Data from: Genomic analysis suggests that mitonuclear coevolution proceeds over rapid timescales in the Amazonian Pipra manakin complex

Mitonuclear coevolution is defined as reciprocal selection between the
nuclear and mitochondrial genomes. It is necessary to maintain
compatibility between nuclear- and mitochondrially-encoded products that
interact during mitochondrial processes, including mitochondrial genome
replication, transcription, and translation, and oxidative
phosphorylation. Theory predicts that mitonuclear coevolution may play a
crucial role in the early phases of speciation by generating strong
genetic incompatibilities between recently diverged taxa that have evolved
unique mitochondrial-mitonuclear haplotypes. However, the timescale over
which mitonuclear coevolution proceeds remains unclear, making it
difficult to definitively link this process with early speciation. Here,
we test for expected genomic signals of mitonuclear coevolution across the
Amazonian Pipra manakin complex, which includes recently and more deeply
diverged avian lineages. Using dN/dS ratio analyses, we compared signals
of positive selection in mitonuclear gene categories and functionally
equivalent nuclear gene categories that do not participate in mitonuclear
coevolution for each pair of Pipra lineages separately and for all the
lineages simultaneously. For the ribosomal protein and aminoacyl tRNA
synthetase (AARS) gene categories, we identified genomic patterns
consistent with stronger positive selection in mitonuclear versus nuclear
genes which is suggestive of mitonuclear coevolution having occurred
across the Pipra complex. Significantly, we determined that expected
genomic signals of mitonuclear coevolution could be identified between
lineages that diverged as recently as 0.35-0.4 MYA. This time span is in
keeping with the initial stages of avian speciation and suggests that
mitonuclear coevolution may operate on a timescale that would allow it to
play an important role during early speciation.