Data "Weak but repeated patterns of co-introgression of nuclear OXPHOS genes and mitochondrial DNA in Iberian wall lizards"

Abstract The role of mitonuclear interactions in shaping patterns of introgression remains poorly understood. Here we studied multiple independent cases of mitochondrial capture in Iberian Podarcis lizards, we tested whether nuclear OXPHOS genes preferentially co-introgress with mitochondria allowing for incompatibilities mitigation. Using dense sampling and targeted sequencing, we uncovered a weak but consistent signal of preferential co-introgression in three of four events, some of which involved complete mitochondrial DNA replacements from ghost lineages. These findings reveal that mitonuclear co-introgression, though subtle, can leave detectable signatures across repeated introgression events. Methods We used capture target enchirment of DNA samples to obtain sequences of 240 nuclear genes and 13 mitochondrial genes of 288 lizards. We mapped the raw reads against the Podarcis muralis reference genome (BioProject PRJNA515813) and retained 67 nuclear OXPHOS genes, 144 nuclear control genes and the 13 mitochondrial protein-coding genes. The dataset includes individuals of every recognized or suspected species of the Iberian group: 17 P. bocagei, 22 P. carbonelli, 4 P. guadarramae, 44 P. hispanicus, 123 P. liolepis, 4 P. lusitanicus, 44 P. vaucheri, 6 P. virescens and 15 P. sp. Maghreb from two undescribed lineages (candidate species). Moreover, 2 Teira dugesii, 2 P. tiliguerta and 2 P. muralis were included as outgroups for phylogenetic analysis.