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

E. M. Joyce; A. N. Schmidt-Lebuhn; H. K. Orel; F. J. Nge; B. M. Anderson; T. A. Hammer; T. G. B. McLay

doi:10.1071/SB24011

RESEARCH ARTICLE (Open Access)

Previous Next Contents Vol 38(3)

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

E. M. Joyce

^A ^* , A. N. Schmidt-Lebuhn

^B , H. K. Orel

^C , F. J. Nge

^D , B. M. Anderson ^E , T. A. Hammer

^F ^G and T. G. B. McLay ^C ^H ^I ^*

+ Author Affiliations

- Author Affiliations

^A Systematik, Biodiversität und Evolution der Pflanzen, Ludwig-Maximilians-Universität München, Menzinger Straße 67, D-80638 Munich, Germany.

^B Centre for Australian National Biodiversity Research (a joint venture of Parks Australia and CSIRO), Clunies Ross Street, Canberra, ACT 2601, Australia.

^C School of BioSciences, The University of Melbourne, Parkville, Vic. 3010, Australia.

^D National Herbarium of New South Wales, Botanic Gardens of Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia.

^E Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983, Australia.

^F School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.

^G State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA 5000, Australia.

^H National Biodiversity DNA Library, Environomics, CSIRO, Parkville, Vic. 3010, Australia.

^I Royal Botanic Gardens Victoria, Melbourne, Vic. 3004, Australia.

^* Correspondence to: e.joyce@lmu.de, todd.mclay@csiro.au

Handling Editor: Caroline Puente-Lelievre

Australian Systematic Botany 38, SB24011 https://doi.org/10.1071/SB24011

Submitted: 15 May 2024 Accepted: 7 March 2025 Published: 7 May 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC)

Abstract

Target capture has rapidly become a preferred approach for plant systematic and evolutionary research, marking a step change in the generation of data for phylogenetic inference. Although this advancement has facilitated the resolution of many relationships, phylogenetic conflict continues to be reported and is 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. Although 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 phylogenomic datasets, and, although further methodological development is needed, when conflict is carefully investigated, target-capture data can provide unprecedented insight into the extraordinary evolutionary histories of plants.

Keywords: Angiosperms353, deep coalescence, discordance, GAP, Genomics for Australian Plants, hybridisation, HybSeq, incomplete lineage sorting, incongruence, PAFTOL, paralogy, polyploidy, polytomy, target enrichment.

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