Abstract

Early work on male colour diversity in guppies found a that a substantial proportion of colour pattern variation is Y-linked, and this association inspired our current models of sex chromosome evolution. This Y diversity is curious, given that the loss of recombination between sex chromosomes often depletes Y chromosomes of functional content and genetic variation, which might limit their potential to generate adaptive diversity. We have mapped out Y degeneration and Y haplotype diversity across guppies and several related species, and used this in conjunction with deep learning image analysis of colouration to determine the role of the Y in male phenotypic variation. Our results indicate a remarkable amount of Y haplotype diversity, likely maintained by balancing selection related to sexual selection.