I discuss three problems with the argument that ancient asexual lineages lack meiosis and recombination resulting in a diminution of (potentially disadvantageous) transposable elements and other forms of repetitive DNA. First, all ancient asexuals are probably automictic, hence could retain meiotic recombination in the guise of gene conversion. Second, transposable elements alter recombination rates, not vice versa. Third, increasing the number of transposable elements and other forms of repetitive DNA reduces meiotic recombination rate. Ancient asexuals lack those transposable elements that are transmitted via outcrossing, and this has nothing to do with meiotic recombination.
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Root Gorelick (2003) studied this question.
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