Characterizing a lethal mitonuclear incompatibility in naturally hybridizing Xiphophorus swordtails

The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of “hybrid incompatibilities,” where alleles derived from two different species no longer interact properly in hybrids. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes and that incompatibilities involving multiple genes should be common, but there has been sparse empirical data to evaluate these predictions. Here, we describe a mitonuclear incompatibility involving three genes in physical contact within respiratory Complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations fail to complete embryonic development or die as juveniles, while those heterozygous for the incompatibility have reduced Complex I function and unbalanced representation of parental alleles in the mitochondria..., This project was based genomic DNA samples collected from live fish in Hidalgo, Mexico and lab populations in Stanford, California, followed by low-coverage sequencing and local ancestry inference using an HMM-based approach. The resulting ancestry information was used for QTL and admixture mapping to identify mito-nuclear associations, and estimation of selection on particular genotype combinations. We also genotyped embryos dissected from in utero after performing developmental staging, respirometry measurements, and morphometrics. We isolated mitochondria from adult heterozygotes, then used these samples to perform respirometry using an Oroboros O2K respirometer, and a Parallel Reaction Monitoring proteomics experiment. Using inferred protein sequences from the relevant species, we performed in silico modeling in RaptorX and MODELLER of Complex I genes of interest, analyses of evolutionary rates using codeml, and tested for historical introgression using a combination of phylogentics..., , # Characterizing a lethal mitonuclear incompatibility in naturally hybridizing Xiphophorus swordtails

[https://doi.org/10.5061/dryad.j3tx95xmx](https://doi.org/10.5061/dryad.j3tx95xmx)

This dataset includes a variety of data types, all of which aim to comprehensively explore a complex, lethal mitonuclear incompatibility in hybridizing swordtails of the genus *Xiphophorus.* This includes large amounts of local ancestry information from *Xiphophorus* hybrids, simulation input and output files, structures from *in silico* modelling of proteins, phylogenetic analyses, and miscellaneous tabular data from organismal and morphological measurements.

In general, the local ancestry information is either presented as the raw output of the ancestryinfer pipeline ([https://doi.org/10.1111/1755-0998.13175](https://doi.org/10.1111/1755-0998.13175)), or a processed genotype file. The former is identified with the naming convention \"ancestry-probs-par[1 or 2]_.txt\", where 1 is birchmanni and 2 is mal...