Conspicuous innovations in the history of life are often preceded by more cryptic genetic and developmental precursors. In many cases, these appear to be associated with recurring origins of very similar traits in close relatives (parallelisms) or striking convergences separated by deep time (“deep homologies”). Although the phylogenetic distribution of gain and loss of traits hints strongly at the existence of such precursors, no models of trait evolution currently permit inference about their location on a tree. Here we develop a new stochastic model which explicitly captures the dependency implied by a precursor and permits estimation of precursor locations. We apply it to the evolution of extrafloral nectaries (EFNs), an ecologically significant trait mediating a widespread mutualism between plants and ants. In legumes, a species-rich clade with morphologically diverse EFNs, the precursor model fits the data on EFN occurrences significantly better than conventional models. The model generates explicit hypotheses about the phylogenetic location of hypothetical precursors, which may help guide future studies of molecular genetic pathways underlying nectary position, development and function.

Trait data in Nexus formatThis is a gzip compressed tar archive of six nexus files (and a README file). Each nexus file contains the trait data for one of the six types of extra-floral nectary as described in the paper. Each file also contains a trees block with the same MCC tree used in places in the paper. The nexus file is plain text.EFN_traits.tar.gz