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According to this theory, if a population carries several different alleles of a particular gene, odds are that each of those alleles is equally good at performing its job in other words, that variation is neutral: whether you carry allele A or allele B does not affect your fitness.
It is well known that most SSR variation is neutral, and that functional variation is much more likely to be associated with SNPs and indels in and around genes.
However, protein predictions by PON-P suggest that variation is neutral.
Of course, whether particular variation is neutral, detrimental, or adaptive depends upon the environment, population size, genetic background, etc.
In sum, while regions of relaxed constraint certainly harbor more variation, this does not mean such variation is neutral.
If base composition variation is neutral, the ratio of AT-to-GC versus GC-to-AT polymorphisms should be similar to the ratio of AT-to-GC versus GC-to-AT fixations.
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Measurement of selective forces is still generally undertaken at a whole-gene level, an approach that falls down if pressures vary considerably within individual genes, preventing determination of the true baseline for variation which is neutral evolution within and between malaria species.
We note that even if the dendritic transcriptome variation is functionally neutral, neutral variation can provide the substrate for rapid adaptive evolution under a different selective regime by presenting segregating variation.
Assuming that variation at R37 is neutral, then the mutations in the heterozygous lines may have occurred quite recently (perhaps within the last eight generations, taking into account the expected two-fold decay of heterozygosity per generation with selfing and an average of eight replicas per line).
The pleiotropy hypothesis assumes that genital variation is largely neutral.
We discuss below some methods that can be applied to the question of whether within-population variation is largely neutral or has adaptive significance.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com