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 phylogenetic relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common in plant evolution. The proliferation of methods designed to analyse target capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we guide researchers through the 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, synthesise strategies for managing paralogs, explain the causes and measurement of conflict, and summarise current methods for investigating biological processes underlying 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 and inevitable in plant phylogenetic research, but when properly managed, target capture data can provide unprecedented insight into the extraordinary and complex evolutionary histories of plants.