Data from: Molecular phylogeny and pollen evolution of Euphorbiaceae tribe Plukenetieae

Tribe Plukenetieae (Euphorbiaceae, Acalyphoideae) is a pantropical lineage of mostly stinging, twining vines and lianas with diverse floral and pollen morphology. To elucidate generic relationships in the tribe and examine patterns of pollen morphology evolution, we conducted phylogenetic analyses of nuclear ribosomal ITS and plastid psbA-trnH DNA sequence and indel gap-scored data. We sampled all genera in subtribes Dalechampiinae and Tragiinae, and most in Plukenetiinae; species sampling was broad in the latter two subtribes. Our efforts produced a 2,207 character dataset of 154 terminals (representing ca. 93 species). Analyses of these data support the monophyly of each subtribe and weakly suggest Dalechampiinae (Dalechampia) is sister to Plukenetiinae + Tragiinae. Within Plukenetiinae, Haematostemon is resolved as sister to Romanoa + Plukenetia, and Plukenetia is divided into five subclades that mostly correspond to the current infrageneric classification. Tragiinae is resolved into an Old World lineage and a mostly New World lineage, and is divided into ten subclades also supported by floral and/or pollen morphology. Species-rich Tragia is recovered as para- or polyphyletic and intermixed with all other currently recognized Tragiinae genera. The recently segregated genera, Bia, Ctenomeria, and Zuckertia, are upheld, and Gitara is resurrected from Acidoton, resulting in two new combinations: Gitara nicaraguensis and Zuckertia manuelii. Pollen aperture and exine morphology are largely correlated with phylogeny. The loss of pollen endopores is a potential synapomorphy of Plukenetiinae + Tragiinae, and we hypothesize that weakly defined apertures and inaperturate pollen originated independently four and three times, respectively

Plukenetieae combined partitioned dataset

154 terminal, 2381 character, combined psbA-trnH, psbA-trnH indels, and ITS dataset of tribe Plukenetieae and outgroups (Euphorbiaceae). This nexus file includes the full alignment, exclusion sets, and partitions

Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species

Abstract Background Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BioGeoBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. Results Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. Conclusions The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia

Data from: Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species

Background: Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5,069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BioGeoBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. Results: Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. Conclusions: The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia

Cardinal-McTeague_2018

This package includes the LiteBlueDevil v0.3 python script, archived alignment, tree files, and seed dimension dataset, and R script and files needed to reproduce the seed evolution analyses in the following paper: Cardinal-McTeague et al. 2018. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evolutionary Biology

Phylogeny, Classification, and Character Evolution of Acalypha (Euphorbiaceae Acalyphoideae)

Acalypha (Euphorbiaceae Acalyphoideae) is a large; monophyletic genus distributed worldwide in tropical and subtropical regions; with a few species extending into temperate Asia and North America. We reconstructed phylogenetic relationships within the genus using DNA sequences from the plastid ndhF and trnL-F regions and the nuclear ribosomal ITS region; sampling 143 species to represent the geographic; morphologic; and taxonomic diversity with the genus; resulting in a 162 (158 in Acalypha) terminal and 3847 character combined dataset. Bayesian and maximum likelihood reconstructions based on the combined dataset yielded a tree with a generally well-supported backbone and several strongly supported clades. Our results strongly supported the monophyly of subg. Acalypha as currently recognized but showed that subg. Linostachys and almost all other infrageneric taxa recognized in the most recent comprehensive classification of the genus were not monophyletic. We therefore propose a new subgeneric classification comprising subg. Acalypha; subg. Androcephala; subg. Hypandrae; and subg. Linostachys (s.s.). Our results also shed light on relationships within some species groups; including in what has been treated as a broadly defined A. amentacea; in which we recognize A. amentacea; A. palauensis comb. nov.; and A. wilkesiana as distinct species. Bayesian ancestral state estimations based on the phylogeny of Acalypha demonstrated that plant habit and inflorescence position and sexuality are highly homoplastic; especially within subg. Acalypha; and that inflorescence position and habit exhibit correlated evolution