A panel of diverse mitonucleogenotypes in <i>D</i>. <i>melanogaster</i>: Population setup and grouping according to mitochondrial and nuclear SNPs.

<p>(<b>A</b>) Fly populations from Australia, Benin, and Canada were introgressed in all possible pairwise combinations, generating novel combinations of mitochondrial and nuclear genomes. Three biologically independent replicate populations were established per introgression. In every generation, 45 females and 45 males were crossed, allowing the potential for variation to segregate within each population. Map created in R with Natural Earth data. (<b>B</b>) PCA indicates purging of F<sub>0</sub> mothers’ nucleogenotypes, and homogeneous substitution with nuclear genomes from donor populations. PCA was performed on per-population allele frequencies, of all observed nuclear SNPs on the major chromosome arms (2L, 2R, 3L, 3R, and X). Each point represents a distinct population, color-coded as per panel (A). Points representing diverse nucleogenotypes sit on top of one another, suggesting homogenized nuclear genomes even in the presence of distinct mitochondria. (<b>C</b>) Proportional assignment of populations to clusters (“layers”) according to nuclear SNP frequency, by admixture analysis. Admixture proportions for each population were inferred by model-based clustering with ConStruct. Colors represent the proportion variants in each populations’ genome assigned to arbitrary clusters (“layers”). The analysis was instructed to assign populations to 3 layers (K = 3), because we expected 3 major groupings resulting from the 3 distinct geographic origins. Most variation in genomes originating from Australia, Benin, and Canada was assigned to clusters/layers 1, 2, and 3, respectively. To minimize effects of LD, only nuclear SNPs at least 1 kb apart and outside regions of no recombination were considered for PCA and admixture analyses. Population IDs are given below the barplot (mito. = mitogenotype, nuclear = nucleogenotype, rep = population replicate). Note that only 2 populations were sequenced per mito-nuclear combination, assuming that the anticipated nuclear homogenization would be equivalent in all 3 populations: The equivalent assignments of nucleogenotypes to layers suggest that this assumption was correct, and nuclear genotype is shaped by the nuclear intogression, independent of mitochondrial genotype, This recapitulates the PCA result (Panel B). (<b>D</b>) PCA shows 2 major groupings of mitogenotypes according to all observed mtDNA SNPs. Each point represents a distinct population, colour-coded as per panel (A). The intermediate population on PC1 represents population AA<sub>3</sub>, suggesting a mitogenotype in this population that is intermediate between the major clusters comprising mitogenotypes A (to the right) and mitogenotypes B and C (to the left). (<b>E</b>) Mitochondrial admixture proportions, showing assignment of populations to layers according to mtDNA SNP frequency. Admixture proportions for each population were inferred by model-based clustering with ConStruct (K = 3). Colors represent proportion assigned to each layer. Most variation in mtDNA originating from Australia, Benin, and Canada was assigned to clusters/layers 1, 2, and 3, respectively. The result suggests high levels of similarity among replicate mitogenotypes, largely independent of nucleogenotype, i.e., recapitulating the PCA result (Panel D). (<b>F</b>) Network analysis based on the major alleles in each population at the 27 differentiated sites. Populations are grouped according to allele frequency at indicated loci on mtDNA. SNPs distinguishing each cluster of populations are indicated in text, showing mtDNA position, gene, and whether for protein-coding genes whether the SNP was synonymous or not. (<b>G</b>) Segregation of major alleles for significantly differentiated mitochondrial SNPs. Heatmap shows nucleotide identity at positions in mitochondrial genome indicated at top. Gene for each position and SNP classification (synonymous/nonsynonymous) indicated by color bar at top, and geographic origin of mitochondrial and nuclear genomes indicated on right. Hierarchical clustering (dendrogram on left) shows separation of SNPs by geographic origin, with 5 constituent clusters. Concatenating SNP clusters with nucleogenotype reveals 8 mitonucleogenotypes, indicated to right. Data underlying the graphs shown in the figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002218#pbio.3002218.s020" target="_blank">S11</a>–<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002218#pbio.3002218.s023" target="_blank">S14</a> Tables. LD, linkage disequilibrium; PCA, principal components analysis; SNP, single nucleotide polymorphism.</p>

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