Table 2.

Correlation coefficients (r) of allele frequency differences for SNPs between the early‐ and late‐eclosing quantiles of flies in the eclosion time GWAS (Ragland et al., 2017) vs. geographic allele frequency differences within the host races between Grant, MI, and Urbana, IL, for apple fly (upper table) and hawthorn fly populations (lower table)

	chr 1	chr 2	chr 3	chr 4	chr 5	chr 1–5
Apple
Map SNPs	n = 949	n = 675	n = 996	n = 436	n = 1,188	n = 4,244
	0.07	0.72 ****	0.72 ****	0.14	0.02	0.42 ***
High LD	n = 263	n = 129	n = 223	n = 42	n = 374	n = 1,031
	0.49 ****	0.85 ****	0.37 ***	0.02	0.06	0.48 ***
Int. LD	n = 558	n = 459	n = 599	n = 159	n = 593	n = 2,368
	0.05	0.65 ****	0.63 ****	0.13	−0.01	0.39 ****
Low LD	n = 128	n = 87	n = 174	n = 235	n = 221	n = 845
	−0.05	0.43 **	0.15	0.03	−0.03	0.09
Hawthorn
Map SNPs	n = 949	n = 675	n = 996	n = 436	n = 1,188	n = 4,244
	0.82 ****	0.73 ****	0.69 ****	0.04	0.11	0.72 ****
High LD	n = 263	n = 129	n = 223	n = 42	n = 374	n = 1,031
	0.59 ****	0.86 ****	0.41 ****	0.17	−0.03	0.84 ****
Int. LD	n = 558	n = 459	n = 599	n = 159	n = 593	n = 2,368
	0.75 ****	0.67 ****	0.61 ****	−0.09	0.10	0.63 ****
Low LD	n = 128	n = 87	n = 174	n = 235	n = 221	n = 845
	0.37 ***	0.44 **	0.19	0.10	0.01	0.18 ***

Results are given for all mapped SNPs (Map SNPs), and for high, intermediate (Int.), and low LD classes of SNPs considered separately for each chromosome, as well as for all chromosomes together (chr 1–5). Significant relationships, as determined by Monte Carlo simulations, are in bold. n = # of SNPs genotyped in the class.

*p ≤ 0.05;

^a**p ≤ 0.01;

^b***p ≤ 0.001;

^c****p ≤ 0.0001.