Data from: Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)

Crassulacean acid metabolism (CAM) is a modified form of photosynthesis that has arisen independently at least 35 times in flowering plants. The occurrence of CAM is often correlated with shifts to arid, semiarid, or epiphytic habits, as well as transitions in leaf morphology (e.g. increased leaf thickness) and anatomy (e.g. increased cell size and packing). We assess shifts between C3 and CAM photosynthesis in the subfamily Agavoideae (Asparagaceae) through phylogenetic analysis of targeted loci captured from the nuclear and chloroplast genomes of over 60 species. Carbon isotope data was used as a proxy for mode of photosynthesis in extant species and ancestral states were estimated on the phylogeny. Ancestral character state mapping suggests three independent origins of CAM in the Agavoideae. CAM species differ from C3 species in climate space and are found to have thicker leaves with densely packed cells. C3 ancestors of CAM species show a predisposition toward CAM-like morphology. Leaf characteristics in the ancestral C3 species may have enabled the repeated evolution of CAM in the Agavoideae subfamily. Anatomical changes, including a tendency toward 3D venation, may have initially arisen in C3 ancestors in response to aridity as a way to increase leaf succulence for water storage.CrossSectionMeasurementsCross section data generated from leaf cross sections, imaged using a Zeiss microscope and analyzed in ImageJ.Gene treesGene trees produced from 272 single copy genes, using RAxML. Trees are the consensus of 500 bootstrap replicates (RAxML_bipartitions.*).genetrees.zipGene alignmentsNucleotide alignments of 272 single copy genes.alignments.zipChloroplast treeRAxML bipartition tree from chloroplast alignment. 500 bootstrap replicates.chloroplast_RAxML.treChloroplast alignmentChloroplast alignment file.all.merged.fa.align-gb.68Concatenated nuclear treeRAxML bipartition (bootstraps=500) tree for the concatenated nuclear data.concatenated_nuclear_RAxML.treNuclear ASTRALII treeASTRAL-II species tree, based on 272 single copy gene trees. 400 bootstrap replicates.nuclear_astral.treFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB 144219