Inferring the relative contributions of evolutionary processes shaping X chromosome dynamics in the common marmoset ( Callithrix jacchus ) in the presence of twinning and hematopoietic chimerism

Abstract The common marmoset (Callithrix jacchus) is a biomedically important species that is characterized by two unusual biological traits—a high frequency of twin births and hematopoietic chimerism—that preclude the application of many commonly used population genomic approaches for quantifying evolutionary processes. In this study, we directly account for both factors in order to estimate fine-scale mutation and recombination rate maps, as well as to infer the demographic and selective processes shaping variation, on the common marmoset X chromosome. Comparing our findings to estimates recently inferred on the autosomes of this species, we find reduced rates of mutation and recombination on the X, as expected. Furthermore, population sex ratios are inferred to be nearly equal, and the appropriately rescaled autosomal population history fits the X chromosome well. Finally, we report evidence of recent selective sweeps targeting a number of X-linked genes, including several of significant biomedical relevance. Overall, these analyses provide novel insights into the evolutionary processes shaping X chromosome evolution in this biomedically-relevant primate model.