Most readers of a special issue of Plant Physiology on legumes will be familiar with only a handful of species, primarily pea (Pisum sativum) and the various economically important "beans" such as soybean (Glycine max), and of course, the model legumes Medicago truncatula and Lotus japonicus. That leaves around 700 other legume genera and 20,000 species left to consider-legumes are the third largest flowering plant family, behind only orchids (Orchidaceae) and asters (Asteraceae). And the numbers tell only part of the story. Neither these two larger families, nor the grasses, another large group, even begin to approach the legumes in their overall range of variation. The legumes are incredibly diverse in every way imaginable and defy generalization about almost any attribute. Even the characteristic fruit type that gives legumes their name is highly variable and ranges from tiny single-seeded forms to meterlong woody pods and from typical dehiscent legumes to indehiscent wind-dispersed winged fruits and articulated loments with "stick-tight" dispersal strategies.Ecologically the family ranges from rain forests to deserts, and from lowland to alpine habitats; there are even aquatic species. They include giant forest trees that are prominent sources of lumber and expensive woods (e.g. Brazilian rosewood [Dalbergia nigra]), shrubs of all sizes and habits, lianas from annual twiners to woody behemoths such as wisteria or kudzu, and tiny annual herbs. Nodulation, that trademark symbiosis of legumes, is conspicuously absent in several major lineages. If you think you could recognize all legume genera by the butterflyshaped ("papilionoid") flowers so familiar from pea and its relatives, think again (Fig. 1). The earlydiverging lineages have flowers that look more like those of a wild rose, and many modifications exist, from the reduced flowers of the aptly named Amorpha (not too far in the family tree from soybean and pea) to spectacular orchid-like flowers of species that share only a more distant ancestry with these models. There are flowers with one stamen, and whole groups of genera with flowers that compensate for their nondescript petals with their many, showy stamens. There is pollination by bees, moths, butterflies, perching birds, hummingbirds, and bats, not to mention the do-it-your-selfers. Many species shed their pollen in tetrads or larger masses rather than as individual grains (might some geneticist be interested in developing a Neurospora-like legume system of tetrad analysis?). There is a tremendous diversity of secondary compounds, particularly alkaloids, many of them biologically active, such as the fish poisons of several woody tropical groups.Current model legumes cover only a fraction of this diversity-the tip of the iceberg of variation in the family. New models would be useful to provide the kind of phylogenetic coverage that exists in grasses, for example, where the primary model, rice (Oryza sativa), is about as distantly related from the other well-studied taxa, maize (Zea mays) and the triti...

The field of molecular plant phylogenetics has had tremendous impacts on botanical studies and taxonomic classification, macroevolution and biogeography, ever since the pioneering studies of Chase et al. (1993) based on DNA sequence data. While those early studies used just a single locus, the plastid gene rbcL, modern studies often employ hundreds to several thousands of genes to infer phylogenetic relationships (e.g.,

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.

The boreotropics hypothesis postulates a preferential tropical biotic interchange between North America and Eurasia during the early Tertiary that was directed by Eocene thermal maxima and the close proximity of these two continental plates. This preferential interchange occurred at a time when South America was geologically and biotically isolated. A prediction of this hypothesis posits that a taxon with a present‐day center of diversity in tropical North America, and with an early Tertiary fossil record from any region there, has a high probability of having sister‐group relatives in the Paleotropics and derived relatives in South America. We propose a test of this prediction with phylogenetic studies of two pantropical taxa of Leguminosae that have early Tertiary North American fossil records. Our findings are consistent with the boreotropics hypothesis, and additional evidence suggests that many tropical elements in North America could be descendants of northern tropical progenitors. Ramifications of this hypothesis include the importance of integrating the fossil record with cladistic biogeographic studies, theoretical bases for recognizing tropical taxa with such disjunct distributions as Mexico and Madagascar, identification of taxa that may be most useful for testing vicariance models of Caribbean biogeography, and integrating the study of disjunct distributions in temperate regions of the northern hemisphere with those in the neo‐ and paleotropics.

No abstract