LD cline
The total fraction of locus pairs across populations and linked loci with positiver LD was 0.65 (95% CI: 0.52-0.77), which is higher than expected under random association (LD test 1: N = 55, exact P = 0.030; r LD values for all locus pairs and populations are presented in Table S4). The fraction with positiver LD was >0.5 at all five linked locus pairs (Sign test: P = 0.063) but was particularly high for interlocus distances ≥18 Mb (three locus pairs: 0.69, N = 42, exact P = 0.020). Surprisingly, the fraction with positiver LD was also relatively high in East Africa (four locus pairs: 0.69, N = 26, exact P = 0.076). Both among randomized genotypes at the former five locus pairs and among observed genotypes at the remaining unlinked locus pairs the total fraction with positive r LD was very close to the expected value of 0.5 (randomized genotypes: 0.501; 95% CI: 0.476, 0.526; N = 1541, χ2 = 0.006, P = 0.94; remaining loci: 0.484; 95% CI: 0.457, 0.512; N = 1255, χ2 = 1.21, P = 0.27; in both cases same subset of populations as with the linked loci, sample size ≥6, |r LD| >0.001).
There was a non-significant logarithmic relationship betweenr LD and latitude (LD test 2: Eq. 3; a = -0.055, b = 0.189, P = 0.26, marginalR 2 = 0.032; Figure 4, Table S5). When considered together, the two LD tests were significant (Z -transform test: P = 0.020). The decreasing trend inr LD with latitude could largely be attributed to the two closest linked locus pairs; BM1824 -CSMM019 andCSMM019 -BM3205 (Eq. 3; a = -0.214, b = 0.595, P = 0.014, marginal R 2 = 0.36; other three locus pairs: a = -0.0006, b = 0.056, P= 0.99; Figure 4, Table S5). Predicted r LDdecreased from 0.45 at 25 °S to -0.13 at 4 °N. Similarly to the allele-frequency clines, the LD cline did not extent beyond 25 °S, with a relatively strong drop of r LD in HiP, being non-significant here despite high sample size (r LD = -0.055, N = 418, P = 0.26), relative to KNP (r LD = 0.32-0.34, N = 155-328, P <0.00002). Significant positiver LD after Bonferroni correction was observed for both locus pairs in the four most southern populations; northern KNP, southern KNP, Limpopo NP and Manguana (P <0.00012; Bonferroni-corrected α = 0.00073; Table S4). The two highestr LD values at any locus pair were observed in the same metapopulation; Limpopo NP-Manguana (BM1824 -CSMM019 :r LD = 0.93, P = 0.00012;INRA006 -TGLA263 : r LD = 0.68,P = 0.017; Table S4).