Table 1.

Sets of taxa with significant D statistics and properties of the pIRs

Trioa	P2	P3	f4-ratio	Mean pIRs (Kb)b	No. genes	Gene densityc	Sweepsd	cM/kbe	Resistance genesf	PDg	Climateh
GAM	arizonica	monticola	8.03%	269.36	2282	0.96	0.27	2.27	1.1	2.19*	1.27*
RAM	arizonica	monticola	2.07%	210.44	597	0.92	0	1.1	0.56	1.12	1.51*
MBC	berlandieri	candicans	3.24%	163.23	746	0.82*	0.39	1.52	1.12	0.59	2.02*
AGR	girdiana	riparia	3.32%	154.49	955	0.99	0.32	1.61	0.52	0.80	1.42*
GRM	riparia	monticola	6.08%	270.68	1325	0.79*	0.57	1.21	1.56*	0.81	1.13
GRB	riparia	berlandieri	7.47%	233.29	1538	0.75*	0.93	1.43	2.00*	1.03	1.13*
ARB	riparia	berlandieri	7.40%	200.07	1607	0.75*	0.77	1.8	1.73*	1.09	1.28*
ARC	riparia	candicans	2.43%	226.25	480	0.77*	1.41*	1.23	3.55*	2.47*	1.14*
GRC	riparia	candicans	2.30%	217.32	455	0.76*	0.43	1.45	3.01*	2.47*	1.33*

^aThe three letters in a trio represent three species that act as P1, P2, and P3, respectively, in introgression tests. The species are A: V. arizonica, B: V. berlandieri, C: V. candicans, G: V. girdiana, M: V. monticola, and R: V. riparia. For each trio, M. rotundifolia was used as the outroup for introgression tests

^b The mean length of pIRs after merging windows separated by < 1 kb in distance

^cGene density inside pIRs relative to the average gene density of the whole genome. Asterisks denote trios with significantly lower values of gene density in pIRs (p < 0.05)

^dSweeps refers to the relative enrichment of selective sweeps in pIR regions. Significant enrichment is denoted by an asterisk, with significance (p < 0.05) assessed by permutation

^ecM/kb refers to the ratio of the average recombination rate within pIR regions, relative to the genomic background

^f Resistance genes refers to the enrichment of annotated disease resistance genes. Asterisks denote trios with significant enrichment (p < 0.05)

^g PD refers to the enrichment of Pierce’s disease associated SNPs within pIRs. Significant enrichment is denoted by an asterisk (p < 0.05), with significance assessed by permutation

^h Climate refers to the enrichment of bioclimate associated SNPs within pIRs. Values correspond to the average relative enrichment of the top three bioclimatic variables. Significant enrichment is denoted by an asterisk, with significance assessed by permutation (p < 0.05)