On the effects of background selection in small populations on comparisons of molecular variation

Deleterious mutations affect genetic variation at linked neutral loci. Neutral variation can be reduced due to background selection, but in small population and with tight linkage such variation may increase due to associative overdominance. Here I report the results of computer simulations of diploid genotypes in small populations, where I look at the effect of deleterious mutations and linkage on comparisons of intra- and interspecific variation. Each chromosome consisted of 2000 loci where deleterious and neutral mutations occurred. The ratio of nonsynonymous to synonymous substitution rates (K-a/K-s) either increases with tight linkage or is unaffected, depending on the strength of selection. The ratio of the numbers of segregating mutations to the number of fixed mutations decreases under the conditions leading to background selection but can increase at tight linkage. Numbers of segregating sites (S-n) are less affected than nucleotide site diversity (pi), pi reduces more than S-n at intermediate linkage, but pi increases more than Sn when linkage is tight. Similar effects as found for S-n and it are observed for heterozygosity and variance in allele size of tandem repeat loci.