Regulatory divergence as a mechanism for X-autosome incompatibilities in Caenorhabditis nematodes

The worlds astounding biodiversity results from speciation, the process of formation of distinct species. Hybrids between species often have reduced fitness due to negative epistatic interactions between divergent genetic factors, as each lineage accumulated substitutions independently in their evolutionary history. Such negative genetic interactions can manifest as gene misexpression due to divergence in gene regulatory controls from mutations in cis-regulatory elements and trans-acting factors. Gene misexpression due to differences in regulatory controls can ultimately contribute to incompatibility within hybrids through developmental defects such as sterility and inviability. We sought to quantify the contributions of regulatory divergence to post-zygotic reproductive isolation using sterile interspecies hybrids of two Caenorhabditis nematodes: C. briggsae and C. nigoni. We analysed previous transcriptome profiles for two introgression lines with distinct homozygous X-linked fragments from C. briggsae in a C. nigoni genomic background that confers male sterility, owing to defects in spermatogenesis (Li et al. 2016). Our analysis identified hundreds of genes that show distinct classes of non-additive expression inheritance and regulatory divergence. We find that these non-overlapping introgressions affect many of the same genes in the same way and demonstrate that the preponderance of transgressive gene expression is due to regulatory divergence involving compensatory and joint effects of cis- and trans-acting factors. The similar transcriptomic responses to non-overlapping genetic perturbations of the X-chromosome implicate multiway incompatibilities as an important feature contributing to hybrid male sterility in this system. Significance statementThe genetic causes of intrinsic post-zygotic reproductive isolation can arise from hybrids experiencing negative gene regulatory interactions. In Caenorhabditis nematodes, hybrid male sterility involves X-autosome incompatibilities that affect small-RNA regulatory pathways. We sought to understand the role of gene regulatory divergence as a related contributor to hybrid misexpression by analyzing transcriptomes of sterile males from two hybrid introgression lines, each containing distinct X-linked fragments from C. briggsae in a C. nigoni genomic background. We show that gene misexpression occurs due to extensive joint divergence of cis- and trans-acting regulatory factors and provide evidence for multiway incompatibilities as an important feature of this system.