Exploring mitonuclear discordance: Ghost introgression from an ancient extinction lineage in the Odorrana swinhoana complex

This study investigates mitonuclear discordance in the Odorrana swinhoana complex (Anura: Ranidae), specifically exploring the hypothesis of ghost introgression, which refers to genetic signatures from an ancient and extinct lineage. Using mtDNA and RADseq, we reconstructed the evolutionary process of the Odorrana swinhoana complex, comprising O. swinhoana, O. utsunomiyaorum, and an unidentified clade with highly divergent mitochondrial sequences. Although this clade appears as a basal lineage in the mitochondrial phylogeny, nuclear data from RADseq reveal it as a mixture of modern O. swinhoana nuclear sequences and ancient mtDNA. Demographic modeling showed that all models incorporating a ghost population outperformed that without it, though the inferred position of the ghost lineage differed from that in the mitochondrial tree. We therefore inferred that this unique lineage likely resulted from an eastward expansion from western O. swinhoana, which replaced an ancient Odorrana species that no longer exist as an independent taxon (i.e., the ghost). This process might left the population with distinct mtDNA and small parts of nuclear signatures. Although we did not find a direct correlation between mitonuclear discordance and ghost introgression, our results still provide one of the first cases of ghost introgression in amphibians. This study further suggests that ghost introgression is likely a widespread phenomenon in nature, which may not occur only one time and should be considered in evolutionary research. Additionally, This study also suggests that using only mtDNA to construct phylogeny or species delimitation could yield false results.