The evolution, diversity, and genetic architecture of sex in waterhemp (Amaranthus tuberculatus)

The evolution of separate sexes is hypothesized to occur through distinct pathways involving few large-effect or many small-effect alleles. However, the genetic architecture of sex may itself evolve through selection to suppress recombination in order to maintain beneficial combinations of alleles, potentially at the cost of losing functional genetic variation. To explore these processes, we leveraged the recent transition of Amaranthus tuberculatus to dioecy within a predominantly monoecious genus, along with a sex-phenotyped population genomic dataset, and six newly generated chromosome-level haplotype phased assemblies. We identify a ~4 Mb region strongly associated with sex through genotype and sequence-depth based analyses. Comparative genomics of these proto-sex chromosomes within the species and across the Amaranthus genus demonstrates remarkable variability in their structure and genic content, including numerous polymorphic inversions. No such inversion underlies the extended linkage we observe associated with sex determination. Instead, we identify a complex copy number polymorphism that is differentiated across sexes, is variable across ancestral lineages, geographical scales, and habitats, but incompletely explains sex as phenotyped--over 10% of individuals show phenotype-genotype mismatch in the sex-linked region. Together with our novel observation of leakiness in expression of sex within the species, these findings imply the presence of multiple interacting determinants of sex. The evolution of separate sexes and its genetic architecture in A. tuberculatus therefore appears to be ongoing, with modifiers of sex that permit gene exchange and the maintenance of diversity in proto-sex chromosomes.