Fig. 3.

Independent gains are less likely than independent losses. Although parsimony approaches may misinfer independent gain substitutions in multiple descendants as single events (A) and independent loss substitutions as single events (B), independent gains in an ancestral sequence one step away from being a binding site can only occur by one type of substitution (represented by two independent T–>A events at position 5), whereas independent loss substitutions can occur by any event anywhere within an existing site (here represented by C–>G at position 3 and A–>T at position 5). Independent, misinferred loss substitutions are therefore much more likely to occur than independent, misinferred gains.