Phylogenomic timetree-calibrated speciation clocks for Caenorhabditis nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation.

Reproductive isolation and genomic divergence both accumulate over time in the formation and persistence of distinct biological species. The pace of "speciation clocks" quantified with pre-zygotic and post-zygotic reproductive isolation, however, differs among taxa, with pre-zygotic isolation tending to evolve sooner in some but not all taxa. To address this issue in nematodes for the first time, here we infer the species tree and divergence times across the phylogeny of 51 species of Caenorhabditis. We incorporate several molecular evolutionary strategies in phylogenomic dating to account for complications in this group due to lack of fossil calibration, deep molecular divergence with synonymous-site saturation, and codon usage bias. By integrating divergence times with experimental data on pre- and post-zygotic reproductive isolation, we infer that post-zygotic isolation accumulates faster than pre-zygotic isolation in Caenorhabditis and that hybrid sterility evolves sooner than hybrid inviability. These findings are consistent with speciation being driven principally by intrinsic isolating barriers and the disproportionate fragility of germline developmental programs to disruption. We estimate that it takes approximately 50 million generations for intrinsic post-zygotic reproductive compatibility to be reduced by half, on average, between diverging pairs of Caenorhabditis. The protracted reproductive isolation clocks in Caenorhabditis may, in part, reflect the capacity to retain population genetic hyperdiversity, the incomplete sampling of global biodiversity, and as-yet uncharacterized incipient or cryptic species.