Target capture sequencing provides insights into hybridogenetic water frogs

Abstract The European water frogs of the genus Pelophylax , with their propensity to hybridize and a non-orthodox inheritance system in some hybrids, present a genetic puzzle that has previously lacked strong genomic tools. This has limited investigation into the remarkable hybridogenetic system observed in the edible frog P. esculentus as well as inhibited monitoring of invasive populations in a genus that is critically vulnerable to this threat. In this study we explore whether a previously developed target capture bait set, FrogCap, can be used to answer genomic questions within the genus, by applying it to the three taxa of Pelophylax native to the Netherlands. We observe that the target capture data cleanly separates the three taxa, confirming significant introgression of P. lessonae mtDNA into P. ridibundus from the Netherlands. We also show that target capture is an efficient method for identifying polyploidy in P. esculentus and is effective at determining ancestral contribution within our sample population. Targeted sequence capture using FrogCap is a useful tool to unravel the intricate evolution of Pelophylax water frogs.