Data from: Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution

Flaveria (Asteraceae) is the prime model for the study of C4 photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C3-C4 intermediate phenotypes, still existing in Flaveria today. Molecular phylogenies of Flaveria based on concatenated data matrices are currently used to reconstruct the complex sequence of trait shifts during C4 evolution. To assess the possible role of hybridization in C4 evolution in Flaveria, we re-analyzed transcriptome data of 17 Flaveria species to infer the extent of gene tree discordance and possible reticulation events. We found massive gene tree discordance as well as reticulation along the backbone and within clades containing C3-C4 intermediate and C4-like species. An early hybridization event between two C3 species might have triggered C4 evolution in the genus. The clade containing all C4 species plus the C4-like species F. vaginata and F. palmeri is highly supported in our phylogenetic analyses, but it might be of hybrid origin involving F. angustifolia and F. sonorensis (both C3-C4 intermediate) as parental lineages. Hybridization seems to be a driver of C4 evolution in Flaveria and likely promoted the fast acquisition of C4 traits. This new insight can be used in further exploring C4 evolution and can inform C4 bioengineering efforts.Data package from Morales-Brioned and Kadereit Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution - https://doi.org/10.18061/bssb.v2i3.8992 This package contains the supplemental material and the data and software outputs (i.e. fasta files, alignments, trees, etc). - Supplemental material Table S1. Taxon sampling and source of data Table S2. HyDe significant hybridization tests for all species of Flaveria. Table S3. HyDe significant hybridization tests for all species of Flaveria excluding F. pringlei (C3). Fig. S1. a) Maximum likelihood phylogeny of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene supermatrix. Numbers above branches represent bootstrap support (BS). Branch lengths as substitutions per site (scale bar on the bottom). b) ASTRAL tree of Flaveria inferred from the 2,127 nuclear gene trees. Local posterior probabilities (LPP) are shown next to nodes. Internal branch lengths are in coalescent units (scale bar on the bottom). Fig. S2. a) Maximum likelihood cladogram of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene supermatrix. b) ASTRAL cladogram of Flaveria inferred from the 2,127 nuclear gene trees. Pie charts represent the proportion of gene trees that support that clade (blue), the main alternative bifurcation (green), the remaining alternatives (red), and conflict or support that have