Exploring Mitonuclear Discordance: Ghost Introgression From an Ancient Extinction Lineage in the Odorrana swinhoana Complex

Mitonuclear discordance, the incongruence between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA), is a well-documented phenomenon with various potential explanations. One emerging hypothesis, ghost introgression, refers to the genetic contribution of an ancient, extinct or unsampled lineage and can now be tested using modern genomic data and demographic models. In this study, we investigated the evolutionary history of the Odorrana swinhoana complex (Anura: Ranidae), which includes O. swinhoana, O. utsunomiyaorum and an unidentified population with highly divergent mtDNA. While mitochondrial phylogeny suggested this population as a basal lineage, nuclear data from ddRADseq revealed it as a mixture of the most derived O. swinhoana nuclear sequences combined with ancient mtDNA. Demographic modelling further supported ghost introgression, as all models incorporating a ghost population outperformed those without it. These findings suggest that an eastward expansion of western O. swinhoana replaced an ancient Odorrana lineage, leaving only its mtDNA and fragments of its nuclear genome in the hybrid population. Our results provide one of the first documented cases of ghost introgression in amphibians and highlight its potential as a widespread evolutionary process. This study also underscores the risks of relying solely on mtDNA for phylogenetic reconstruction and species delimitation.