Figure 3. Candidate RI genes revealed by genomic cline analysis.

(A–B) Markers are ordered along chromosomes as in Table S3. (A) BGC run 2 estimates of genomic cline center (α) with 95% credibility intervals for all 86 SNP markers. Red dots indicate markers with significant excess house sparrow ancestry, blue dots indicate markers with significant excess Spanish sparrow ancestry, grey dots indicate markers with either significant house or Spanish excess ancestry but where the difference in allele frequency between the parent species are below 0.5, and black dots indicate markers that do not differ from neutral expectations. (B) BGC run 2 estimates of genomic cline rate (β) with 95% credibility intervals for all 86 SNP markers. Orange dots indicate markers with clines significantly steeper than neutral expectations, white dots indicate markers with significantly shallower clines than neutral expectations, grey dots indicate markers with either significantly steeper or shallower clines than neutral expectations but where the difference in allele frequency between the parent species is below 0.5, and black dots indicate markers that do not differ from neutral expectations. (C) Genomic cline center (α) plotted against genomic cline rate (β). Red dots indicate markers that exhibit significant excess house sparrow (P. d.) ancestry, clines steeper than neutral expectations and where the difference in allele frequency between the parent species is greater than 0.5. The red dots that are encircled and named shift at the Italian-Spanish boundary and are hence candidate RI genes. Blue dots indicate markers that exhibit significant excess Spanish sparrow (P. h.) ancestry, clines steeper than neutral expectations and where the difference in allele frequency between the parent species is greater than 0.5. The blue dots that are encircled and named shift at the Italian-house boundary and are hence candidate RI genes. Green dots indicate markers that have allele frequency differences between the parent species greater than 0.5 and clines steeper than neutral expectations but do not exhibit excess house or Spanish sparrow ancestry. These markers are candidates for being incompatibilities within the Italian sparrow. Grey dots indicate markers in which the allele frequency difference between the parent species is less than 0.5. (D). Examples of BGC genomic clines representative of the marker categories described in panel (C). For illustrations of all clines, see Figure S2.