Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

Area of Science:

• Evolutionary Biology
• Genetics
• Mitochondrial Genomics

Background:

• Mitochondrial-nuclear gene mismatches are hypothesized to contribute to species boundaries.
• Genetic incompatibilities arise when mitochondrial DNA (mtDNA) is in a cellular environment lacking coevolved nuclear-encoded mitochondrial (n-mt) proteins.
• Previous studies suggest disruptions in mitonuclear coevolution can cause reproductive isolation.

Purpose of the Study:

• To investigate if mitonuclear incompatibilities generate selection impacting multiple n-mt loci.
• To determine if mitonuclear incompatibilities contribute broadly to speciation across the genome.
• To test the hypothesis using hybridizing Xiphophorus fish species with known large-effect mitonuclear incompatibilities.

Main Methods:

• Categorized nuclear-encoded genes based on interaction levels with mitochondrial gene products.
• Analyzed patterns of covariation in mitonuclear ancestry across gene classes.
• Evaluated the influence of non-synonymous divergence and hybridization age on analyses.

Main Results:

• Found inconsistent statistical support for differences in mitonuclear ancestry covariation between gene classes.
• Analysis sensitivity was affected by non-synonymous divergence in interacting n-mt genes and hybridization age.
• Genome-wide scans focusing on broad functional gene classes may not reliably detect mitonuclear coevolution history.

Conclusions:

• Mitonuclear incompatibilities may exert strong selection at multiple loci without clear genome-wide signals.
• Detecting mitonuclear coevolutionary history requires nuanced approaches beyond broad functional gene enrichment.
• The study highlights limitations in current methods for identifying the role of mitonuclear interactions in speciation.