[attractivechaos]

The Trends in Genetics (not Cell) paper seems plausible. I don't study fish genetics or evolution. As I remember, fish genomes tend to have more genome-wide duplications and losses in comparison to other vertebrates. One possibility is that some fish lose AFPs because they don't need them – i.e. the observation could be caused by loss of function instead of gain of function due to HGT. I have to admit that the chance of gene losses across multiple fish lineages is pretty tiny but it is at least associated with a known mechanism.

Anyways, an interesting article.