Historical effective population size by SNeP

The pattern of variations in the census population is demonstrated by recent demographic history, as is the variation in the N_e of various breeds.

Past N_e of all the breeds were derived by SNeP software, utilizing estimates of LD decay in relation to distinct SNP distances. SNeP uses the formula to estimate N_e from LD given by Corbin et al [27]:

Where N_T(t) is the effective population size estimated t generations ago in the past c_t is the recombination rate t generations ago in the past r²_adj is the LD estimation, adjusted for sampling bias (r²_adj = r²−(βn)⁻¹ where n is the sample size, and β = 1 if the gametic phase is unknown and 2 when it’s known), and α is a correction for the occurrence of mutation (default = 1). Firstly, recombination is inferred between a pair of SNPs considering the relation between physical distance (δ) and linkage distance (d) as δ = kd (k = 10⁻⁸). Instead of using the approximation of d = c (1 Mb = 1 cM), the recombination modifier given by Sved and Feldman [28] was used, which is, c = d(1–(d/2)).

The maximum distance between SNPs to be analyzed was kept much higher than the default value to get N_e of more recent generations, up to the 5th generation ago (with default settings we were getting N_e up to 13 generations ago). The number of bins was also increased to a higher value to get a smoother curve.