Final answer:
It's logical to infer positive natural selection when replacement substitutions outnumber silent substitutions in gene comparisons of closely related species, as this indicates adaptive changes being favored by selection and often results in a dN/dS ratio greater than one.
Step-by-step explanation:
When researchers compare a gene in closely related species and find that replacement substitutions (non-synonymous substitutions) outnumber silent substitutions (synonymous substitutions), it is logical to infer that positive natural selection has taken place.
The measure of the rate of non-synonymous to synonymous substitutions is often expressed as the dN/dS ratio or ω ratio. A ratio of greater than one (ω > 1) indicates that non-synonymous substitutions are being favored and are therefore beneficial, which is evidence of positive selection.