Multiplex shotgun genotype (MSG) reduced representation genomic data for the long-tailed finch (Poephila acuticauda) and black-throated finch (Poephila cincta).

Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyze the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill color, using reduced representation genomic sequencing for 293 individuals over a 1530 km transect. Autosomal differentiation between subspecies is minimal. In contrast, 75% of the Z chromosome is highly differentiated and shows a steep genomic cline which is displaced 350 km to the west of the cline in bill color. Differentiation is associated with two or more putative chromosomal inversions, each predominating in one subspecies. If inversions reduce recombination between hybrid incompatibilities, they are selectively favored and should therefore accumulate in hybrid zones. We argue that this predisposes inversions to differentially accumulate on the Z chromosome. One genomic region affecting bill color is on the Z, but the main candidates are on chromosome 8. This, and the displacement of the bill color and Z chromosome cline centers suggest that bill color has not strongly contributed to inversion accumulation. Based on cline width, the Z chromosome and bill color both contribute to reproductive isolation established between this pair of subspecies.