Speciation in the Patelloida saccharina species complex across the Japanese Archipelago

概要

The process of speciation among closely-related species and the underlying dynamics
have long been challenging subjects in the field of evolutionary biology. Cytoplasmic
DNA markers, which are commonly employed in molecular barcoding, have often proven
insufficient in resolving phylogenies and other related subjects. However, the advent of
next-generation sequencing technologies and reduced genome representation techniques
have resulted in a significant improvement to resolve phylogenies of closely related
species with greater detail. Furthermore, these approaches have enabled a much better
understanding of the divergence and speciation patterns and processes. This study
examined the extent of speciation in the Patelloida saccharina species complex using a
combination of single-locus sequencing and single nucleotide polymorphism (SNP)
discovery technology.
METHODOLOGY
The mitochondrial cytochrome oxidase I gene (COI), the 16S RNA (16S), and the
nuclear histone3 gene (H3), as well as SNP markers, were sequenced from 165 specimens
collected across 37 localities in the Japanese Archipelago. In total, 28 unique COI
haplotypes, 16 16S haplotypes, 11 H3 haplotypes, and 13847 unlinked SNPs were
obtained. The phylogenetic trees and genetic assignment analyses revealed three
genetically distinct lineages: Patelloida saccharina saccharina (Linnæus, 1758),
Patelloida saccharina lanx (Reeve, 1855), and an unknown Patelloida sp. From
Shionomisaki, Kushimoto, Wakayama Prefecture.
RESULTS
Divergence time analysis estimated that the split between P. saccharina saccharina and
P. saccharina lanx occurred ~45,000 years ago, which is too recent to accumulate
morphological differences that would make it difficult for taxonomic identification.
Demographic history analyses suggest that continuous gene exchange occurred after the
initial split, allowing for the introgression of the P. saccharina lanx genome and the
proliferation of intermediate individuals. ...