Format: ORAL

Rong Zhang1, Ting-Shuang Yi1, Jin Jian-Jun1,2, Yin-Huang Wang1,3, De-Zhu Li1, Joseph Charboneau4, Xing-Xing Shen5, Stephen A. Smith4, Domingos Cardoso6, Luciano P. de Queiroz7, Anne Bruneau8

1. Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China 2. Present Address: Columbia University New York, USA 3. Present Address: Chongqing Normal University, Chongqing, China 4. University of Michigan, Ann Arbor, USA 5. Zhejiang University, Hangzhou, China 6. Rio de Janeiro Botanical Garden, Rio de Janeiro, Brazil 7. Universidade Estadual de Feira de Santana, Feira de Santana, Brazil 8. Université de Montréal, Montréal, Canada

Tree of Life lies at the heart of almost all studies in evolutionary biology. However, it is challenging to resolve recalcitrant phylogenetic relationships caused by rapid evolutionary radiations, hybridizations, and whole genome duplications. Despite the ecological and economical importance of Fabaceae (Leguminosae), phylogenetic relationships among some subfamilial and tribal lineages remain poorly resolved. We reconstructed the backbone phylogeny of Fabaceae using plastomes, mitochondrial genes and transcriptome data of 909 species across 486 genera, representing all six subfamilies and almost all tribal lineages. Our results strongly supported the monophyly of the six subfamilies and 64 tribal clades, and clarified many long-controversial relationships. However, 14 sets of nodes remained unresolved due to conflicts among trees based on plastid and nuclear data, or different analysis methods. Through gene-tree quartet analyses evaluating alternative topologies and consistently strong support in ML and Astral tree both on the nuclear data sets, we resolved 18 of these recalcitrant nodes. Using relative quantification analyses, our study identified incomplete lineage sorting as the main source of conflict for deeper nodes (e.g., the root of Fabaceae), gene flow is the main source for shallower nodes (e.g., Griffonia, ADA clade, Wisterieae), both are involved conflicts for some nodes (e.g., core Papilionoideae, Erythrophleeae, Tachigalieae, Moldenhawereae). The study suggested when ILS and gene flow coexist to a considerable extent, resolving contentious relationships becomes exceedingly difficult. Our study provides a robust phylogenomic framework for exploring legume evolution and supplies a typical case to apply multiple types of molecular data and analysis methods to resolve recalcitrant phylogenetic relationships and explore the underlying conflict.