Natural hybrid zones provide opportunities for studies of the evolution
of reproductive isolation in wild populations. Although recent
investigations have found that the formation of neo-sex chromosomes is
associated with reproductive isolation, the mechanisms remain unclear in
most cases. Here, we assess the contemporary structure of gene flow in
the contact zone between largely allopatric cytotypes of the dioecious
plant Rumex hastatulus, a species with evidence of sex chromosome
turn-over. Males to the west of the Mississippi river, USA, have an X
and a single Y chromosome, whereas populations to the east of the river
have undergone a chromosomal rearrangement giving rise to a larger X and
two Y chromosomes. Using reduced-representation sequencing, we provide
evidence that hybrids form readily and survive multiple backcross
generations in the field, demonstrating the potential for ongoing gene
flow between the cytotypes. Cline analysis of each chromosome separately
captured no signals of difference in cline shape between chromosomes.
However, principal component regression revealed a significant increase
in the contribution of individual SNPs to inter-cytotype differentiation
on the neo-X chromosome, but no correlation with recombination rate.
Cline analysis revealed that the only SNPs with significantly shallower
clines than the genome-average were located on the neo-X. Our data are
consistent with a role for neo-sex chromosomes in reproductive isolation
between R. hastatulus cytotypes. Our investigation highlights the
importance of studying plant hybrid zones in species with sex
chromosomes for understanding mechanisms of reproductive isolation and
the role of gene flow in the spread of neo-X chromosomes.