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Seed markets are vital to scaling up ecosystem restoration in the Brazilian Cerrado, home of the world’s most species-rich grasslands and savannas. We compiled lists of species traded by four major Cerrado seed supply systems to investigate the representativeness of the species currently available for seed-based restoration. We also identified whether dominant ground-layer species are being sourced for seed production. Seeds from 263 Cerrado species can be purchased for restoration, of which 68% are trees, particularly legumes (24%). 63% of the traded species were found in only one seed supply system. The five most dominant graminoids of the Cerrado ground layer were available for sale, but two additional species uncommon in old-growth areas represented 44% of the sales of a key seed trader in Central Brazil. The expansion of Cerrado seed supply systems should be supported to further increase the number of species on the market. Sourcing seeds from a diversity of herbaceous species is central to facilitating the restoration of species-rich grasslands and savannas in the Cerrado. Recovering the diversity and functioning of old-growth open ecosystems through seeds will depend on increasing the supply and demand for species typical of Cerrado’s ground layer.

The Brazilian Caatinga is considered the richest nucleus of the Seasonally Dry Tropical Forests (SDTF) in the Neotropics, also exhibiting high levels of endemism, but the timing of origin and the evolutionary causes of its plant diversification are still poorly understood. In this study, we integrate comprehensive sampled dated molecular phylogenies of multiple flowering plant groups and estimations of ancestral areas to elucidate the forces driving diversification and historical assembly in the Caatinga flowering plants. Our results show a pervasive floristic exchange between Caatinga and other neotropical regions, particularly those adjacent. While some Caatinga lineages arose in the Eocene/Oligocene, most dry-adapted endemic plant lineages found in region emerged from the middle to late Miocene until the Pleistocene, indicating that only during this period the Caatinga started to coalesce into a SDTF like we see today. Our findings are temporally congruent with global and regional aridification events and extensive denudation of thick layers of sediments in Northeast (NE) Brazil. We hypothesize that global aridification processes have played important role in the ancient plant assembly and long-term Caatinga SDTF biome stability, whereas climate-induced vegetation shifts, as well as the newly opened habitats have largely contributed as drivers of in situ diversification in the region. Patterns of phylogenetic relatedness of Caatinga endemic clades revealed that much modern species diversity has originated in situ and likely evolved via recent (Pliocene/Pleistocene) ecological specialization triggered by increased environmental heterogeneity and the exhumation of edaphically disparate substrates. The continuous assembly of dry-adapted flora of the Caatinga has been complex, adding to growing evidence that the origins and historical assembly of the distinct SDTF patches are idiosyncratic across the Neotropics, driven not just by continental-scale processes but also by unique features of regional-scale geological history.

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a subset of 60 loci in a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories in the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.