- The inference of phylogenetic relationships is often complicated by differing evolutionary histories of independently‐inherited markers. The causes of the resulting gene tree incongruence can be challenging to identify, often relying on coalescent simulations dependent on unverifiable assumptions. We investigated alternative techniques using the South African rosulate species of Streptocarpus as a study group.
- Two independent gene trees – from the nuclear ITS region and from three concatenated plastid regions (trnL‐F, rpl20‐rps12 and trnC‐D) – displayed widespread, strongly supported incongruence. We investigated the causes by detecting genetic exchange across morphological borders using morphological optimizations and genetic exchange across species boundaries using the genealogical sorting index.
- Incongruence between gene trees was associated with ancestral shifts in growth form (in four species) but not in pollination syndrome, suggesting introgression limited by reproductive barriers. Genealogical sorting index calculations showed polyphyly of two additional species, while individuals of all others were significantly associated. In one case the association was stronger according to the internal transcribed spacer data than according to the plastid data, which, given the smaller effective population size of the plastid, may also indicate introgression.
- These approaches offer alternative ways to identify potential hybridization events where incomplete lineage sorting cannot be rejected using simulations.