Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Elizabeth M Joyce , Alexander N Schmidt-Lebuhn, Harvey K Orel, Francis J Nge, Benjamin M Anderson, Timothy A Hammer, Todd GB McLay

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking a step-change in the generation of data for phylogenetic inference. While this advancement has facilitated the resolution of many relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, incomplete lineage sorting or rapid speciation – common processes in plant evolution. The proliferation of methods for analysing target capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we break down the causes of conflict and guide researchers through a target capture bioinformatic workflow, with a particular focus on robust phylogenetic inference in the presence of conflict. Through the workflow, we highlight key considerations for reducing artefactual conflict, managing paralogs, and assessing conflict, and discuss current methods for investigating causes of conflict. While we draw from examples in the Australian flora, this review is broadly relevant for any researcher working with target capture data. We conclude that conflict is often inherent in plant phylogenetic research, and that although further methodological development is needed, target capture data can still provide unprecedented insight into the extraordinary evolutionary histories of plants when carefully analysed.