Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

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

A new cryptic species in a new cryptic genus in the Caesalpinia group (Leguminosae) from the seasonally dry inter-Andean valleys of South America

The generic affiliation of the Andean species Caesalpinia trichocarpa, C. mimosifolia, and their close relatives has remained uncertain in all recent studies of Caesalpinia s.l. (Leguminosae, subfamily Caesalpinioideae). A new densely sampled phylogeny based on four DNA sequence regions (rps16, trn D-trnT, ycf6- psbM, ITS) strongly supports the monophyly of an Andean clade. We propose that despite the lack of obvious diagnostic morphological synapomorphies, this Andean group should be considered as a distinct genus, here described as the new genus Arquita. Phylogenetic analyses also suggest a problem with species delimitation in this group. Within C. trichocarpa, accessions from disjunct geographic areas in Argentina, Bolivia and Peru each form a robustly supported, unresolved clade that includes C. mimosifolia. The morphological and genetic cohesiveness of the C. trichocarpa complex is investigated using morphometric phenetic analyses of qualitative and quantitative flower and leaf traits, and reconstruction of a densely sampled phylogeny using three plastid and one nuclear ribosomal DNA sequence loci. Our results suggest that the most geographically isolated of these clades, narrowly endemic to two inter-Andean valleys in central-north Peru and separated by ∼1350 km, and extensive high Andean cordilleras above 4000 m, from the nearest populations in Bolivia, represents a genetically highly distinct and morphologically cryptic lineage here described as a new species (Arquita grandiflora). A full taxonomic account of the new genus Arquita and its component species is provided, with a distribution map and a key to the species

Molecular and Morphological Analysis Supports the Separation of Robrichia as a Genus Distinct from Enterolobium (Leguminosae: Caesalpinioideae: Mimosoid Clade).

As currently circumscribed, the legume genus comprises 11 species in two sections: sect. and sect. , with an overall distribution from Mexico to Argentina and a centre of diversity in Amazonia. In the absence of the characteristic indehiscent fruits, is difficult to distinguish from other genera in the ingoid clade, including sensu lato, , and . Previous phylogenetic studies which have included have sampled few species of the genus, leaving questions about its monophyly and interspecific relationships. Here we evaluate the circumscription of and its two infrageneric taxa, their phylogenetic placement in the ingoid clade, and interspecific relationships within the two sections of the genus. Our study includes all species, and analyses of nuclear (ITS and ETS) and plastid ( and ) molecular regions, and morphology. Bayesian inference, maximum parsimony, and maximum likelihood analyses show that , as presently circumscribed, is not monophyletic. The genus is divided into two well-supported independent clades, corresponding to the two previously recognized sections; one of them is sister to the genus and is here raised to generic rank as the genus , with three species, , and . The genus consequently now comprises eight species and is more closely related to a clade composed of and . This new arrangement is reinforced by morphological synapomorphies recovered by ancestral character state reconstructions. Indumentum type, the number of pinnae pairs per bipinnate leaf and leaflet pairs per pinna, inflorescence type, and fruit shape characterize , while the recognition of remains based on fruit traits. We also provide the formal lectotypifications for , , , , , and

Data from: A new generic system for the pantropical Caesalpinia group (Leguminosae)

The Caesalpinia group is a large pantropical clade of ca. 205 species in subfamily Caesalpinioideae (Leguminosae) in which generic delimitation has been in a state of considerable flux. Here we present new phylogenetic analyses based on five plastid and one nuclear ribosomal marker, with dense taxon sampling including 172 (84%) of the species and representatives of all previously described genera in the Caesalpinia group. These analyses show that the current classification of the Caesalpinia group into 21 genera needs to be revised. Several genera (Poincianella, Erythrostemon, Cenostigma and Caesalpinia sensu Lewis, 2005) are non-monophyletic and several previously unclassified Asian species segregate into clades that merit recognition at generic rank. In addition, the near-completeness of our taxon sampling identifies three species that do not belong in any of the main clades and these are recognised as new monospecific genera. A new generic classification of the Caesalpinia group is presented including a key for the identification of genera, full generic descriptions, illustrations (drawings and photo plates of all genera), and (for most genera) the nomenclatural transfer of species to their correct genus. We recognise 26 genera, with reinstatement of two previously described genera (Biancaea Tod., Denisophytum R. Vig.), re-delimitation and expansion of several others (Moullava, Cenostigma, Libidibia and Erythrostemon), contraction of Caesalpinia s.s. and description of four new ones (Gelrebia, Paubrasilia, Hererolandia and Hultholia), and make 75 new nomenclatural combinations in this new generic system

DNA_matrix_trees_Caesalpinia

This zip files contains the DNA alignments used to study the phylogeny of the Caesalpinia group. It also contains the files used in the Bayesian, Parsimony and Maximum likelihood phylogenetic analyses, along with the main results

DNA_matrix_trees_Caesalpinia

This zip files contains the DNA alignments used to study the phylogeny of the Caesalpinia group. It also contains the files used in the Bayesian, Parsimony and Maximum likelihood phylogenetic analyses, along with the main results

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes

Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades

The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny-based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next-generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species-rich angiosperm clades.Fil: Bruneau, Anne. University of Montreal; CanadáFil: Doyle, Jeff J.. Cornell University; Estados UnidosFil: Herendeen, Patrick. Chicago Botanic Garden; Estados UnidosFil: Hughes, Colin. Universitat Zurich; SuizaFil: Kenicer, Greg. Royal Botanic Garden Edinburgh; Reino UnidoFil: Lewis, Gwilym. Royal Botanic Gardens; Reino UnidoFil: Mackinder, Barbara. Royal Botanic Gardens; Reino Unido. Royal Botanic Garden Edinburgh; Reino UnidoFil: Pennington, R. Toby. Royal Botanic Garden Edinburgh; Reino UnidoFil: Sanderson, Michael J.. University of Arizona; Estados UnidosFil: Wojciechowski, Martin F.. Arizona State University; Estados UnidosFil: Boatwright, Stephen. University of the Western Cape; SudáfricaFil: Brown, Gillian. The University of Melbourne; AustraliaFil: Cardoso, Domingos. Universidade Estadual de Feira de Santana; BrasilFil: Crisp, Michael. Australian National University; AustraliaFil: Egan, Ashley. East Carolina University; Estados UnidosFil: Fortunato, Renée Hersilia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Hawkins, Julie. University of Reading; Reino UnidoFil: Kajita, Tadashi. Chiba University; JapónFil: Klitgaard, Bente. Royal Botanic Gardens; Reino UnidoFil: Koenen, Erik. Universitat Zurich; SuizaFil: Lavin, Matt. State University of Montana; Estados UnidosFil: Luckow, Melissa. Cornell University; Estados UnidosFil: Marazzi, Brigitte. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: McMahon, Michelle M.. University of Arizona; Estados UnidosFil: Miller, Joseph T.. Australian National Herbarium. CSIRO Plant Industry. Centre for Australian National Biodiversity Research; AustraliaFil: Murphy, Daniel J.. Royal Botanic Gardens Melbourne; AustraliaFil: Ohashi, Hiroyoshi. Tohoku University; JapónFil: Queiroz, Luciano P. de. Universidade Estadual de Feira de Santana; BrasilFil: Rico, Lourdes. Royal Botanic Gardens; Reino UnidoFil: Särkinen, Tiina. Natural History Museum; Reino UnidoFil: Schrire, Brian. Royal Botanic Gardens; Reino UnidoFil: Simon, Marcelo F.. Embrapa Recursos Genéticos e Biotecnologia; BrasilFil: Souza, Elvia R.. Universidade Estadual de Feira de Santana; BrasilFil: Steele, Kelly. Arizona State University; Estados UnidosFil: Torke, Benjamin M.. New York Botanical Garden; Estados UnidosFil: Wieringa, Jan J.. University of Agriculture Wageningen; Países Bajos. Wageningen University. Netherlands Centre for Biodiversity Naturalis; Países BajosFil: van Wyk, Ben Erik. University of Johannesburgo; SudáfricaFil: Legume Phylogeny Working Group. No especifica