Fig 4. Evidence for repeated hybrid incompatibilities between X. birchmanni × X. malinche and X. birchmanni × X. cortezi hybrids.

A. Interacting locus of the shared chromosome 6 ancestry desert identified in a genome-wide scan. This region was identified scanning for deviations from expected two locus genotypes using a χ² test in F₂ hybrids, based on observed genotypes at the shared chromosome 6 desert and genotypes at other loci throughout the genome. Genome-wide significance threshold (FPR 5%; blue line) was determined using permutations, see Methods for details. Inset shows STRING network with experimentally verified interactions between ndufa13 (contained in the chromosome 6 region) and ndufs5 (contained in the chromosome 13 region). B. Ratio of expected to observed two-locus genotype combinations in F₂ hybrids between X. birchmanni × X. malinche at the shared chromosome 6 desert and associated chromosome 13 region. Capital letters indicate genotype at chromosome 6 and lowercase letters indicate genotype at the chromosome 13 region. For visualization, certain genotype combinations are collapsed (i.e. homozygous parental–BBbb & MMmm; heterozygous locus 1, homozygous locus 2 –MBbb & MBmm). Note that several genotype combinations were expected to be found at low frequency due to low X. birchmanni ancestry on chromosome 13 (MMbb, MBbb, BBbb). C. A second interaction between the minor parent desert on chromosome 9 and a region on chromosome 4 is detected at a relaxed FPR of 10%. D. This minor parent desert is shared between X. birchmanni × X. cortezi hybrid populations and the Acuapa X. birchmanni × X. malinche hybrid population and occurs on chromosome 9 at 12.1 Mb. Points represent minor parent ancestry calculated in 10 kb non-overlapping windows divided by the proportion of the genome derived from the minor parent species. Red–Tlatemaco (malinche × birchmanni), Blue–Acuapa and Aguazarca (birchmanni × malinche), Green–Santa Cruz (birchmanni × cortezi).