-genome sequencing of mtDNA suggest that the Japanese lineage diverged from the continental P. glacialis approximately 3.08 ..., SNPs were detected from the extracted DNA using the genotyping by random amplicon sequencing, direct (GRAS-Di) method designed by Enoki and Takeuchi (2018) and described by Hosoya et al. (2019); this method offers simple library construction and the capacity to detect many SNPs. Briefly, libraries were constructed through two sequential PCR steps, similar to multiplexed inter-simple sequence repeat genotyping by sequencing (Suyama and Matsuki 2015). The first PCR primers consisted of 10 bases of Illumina Nextera adaptor 3-end sequences plus 3-base random oligomers (13 bases). The final PCR product was purified using columns or magnetic beads without size selection and then employed for sequencing on an Illumina platform (Illumina, San Diego, CA, USA). Cyclized DNA was prepared using the produced library and the MGIEasy universal library conversion kit (App-A, MGI Tech) according to the manufacturer’s instructions. DNBs were prepared using the DNBSEQ DNB Rapid Make reagent kit (MGI Tech)..., , # Dual expansion routes likely underlie the present-day population structure in a Parnassius butterfly across the Japanese Archipelago

[https://doi.org/10.5061/dryad.69p8cz9d3](https://doi.org/10.5061/dryad.69p8cz9d3)

## Description of the data and file structure

Each sample’s raw fastq sequence data for SNP and haplotype of mtDNA

### Files and variables

#### File: Supporting\_Material\_PG.xls

**Description:** Each sample’s raw fastq sequence data and haplotype

##### Variables

* Sheet 1: an overview of each sheet.
* Sheet 2: raw sequence data for each  SNP detected with the Grass-Di method.
* Sheet 3: haplotype number for each collected individual (collected year, individual code, collection site, Prefecture, Prefecture number, haplotype number)