Table 1.

Percentages of SNPs displaying significant geographic allele frequency differences between Grant, MI, and Urbana, IL, for the apple race (upper table) and hawthorn race (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
	10.2 (0.06)	38.9 (0.11)***	43.1 (0.13)****	29.1 (0.09)***	9.3 (0.06)	24.2 (0.09)**
High LD	n = 263	n = 129	n = 223	n = 42	n = 374	n = 1,031
	7.2 (0.06)	56.6 (0.14)**	86.1 (0.24)****	78.6 (0.17)**	6.7 (0.05)	33.2 (0.11)**
Int. LD	n = 558	n = 459	n = 599	n = 159	n = 593	n = 2,368
	11.6 (0.06)	38.6 (0.10)***	35.2 (0.10)****	40.3 (0.10)***	11.5 (0.06)	24.7 (0.08)****
Low LD	n = 128	n = 87	n = 174	n = 235	n = 221	n = 845
	10.2 (0.06)	14.9 (0.07)	14.9 (0.07)	12.8 (0.06)	8.1 (0.06)	11.8 (0.06)
Hawthorn
Map SNPs	n = 949	n = 675	n = 996	n = 436	n = 1,188	n = 4,244
	54.4 (0.14)****	50.4 (0.11)****	47.7 (0.11)****	12.0 (0.06)	15.4 (0.06)	37.0 (0.10)****
High LD	n = 263	n = 129	n = 223	n = 42	n = 374	n = 1,031
	92.0 (0.25)****	82.2 (0.16)****	83.9 (0.20)***	4.8 (0.05)	17.1 (0.07)	58.3 (0.15)****
Int. LD	n = 558	n = 459	n = 599	n = 159	n = 593	n = 2,368
	45.5 (0.11)****	47.1 (0.11)****	42.1 (0.09)****	12.0 (0.06)	14.2 (0.06)	34.8 (0.09)****
Low LD	n = 128	n = 87	n = 174	n = 235	n = 221	n = 845
	15.6 (0.05)**	20.7 (0.06)**	20.7 (0.07)***	14.9 (0.06)*	15.8 (0.06)*	17.0 (0.06)**

Results are given for all mapped SNPs (Map SNPs), and for high, intermediate (Int.), and low LD classes of SNPs for each chromosome considered separately, as well as for all chromosomes together (chr 1–5). Also given in parentheses are the mean SNP allele frequency differences between Grant, MI, and Urbana, IL, for apple and hawthorn fly populations for each class of SNP considered.

^* p ≤ 0.05;

^** p ≤ 0.01;

^*** p ≤ 0.001;

^**** p ≤ 0.0001; Significant percentages above null expectation for a class of SNPs, as determined by Monte Carlo simulations, are in bold. n = # SNPs genotyped in the class.