Posted: Jul 02, 2019 7:02 am
by Rumraket
Yeah it's a badly worded sentence, as I initially stated. That's still all it is. They don't make it clear that they're talking about stage F in their later Figure 4, not stage C.
Fig. 4.
Evolutionary mechanism of the gadid AFGP gene from noncoding DNA. The color codes of the sequence components follow Fig. 1. (A) The ancestral noncoding DNA contained latent signal peptide-coding exons with a 5′ Kozak motif, adjacent to a duplication-prone 27-nt GCA-rich sequence. (B) The 27-nt GCA(Ala)-rich sequence duplicated forming four tandem copies. (C) A 9-nt in the midst of the four 27-nt duplicates became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF. (D) A proximal upstream regulatory region acquired through a putative translocation event. (E) A 1-nt frameshift led to a contiguous SP, a propeptide, and a Thr-Ala-Ala-like cds in a read-through ORF. (F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection.

Natural selection is only mentioned in the final step F.

So here you are confused having found other people confused by the same sentence. Now you're three people who are confused by a badly worded sentence. Great, that's just further evidence it's a badly worded sentence. Yet there's still nothing in the context of the discussion that contains the sentence in question which suggests they must be talking about stage C.

There's no reason to think the authors actually believe selection drove fixation of duplications in an unexpressed noncoding region, that wouldn't make sense and we don't have to assume the authors are so stupid and ignorant they don't know this.

They should have just added this to remove any confusion:
"We hypothesize that, following acquisition of a transcriptional promoter, upon the onset of selective pressure from cold polar marine conditions, additional duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred. As the number of AFGP tripeptide-coding repeats increased, the antifreeze function would become augmented."

That's it, then there would have been no confusion. If you read the legend to figure 4 you will see that natural selection is only mentioned in step F.