The neutrality of coding-site allele-frequency spectra. The allele-frequency spectrum for SNPs at nonsynonymous (black line) and synonymous (dashed line) sites among the 17 samples for the genome. Allele frequencies were computed using read-depth coverage values and were folded because the selective process may act on both the ancestral alleles inferred from L. infantum as well as the derived version with the L. donovani population. The ratio of nonsynonymous to synonymous SNPs approaches one as the allele frequencies increase, suggesting that higher frequency variants are subject to stronger purifying selection to remove deleterious alleles.