Table 2 . Polymorphism and LD data summary.

Parameter	Tef-rht1-1	Tef-rht1-2	Tef-sd1-1	Tef-sd1-2	Tef-sd1-3
Number of tef accessions analyzed	31	31	31	31	31
Number of haplotypes observed	10	4	3	3	2
Total length of region analyzed, bp	2291	2293	4585	4585	4577
Length of coding region analyzed, bp	1857	1854	1065	1065	1065
Length of non-coding region analyzed, bp	434	439	3520	3520	3512
Number of indels	0	3	6	1	9
Number of nucleotide substitutions	32	35	14	17	15
Overall frequency of polymorphic sites per bp	1 per 71.5	1 per 65.5	1 per 327.5	1 per 269.7	1 per 305.1
Frequency of polymorphic sites per bp, coding	1 per 371.4	1 per 123.6	1 per 355	1 per 177.5	1 per 1065
Frequency of polymorphic sites per bp, noncoding	1 per 20.6	1 per 21.9	1 per 320	1 per 320	1 per 250
(π), Average pairwise diversity	0.00382	0.00575	0.00147	0.00182	0.00166
(Θ), Number of segregating sites	0.00350	0.00383	0.00077	0.00093	0.00082
Gene diversity, haplotypes	0.892	0.647	0.671	0.609	0.503
Nonsynonymous amino acid substitutions	4	3	2	3	1
LD pairwise comparisons	465	595	91	136	105
Significant pairwise comparisonsa	112	409	91	136	105
Bonferroni correctionb	17	174	78	136	105
Magnitude of LDc	0.216	0.472	0.828	0.816	1

LD, linkage disequilibrium

^aFisher’s exact test at P < 0.001.

^bCorrection at P < 0.001.

^cMeasured as a function of distance across loci ranging for 0.0 (no LD) to 1 (complete LD).