Estimating Effective Population Size Using SNeP

We tested SNeP with two published datasets that had been previously used to describe trends in N_e over time using LD, Bos indicus [54,436 SNPs of 423 East African Shorthorn Zebu (SHZ)–Mbole-Kariuki et al., 2014 (link), data available at Dryad Digital Repository: doi:10.5061/dryad.bc598.] and Ovis aries [49,034 SNPs genotyped in 24 Swiss White Alpine (SWA), 24 Swiss Black-Brown Mountain sheep (SBS), 24 Valais Blacknose sheep (VBS), 23 Valais Red sheep (VRS), 24 Swiss Mirror sheep (SMS) and 24 Bundner Oberländer sheep (BOS)–Burren et al., 2014 (link)]. The r² estimates for the cattle datasets were obtained by the authors using GenABLE (Aulchenko et al., 2007 (link)) using a minimum allele frequency (MAF) < 0.01 and adjusting the recombination rate using Haldane's mapping function (Haldane, 1919 ). The r² estimates of the sheep data were calculated by the authors using PLINK-1.07 (Purcell et al., 2007 (link)), with a MAF < 0.05 and no further corrections. For both autosomal datasets r² estimates where corrected for sample size using equation (4) with β = 2. For these comparative analyses the SNeP command line included the same parameters used for the published data apart from the r² estimates, calculated through genotype count and the use of SNeP's novel binning strategy.