Figure S1. Distribution of hybrid indices calculated based on all markers (N =110), autosomal
markers (N =99) and markers with abrupt (N = 50) and gradual clines (N = 60) (based on
genomic cline estimates in Connecticut).
Figure S2. Individual genomic clines, concordance clines and geographic clines for all 110
genes analyzed in Connecticut (N = 260). A) Each genomic cline depicts the extent of genomic
introgression for a focal gene. The hybrid index represents genome-wide admixture based on the
proportion of alleles inherited from G. firmus (hybrid index: 0 = G. pennsylvanicus, 1 = G.
firmus). The shaded gray areas represent the 95% confidence intervals for the probability of
observing a homozygous G. pennsylvanicus genotype (dark grey) or heterozygous genotype
(light grey) at the focal gene, given the hybrid index. Observed genotype classes are plotted
against the hybrid index as open circles (top: homozygous G. pennsylvanicus, middle:
heterozygous, bottom homozygous G. firmus), and the frequency of observed genotypes is
indicated on the right of the panel. The genomic clines for homozygous G. pennsylvanicus
genotype (solid line) and heterozygous genotype (dashed line) are overlaid onto the 95%
confidence intervals for the genotype probabilities; genomics clines that fall outside of the
expected distribution represent significant deviations from neutral expectations. Excess (+) or
deficit (-) of observed genotype classes are indicated above. B) The concordance clines are
plotted as the individual per locus hybrid index against the hybrid index calculated from all
markers. Clines that are concordant (their introgression is equal to the expectation based on all
loci) lie on the diagonal. Cline shape (v) is estimated by deviations above (abrupt) or below
(gradual) concordance and cline position (u) is estimated by deviations toward either genomic
background (e.g., negative values represent G. pennsylvanicus alleles present in the G. firmus
genetic background). Dashed lines represent upper and lower confidence intervals. C)
Geographic clines are plotted as the change in the frequency of the G. pennsylvanicus allele from
G. pennsylvanicus habitat (loamy soil, 0 m) to G. firmus habitat (sandy soil, 500 m).