Target Capture Sequencing Provides Insights Into Hybridogenetic Water Frogs

ABSTRACT The European water frogs of the genus Pelophylax present a genetic puzzle that has not yet been studied with strong genomic tools. This limitation has hampered investigation into, for example, the remarkable hybridogenetic system observed in the genus, as well as the monitoring of invasive populations—a critically vulnerable threat to Pelophylax . 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: the marsh frog P. ridibundus , the pool frog P. lessonae , and their hybridogenetic hybrid, the edible frog P. esculentus . We ask if we can obtain high coverage genomic data, distinguish the different species, identify ploidy level, and detect putative interspecific nuclear gene flow. We observe that the high‐quality target capture data obtained 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.