These high-frequency selected variants lead to higher colocalization success. There are other differences we look at in the paper, including the spatial distribution of ascertained eQTLs across species, and the different strengths of selection for eQTLs across species.

These population histories lead to very different allele frequency distributions. When we simulate genomes based on the human population histories, most deleterious variants are uncommon. When we use the cattle population history, we observe many high-frequency deleterious variants.

Why is this? Humans, cattle, and pigs have similar genomes. The main difference is that cattle and pigs have experienced strong recent selection due to agricultural breeding. The breeding has decreased the effective population size, while the human effective population size has increased.

Recently, large eQTL-mapping datasets were released in cattle and pigs. To our surprise, colocalization explained a much higher percentage of GWAS loci. Here we compare the three species (using fastEnloc, a colocalization method).