Jason Grant Bragg, Sally Potter, Ana Afonso-Silva, Mozes Blom, Conrad Hoskin, Huw A Ogilvie, Craig Moritz 

Evolutionary lineages at the tip of the tree of life can be genetically diverged yet phenotypically similar and therefore unrecognized by traditional morphology-based taxonomy. Such lineages, spanning the “grey zone of speciation” 1, are increasingly uncovered using genomic analyses. Here we show that incorporating this unrecognized lineage diversity into macro-evolutionary analyses yields novel insights into the speciation process. Examining a major clade of Australian skinks with extensive sampling of both unrecognised lineages and described species (199 lineages across 124 species) we find that lineages of this group have been forming at a constant net rate over time. In contrast, when including only the described species we see a slow-down in the net rate of diversification. Simulations of lineage formation via a protracted speciation model, extended to include multivariate trait evolution, indicate that phenotypic conservatism can explain the dynamics of taxonomically recognized diversity over time. Including intraspecific lineages in macroevolutionary analyses has provided new insights about the diversification process. In this case, it points to higher net rates of lineage than species formation, and a role for phenotypic constraint in generating cryptic lineage diversity.