[burning_hamster]

I just read the PLOS one paper. The arguments they brought forth were strong. If this had been my paper, I would have been livid if I had been rejected. However, given the fragmented and buggy state of bioinformatics tooling and databases at the time, I can easily imagine how their extraordinary claims did not the cross the "beyond reasonable doubt" threshold. From a reviewer's perspective, a couple matching disulfide bridges and a negative Southern alone might not have convinced me either. Glad it worked out for her in the end though.

[ak217]

The issue with the evidence in that paper is that they used primers to amplify the specific genes of interest. That introduces a strong assumption at the start of their analysis: specifically, that these genes appeared in the genomes by some HGT process instead of independently being duplicated internally in each genome from another gene shared among the species. Whole genome sequences were not available for these species at the time. A modern, more complete analysis would look into homologs across whole genomes and try to reject that hypothesis, which is much less extraordinary than animal germline HGT.

That's precisely why the authors published the new Cell paper https://www.cell.com/action/showPdf?pii=S0168-9525%2821%2900... with stronger evidence from whole genome sequence to support the HGT hypothesis. I'm still trying to wrap my head around Figure 2 there, so I'm on the fence.

[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.