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Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands

Citation

Kimura, Takuma et al. (2022), Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands, Dryad, Dataset, https://doi.org/10.5061/dryad.rn8pk0pbt

Abstract

Aim: Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Except for a few examples such as the Canary Islands, endemic plants on nearshore oceanic islands have received less attention. In this study, we examined the Solidago virgaurea complex on the Japanese mainland Honshu and the adjacent Izu Islands to investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands.

Location: Japanese mainland Honshu and the adjacent Izu Islands

Taxon: Solidago virgaurea (Asteraceae)

Methods: Sixteen and nine populations of S. virgaurea complex were sampled from the mainland and islands, respectively; phylogeographic and population genetics analyses were performed using plastid DNA and nuclear microsatellite DNA variations.

Results: Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of S. virgaurea from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island.

Main conclusions: The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of S. virgaurea are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations.

Methods

Microsatellite genotyping

We used 10 expressed sequence tag-simple sequence repeat markers developed from S. virgaurea subsp. asiatica (Sakaguchi & Ito, 2014) and three genomic simple sequence repeat markers developed from S. altissima (Sakata et al, 2013; Table S1). We conducted PCR amplification in multiplex reactions using the Type-it® Microsatellite PCR Kit (Qiagen, Venlo, Netherlands). The PCR reaction mixture contained 50–100 ng DNA, 1.5 μl of 2 × Type-it Multiplex PCR Master Mix, and each primer at 10 μM, and was brought to a total volume of 3.0 μl with sterilized water. The PCR protocol was as follows: denaturation at 95°C for 1 min; 30 cycles of 95°C for 30 sec, 55°C for 90 sec, and 72°C for 90 sec; and a final extension at 72°C for 10 min. To separate the PCR products, we used the ABI PRISM® 3130 Genetic Analyzer with Gene Scan 600 Liz Size Standard (Thermo Fisher Scientific, Waltham, MA). To determine the length of the amplified fragment and the resultant genotypes, we used Gene Mapper v.4.0 (Thermo Fisher Scientific, Waltham, MA).

Usage Notes

Microsatellite genotype of Solidago virgaurea (GenAlEx data format)

1. All samples

2. Populations with ≥ 10 individuals

3. Populations with ≥ 10 individuals (Short sample name)