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Synonymous codon usage can be under weak selection and lead to non-random use of the codons coding for the same aminoacid.
Such bias can be under weak selection (| Ne s| ≈ 1) and is maintained by the concurrent action of selection, drift, and mutation.
At low densities, mate detection traits may be of paramount importance, while traits involved in mate competition or territory defense may be under weak selection because conspecific encounter rates will be low (Maher and Lott 2000; Knell 2009).
The extent of selection for biosynthetic cost might seem surprising, because accessory genes are traditionally supposed to be under weak selection, yet we find evidence of selection for their amino acid composition.
This also implies that although "measured" levels of variability suggest a ∼50% difference in N e of the X chromosome for the two species, this difference could be an underestimate given that the surveyed synonymous and short intronic sites are themselves likely to be under weak selection in one or both species.
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By extension, populations experiencing higher rates of extrinsic mortality should be under weaker selection against mutations with deleterious effects late in life, and should therefore evolve more rapid senescence [3], [4].
Accordingly, while we may have sampled a few SCPs with large fitness effects, an appreciable proportion of SCPs should be under weaker selection and are only weakly deleterious (Nes ∼ 1).
Indeed, modestly frequent amino acids (or under-represented amino acids in the proteins encoded by strongly expressed genes) may be under weaker selection, and for this reason, their codons may better tolerate changes driven by mutational bias.
The highest P for replacements which involve the most chemically similar pairs of amino acids (Tables 1, 2, 3) is also consistent with this explanation, because such replacements must be under weaker selection than radical replacements.
We also sequenced a 658 bp region on the small segment containing the C-terminal end of the lytic protein P5; the majority of this region (438 bp, or 66.6%) is not protein-coding [ 48] and may be under weaker selection because it seems to be the least translated portion of the virus φ6 genome [ 49, 50].
This result is not unexpected when comparing sites in two species that are under weak selection.
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