Cytonuclear discordance in rock-wallabies

In this study we use a targeted exon capture approach, which enables us to incorporate high coverage genomic data for museum specimens with modern tissue samples, to fill important sampling gaps for the brachyotis group of rock-wallabies. This approach also allows us to capture mitochondrial sequence data as by-catch from the experiments and assemble more extensive mitochondrial genomic data. In this study, we (1) evaluate the relationships and divergence of the previously identified 10 operational taxonomic units (OTUs) in this chromosomal group using phylogenomic and population genomic approaches, (2) compare mitochondrial and nuclear divergence histories for discordance, (3) test for introgression between OTUs, and (4) evaluate processes causing cytonuclear discordance between OTUs. The increased genomic coverage, together with more robust sampling, allows us to test models of isolation versus migration between OTUs and statistically assess the divergence histories in this species complex in the context of body size differences and regional climatic instability.