Dual expansion routes likely underlie the present-day population structure in a Parnassius butterfly across the Japanese Archipelago
Data files
Jan 06, 2025 version files 122.12 KB
-
README.md
774 B
-
Supporting_Material_PG.xls
121.34 KB
Abstract
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 million years ago (Ma). Subsequently, the Eastern Japan and Western Japan lineages diverged from the Chugoku–Shikoku lineage around 1.06 Ma, with subsequent divergence of the Eastern and Western Japan lineages at approximately 0.62 Ma. P. glacialis is estimated to have expanded its distribution via a land bridge that once connected China and the Japanese Archipelago. Population structure analysis based on 3067 SNP genotypes revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. Through mtDNA and SNP variation analyses, four primary genetic barriers were identified: between Hokkaido and Honshu, between Eastern and Central Japan, within the Kansai region, and in the Chugoku region. The first three barriers correspond to notable geographical features, the Blakiston Line, a line parallel to the Itoigawa–Shizuoka Tectonic Line, and a boundary crossing Lake Biwa. These findings suggest that Japanese P. glacialis diverged from the continental P. glacialis and expanded its range across the Japanese Archipelago via western routes, leading to its current distribution.
README: 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
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)
Methods
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) and high-throughput pair-end sequencing primer kit (App-D, MGI Tech) as recommended in the instructions. Sequencing was performed using DNBSEQ-T7RS high-throughput sequencing kit (MGI Tech) using the supplied primers (App-D) and the DNBSEQ-T7 (MGI Tech) platform under 2 × 150 bp conditions. To remove primer sequences, the first three bases of each read were removed using Cutadapt v4.0 (Martin, 2011). Paired reads with QS <30 or fewer than 75 bases were filtered out using Sickle v.1.33 (Joshi and Fass, 2011). Sequences > 75 nucleotides were removed to standardize read length for data analysis.
The isolated DNA was resuspended in Tris-HCl buffer (pH 7.5) and stored at 4°C. Polymerase chain reaction (PCR) was conducted to amplify two gene regions: the contiguous mitochondrial COI region (721 bp) and COII region (470 bp). The primers used to amplify the COI region were JNfwd (5’-GCAGGAACTGGATGAACAG-3’) and Krev (5’-GAGTATCGTCGAGGTATCC-3’) (Dechaine and Martin, 2004), and those used to amplify the COII region PierreIII (5’-AGAGAGTTTCACCTTTAATAGAACA-3’; Nazari et al., 2007) and Eva (5’-GAGAACATTACTTGCTTTCAGTCATCT-3’; Bogdanowicz et al., 1993). Both fragments were amplified using TaKaRa Ex Taq Hot Start Version (TaKaRa, Tokyo, Japan). The PCR conditions for the COI region were 94°C for 5 min, followed by 30 cycles of 94°C for 30 s, 50°C for 30 s, and 72°C for 1 min. For the COII region, the amplification conditions were 95°C for 5 min, followed by 35 cycles of 94°C for 1 min, 50°C for 1 min, 72°C for 1 min, and finally 72°C for 10 min. Sequencing reactions were performed using BigDye Terminator v3.1 (Applied Biosystems, Carlsbad, USA). All samples were sequenced using an ABI PRISM 3100-Avant Genetic Analyzer (Applied Biosystems, Carlsbad, CA, USA).