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Feb 22, 2017 at 21:43 comment added Mike Nichols Epigenetic silencing of transposable elements is intended to prevent them from spreading further, but if a transposon has directly disrupted a gene by inserting into one of its exons there is no way to recover the function of that gene through epigenetic means. Inactivating a transposon or a non-functioning gene won't remove it, nor will it create a functioning replacement. The only way to remove the deleterious allele will be through natural selection, which increased ploidy will work against.
Feb 22, 2017 at 21:19 comment added Willk You may be right about radiation mutations but maybe not about transposons. If there were a process like lyonization en.wikipedia.org/wiki/X-inactivation to inactivate genes which did not make a product that would weed out these damaged genes from the organism. The actual method by which animals defend against transposons has to so with small noncoding rna whatisepigenetics.com/non-coding-rna which as I understand them, cut the transposon and with it the gene it is in.
Feb 22, 2017 at 20:07 comment added Mike Nichols While this idea makes sense in the short term it would almost inevitably lead to the extinction of the species. By going to 4 gene copies you aren’t actually dealing with the issue of increased mutations. You are merely temporarily masking them. The deleterious mutations will build up in the gene pool, hidden by the good copies until the majority of copies in the genome are non-functional. The rate of viable births will decrease dramatically and the species will go extinct. In the face of active transposable elements or increased radiation a species would be better served becoming monoploid.
Feb 22, 2017 at 18:59 history answered Willk CC BY-SA 3.0