Ectopic gene conversion causing quantitative trait variation

  1. Marina Pfalz
  2. SeÏf-Eddine Naàdja
  3. Jacqui Anne Shykoff
  4. Juergen Kroymann

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Abstract

Mutation-selection balance explains the occurrence of genetic variation in populations: mutations arise continuously, and natural selection removes or fixes them at varying rates. However, there is more genetic variation segregating in populations than can be explained by mutation-selection balance alone. Here we elucidate a general mechanism for generating this segregating variation using the example of a gene family involved in plant defense.

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  1. Arcadia Science

    but that selection acts against EGC near codons specifying fixed derived amino acids, i.e., mutations that differentiate Arabidopsis thaliana gene copies from those of Arabidopsis lyrata.

    Very cool result!

  3. Arcadia Science

    deed, visual inspection identified numerous linked specific variants at polymorphic sites, sometimes spanning hundreds of positions, indicative of gene conversion tracts.

    As you point out, it seems some of the strongest evidence for ECG is that polymorphism is not just shared, but shared polymorphisms are linked. One way you could statistically quantify this is by running a tool scanning for evidence of identity by descent (IBD), or use a tree sequence approach, treating each gene from each accession as an individual genome (like in the multiple sequence alignment you construct). This isn't strictly what IBD tools are for, but it should provide a good proxy given that A. thaliana has low polymorphism and high linkage disequilibrium. Relatedly it would help if intervals for putative EGC could be filled in, not just the limits marked as in Fig S6. This would make it easier to see what the length of EGC tracts is.

  4. Arcadia Science

    Given this, I would suggest that this paper does not quite fit the framing of reconciling genetic variation with mutation selection balance. I think as the title suggests the strongest claim is that ECG can create quantitative trait variation, and this is the framing that makes the most sense in the introduction/discussion.

  5. Arcadia Science

    This can explain why there is more segregating fitness variation within populations than predicted under mutation selection balance (1).

    This seems to me as a fairly strong statement that doesn't quite line up with the goals/results of this study. Technically what this study shows is how ECG can contribute to standing genetic variation in a population. The specific paradox of standing genetic variation in phenotypes however, looks to reconcile why there is more variation than expected under mutation selection balance (MSB). MSB in practice is agnostic to the type of mutations, when/where they arose, simply their fitness effects. As detailed in the first reference, it is clear that SNPs alone are inconsistent with MSB which is not surprising since they are only a fraction of genetic variants found in populations. However again as detailed in the first reference, quantitative genetics approaches that use mutation accumulation experiments are agnostic to mutation type, and provide a framework for testing if MSB is sufficient to explain standing levels of genetic variation. Paradoxically they often find that MSB is not enough to explain the high variation in phenotypes (due to genetic effects) we observe (see https://doi.org/10.1098/rspb.2018.1864 for an example), implying that forces such as balancing selection must also be working to maintain excess genetic variation. What this study demonstrates is that non-SNPs can contribute to variation (as other studies have demonstrated for transposons, inversions, indels etc.). This alone does not demonstrate the sufficiency of MSB to explain observed genetic variation in phenotypes though.

  6. Version published to 10.1101/2024.12.26.630369v1 on bioRxiv