[teachingassist]

> that three species should have a near-identical sequence coding for a near-identical protein suggests rather strongly that this version of the gene arose in one species and was then acquired by the other two

We'd strongly expect the amino acid sequence to be similar both by "convergent evolution" (each case evolved independently with the same motivation) and "lateral transfer" (one case evolved and then shared DNA across species), so this wouldn't typically distinguish those two cases.

The sibling answer about structure of introns and exons is a more convincing answer, in my opinion. I don't think we would expect to see that in convergent evolution, but we would in a copy-paste job.

[throwanem]

On what basis do you hold any such expectation? The paper explicitly contrasts its subject with several examples of convergent evolution producing functionally equivalent, but proteomically and genomically highly distinct, outcomes - which is typical of convergent evolution in general.

That said, I agree that the similarity of adjacent noncoding sequence is also a strong indicator that convergent evolution isn't causative here.

[teachingassist]

> On what basis do you hold any such expectation?... The paper explicitly contrasts its subject with several examples of convergent evolution producing functionally equivalent, but proteomically and genomically highly distinct, outcomes

On the basis that the protein is the function here. (antifreeze protein). There might only be one good, or best local maximum, solution for this problem at the protein level. So, we would expect natural selection might converge on that one solution. And, the results of two runs would not be nearly as different as they are in cases where natural selection is optimizing for a system process.

Obligatory coding comparison:

If I asked two programmers to code a webshop, I would expect the underlying code to look substantially different - if the code looked the same, I'd take it as evidence of copying.

If I asked two programmers to code "If A then B", I would expect the underlying code to look substantially the same, whether or not they copied.

A specific antifreeze protein is the second case: both the code and the outcome. It's not part of a system which would have more freedom of variation in its solutions.