The effects of hemiplasy and maintained polymorphisms in fossil clades

One of the most transformative advances in molecular systematics over the past several decades has been our understanding of how population processes like incomplete lineage sorting (ILS) give rise to phylogenetic discordance. Fossil clades, which are known almost exclusively from morphology, have benefited little from these developments. An emerging body of work has shown how processes related to those that cause discordance at the molecular level can also shape patterns at the phenotypic level. Conflicting signal can arise when phenotypic polymorphisms maintained in an ancestral taxon sort among descendant taxa or persist beyond speciation. Here, I explore how ancestral polymorphisms contribute to the landscape of phylogenetic discordance in Pleistocene Homo and late-Cretaceous Micraster. I found rampant discordance stemming from the sorting and persistence of ancestral polymorphisms in both clades. This suggests that mechanisms related to those that drive gene-tree discordance may also shape morphological patterns. Simulations show that explicitly modelling the processes that give rise to this discordance can dramatically improve reconstructions. Further studying how biological processes like ILS generate discordance in phenotypic characters and incorporating them into phylogenetic models can improve tree reconstruction and generate novel biological insights in fossil clades.