Ancestral introgression and dual mitochondrial capture shaped mito-nuclear discordance in sky-island skinks (Scincidae: Sphenomorphus )

Mito-nuclear discordance can obscure the interpretation of evolutionary history, particularly in fragmented systems where multiple processes can generate similar phylogenetic patterns. We investigated pronounced discordance between mitochondrial and nuclear genomes in two parapatric montane skinks, Sphenomorphus taiwanensis and S. luelaiorum, from Taiwan’s sky islands. Using mitochondrial sequences and genome-wide ddRAD-seq SNPs, we evaluated incomplete lineage sorting, introgression, and ghost introgression as alternative explanations, while assessing sex-biased dispersal, selection, and demographic history. Model-based analyses supported historical introgression between extant lineages but provided little evidence for ghost introgression. An expanded coalescent analysis favored bidirectional over unidirectional introgression. Genomic indices showed no consistent sex-biased dispersal, whereas mitochondrial selection signals were restricted to particular lineages. Coalescent estimates and forward simulations indicated that small effective population sizes could increase the probability of mitochondrial capture. We interpret the discordance as the outcome of ancestral bidirectional introgression followed by genetic drift in isolated montane populations, with selection potentially facilitating fixation under high-altitude conditions. These findings illustrate how gene flow and demographic processes in fragmented landscapes can generate persistent mito-nuclear discordance, underscoring the importance of integrating genomic and ecological evidence when interpreting mitochondrial phylogenies.