Abundant selection explains low diversity on human Y chromosomes. M. Wilson Sayres1,2, K. Lohmueller1,2, R. Nielsen1,2 1) Integrative Biology, University of California, Berkeley, Berkeley, CA; 2) Statistics, University of California, Berkeley, Berkeley, CA.

   The human Y chromosome exhibits levels of diversity that are significantly lower than expected under neutral population genetic theory. Variance in male reproductive success (reducing the effective population size of males relative to females) has recently been proposed as an alternative neutral model to explain reduced diversity on the Y relative to mtDNA. Generally Y chromosomes are not included in whole genome analyses, so explicit tests of this hypothesis have yet to be conducted. Here we show that neutral models with unequal male and female effective population sizes are not consistent with observed genome-wide diversity on autosomes, X, Y and mtDNA across completely sequenced males. Instead, a model including selection is needed to explain the departure of observed Y diversity from expectations. We found that models with similar estimates of the strength of background selection can explain diversity for both the Y chromosome and mitochondrial genomes. Our results suggest that strong selection is necessary for explaining the evolutionary history of the human Y chromosome, and argue against the concept of the "junk" Y chromosome .

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