Unearthing the genetic divergence and gene flow of the earthworm Amynthas_YN2017 sp. (Oligochaeta: Megascolecidae) populations based on restriction site-associated DNA sequencing

Abstract

Despite the ecological function of earthworms being of undeniable importance, little is known about their population genetic diversity, dispersal, and gene flow patterns. Here, we applied 769,957 single-nucleotide polymorphisms (SNPs) gathered by restriction site-associated DNA sequencing (RAD-seq) to unearth the genetic variability of populations of the earthworm Amynthas_YN2017 sp. collected from Western Yunnan, China. The neighbor-joining (NJ) tree method revealed that 30 individuals strongly clustered into three lineages (G2, G3, and G5 lineages) that coincided with the geographic distribution proximity of the sampling locations. There was a low level of genetic differentiation among these lineages with an average genetic differentiation (FST) value ranging from 0.080 to 0.135. Clustering analysis demonstrated a clear population genetic structure with a low level of admixture. There was only one migration edge in the population from the G3 lineage to the G2 lineage. Therefore, we presume that a reduction in gene flow caused by geographic isolation influences the population genetic differentiation of Amynthas_YN2017 sp. Additionally, the presence of river (Nujiang River) as geographical barrier is likely to have limited the gene flow. Overall, the large number of SNPs gathered by RAD-seq reveals a significant population genetic structure over a restricted geographic scale, highlighting that the RAD-seq approach could be used to explore the population phylogenetic relationships and population genetic diversity of earthworms.