Data from: Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions
Baris, Tara Z., University of Miami
Wagner, Dominique N., University of Miami
Dayan, David I., University of Miami
Du, Xiao, University of Miami
Blier, Pierre U., Université du Québec à Rimouski
Pichaud, Nicolas, Université du Québec à Rimouski
Oleksiak, Marjorie F., University of Miami
Crawford, Douglas L., University of Miami
Published Jan 05, 2018 on Dryad.
Cite this dataset
Baris, Tara Z. et al. (2018). Data from: Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions [Dataset]. Dryad. https://doi.org/10.5061/dryad.nt461
The oxidative phosphorylation (OxPhos) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins. The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects and how they may affect human health and disease. In many different organisms, healthy nuclear and mitochondrial genome hybrids between species or among distant populations within a species affect fitness and OxPhos functions. However, what is less understood is whether these interactions impact individuals within a single natural population. The significance of this impact depends on the strength of selection for mito-nuclear interactions. We examined whether mito-nuclear interactions alter allele frequencies for ~11,000 nuclear SNPs within a single, natural Fundulus heteroclitus population containing two divergent mitochondrial haplotypes (mt-haplotypes). Between the two mt-haplotypes, there are significant nuclear allele frequency differences for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of the genome, these 349 outlier SNPs form two groups associated with each mt-haplotype, with a minority of individuals having mixed ancestry. We use this mixed ancestry in combination with mt-haplotype as a polygenic factor to explain a significant fraction of the individual OxPhos variation. These data suggest that mito-nuclear interactions affect cardiac OxPhos function. The 349 outlier SNPs occur in genes involved in regulating metabolic processes but are not directly associated with the 79 nuclear OxPhos proteins. Therefore, we postulate that the evolution of mito-nuclear interactions affects OxPhos function by acting upstream of OxPhos.
An unfiltered hapmap including all SNPs and individuals from genotyping by sequencing pipeline. "N" or "S" prior to individual number refers to northern or southern mt-haplotype. "12" or "28" after individual refers to acclimation temperature of individual.
Filtered hapmap with 155 individuals and 11,705 SNPs. Data was filtered so that each SNP was found in at least 70% of individuals, and each individual had at least 50% of all SNPs. "N" or "S" prior to individual number refers to northern or southern mt-haplotype. "12" or "28" after individual refers to acclimation temperature of individual.
Chromosome and start site of 64bp tags from genotyping by sequencing pipeline.
OxPhos data for individuals in filtered hapmap. Includes State 2, State 3, Complex I, Complex II, Complex IV and E State.
National Science Foundation, Award: MCB 1434565, IOS 1147042 and DEB-1265282.