DNA sequence variation and methylation in an arsenic tolerant earthworm population

► Lumbricus rubellus from arsenic contaminated sites were tolerant to the metalloid. ► Mitochondrial and nuclear marker identified L. rubellus as two cryptic lineages. ► Soil As influenced genome structure for both clades, strongly so for Lineage A. ► Lineage B earthworms also showed epigenetic variations related to soil As. ► Two cryptic L. rubellus lineages use different mechanisms to adapt to As exposure.