The danger zone: The joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae.

Abstract

Premise: Rafflesiaceae (Malpighiales) is an iconic parasitic plant clade of species that occur west of Wallace's line in tropical Southeast Asia. This clade has been notoriously difficult to place phylogenetically and is nested within an explosive ancient radiation in Malpighiales, rendering one of the thorniest nodes across the angiosperm Tree of Life. The parasitic family Apodanthaceae has recently been positioned as sister to Rafflesiaceae, offering hope of stabilizing their placements.

Methods: Here, using a data set of 2135 genes and complex methods for species tree inference, we aimed to resolve the phylogenetic placement and divergence time of Rafflesiaceae and Apodanthaceae. We also applied computational simulation to investigate the impact of incomplete lineage sorting (ILS) and long-branch attraction on resolving this ancient radiation.

Results: The clade comprising Rafflesiaceae and Apodanthaceae was variously placed with Euphorbiaceae, Peraceae, Putranjivaceae, and Pandaceae by coalescent and concatenation methods. Such unstable placements appear to be the result of excessive levels of rate heterogeneity and ILS, which contribute to a phylogenetic "danger zone" where simulation suggests that current methods and genomic data may never provide a tidy species tree.

Conclusions: Despite the topological uncertainty, our divergence time estimation identified a mid-Cretaceous origin of stem group Rafflesiaceae and Apodanthaceae, not only making them the oldest parasitic plant lineage reported to date, but also suggesting a likely Gondwana vicariance scenario that explains their initial disjunct distribution in Northern India, Australia, South America, and Africa.