Data from: Repeated mitochondrial capture with limited genomic introgression in a lizard group

Mitochondrial introgression is common among animals and is often first
identified through mitonuclear discordance — discrepancies between
evolutionary relationships inferred from mitochondrial DNA (mtDNA) and
nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed
extensive nuclear introgression in many animal groups, with implications
for genetic and phenotypic diversity. However, the extent to which mtDNA
introgression corresponds to nuDNA introgression varies. Here, we
investigated historical and recent introgression in the Gehyra
nana-occidentalis clade, a complex group of Australian geckos with
documented cases of mitonuclear discordance suggestive of repeated mtDNA
introgression. We hypothesised that mitonuclear discordance in this clade
reflects mtDNA introgression with substantial nuclear introgression.
Despite evidence of repeated mtDNA introgression, however, we found little
to no evidence of historical nuDNA introgression using exon capture and
genome-wide single nucleotide polymorphism (SNP) data. We also found no
evidence of gene flow at modern contact zones and detected only a single
early generation hybrid. Unsurprising given these results, we found no
evidence of transgressive, intermediate, or more variable morphological
phenotypes in taxa with introgressed mtDNA. These findings suggest that
hybridisation in this system has, at least in some cases, resulted in
repeated mitochondrial introgression with little or no nuclear
introgression. This pattern aligns with other studies showing limited
nuDNA introgression in taxa with mitonuclear discordance, highlighting a
potentially broader trend in animal radiations.