PA-X is a fusion protein of influenza A virus encoded in part from a +1 frameshifted ´X-ORF´ in segment 3. We show that the X-ORF of diverse influenza A viruses can be divided into two groups that differ in selection pressure and likely function, reflected in the presence of an internal stop codon and a change in synonymous diversity. Notably, truncated forms of PA-X evolved convergently in swine and dogs, suggesting a strong species-specific effect.