Re-circumscription of the mimosoid genus Entada including new combinations for all species of the phylogenetically nested Elephantorrhiza (Leguminosae, Caesalpinioideae, mimosoid clade)

Recent phylogenomic analyses of 997 nuclear genes support the long-held view that the genus Entada is congeneric with Elephantorrhiza. Entada is resolved as monophyletic only if the genus Elephantorrhiza is subsumed within it. The two genera were distinguished solely by relatively minor differences in the mode of dehiscence of the fruits (a craspedium separating into one-seeded endocarp segments in Entada versus a craspedium with the whole fruit valve breaking away from the persistent replum in Elephantorrhiza) and the craspedial fruit type itself provides a shared synapomorphy for the re-circumscribed Entada. Here, we provide a synopsis of Entada, including 11 new combinations in total, for the eight species, one subspecies and one variety previously placed in Elephantorrhiza, as well as a new combination for a subspecies of Entada rheedei Spreng. not previously dealt with when Entada pursaetha DC. was placed in synonymy. These new combinations are: Entada burkei (Benth.) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada elephantina (Burch.) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada goetzei (Harms) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada goetzei subsp. lata (Brenan & Brummitt) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada obliqua (Burtt Davy) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada praetermissa (J.H. Ross) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada rangei (Harms) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada rheedei subsp. sinohimalensis (Grierson & D.G. Long) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada schinziana (Dinter) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada woodii (E. Phillips) S.A. O’Donnell & G.P. Lewis, comb. nov.; and Entada woodii var. pubescens (E. Phillips) S.A. O’Donnell & G.P. Lewis, comb. nov. We provide a revised circumscription of the genus Entada which now comprises 40 species distributed pantropically, with the greatest diversity of species in tropical Africa. We present a complete taxonomic synopsis, including a map showing the global distribution of the genus and photographs showing variation amongst species in habit, foliage, flowers and fruits. A short discussion about extrafloral nectaries, mainly observed in the Madagascan species, is presented

Disintegration of the genus Prosopis L. (Leguminosae, Caesalpinioideae, mimosoid clade)

Robust evidence from phylogenomic analyses of 997 nuclear genes has recently shown, beyond doubt, that the genus Prosopis is polyphyletic with three separate lineages, each with affinities to other genera of mimosoids: (i) Prosopis africana is an isolated lineage placed in the grade of Plathymenia, Newtonia and Fillaeopsis that subtends the core mimosoid clade; (ii) the remaining Old World species of Prosopis form a clade that is sister to the Indo-Nepalese monospecific genus Indopiptadenia and (iii) New World Prosopis has the Namibian / Namaqualand monospecific endemic genus Xerocladia nested within it. This means that it is now clear that maintaining the unity of the genus Prosopis sensu Burkart (1976) is no longer tenable. These three distinct lineages of Prosopis species correspond directly to Burkart’s (1976) sectional classification of the genus, to previously recognised genera and to the differences in types of armature that underpin Burkart’s sections. Here, we address this non-monophyly by resurrecting three segregate genera – Anonychium, Neltuma and Strombocarpa and provide 57 new name combinations where necessary, while maintaining the morphologically distinctive and geographically isolated genera Xerocladia and Indopiptadenia. The genus Prosopis itself is reduced to just three species and an emended description is presented. The impacts of these name changes for a genus of such high ecological and human use importance are discussed. These impacts are mitigated by clear differences in armature which facilitate identification and by potential benefits from the deeper biological understanding brought about by recognition of these divergent lineages at generic rank. We provide an identification key to genera and present a map showing the distributions of the segregate genera, as well as drawings and photos illustrating variation in armature and fruits

Re-circumscription of the mimosoid genus Entada including new combinations for all species of the phylogenetically nested Elephantorrhiza (Leguminosae, Caesalpinioideae, mimosoid clade)

Recent phylogenomic analyses of 997 nuclear genes support the long-held view that the genus Entada is congeneric with Elephantorrhiza. Entada is resolved as monophyletic only if the genus Elephantorrhiza is subsumed within it. The two genera were distinguished solely by relatively minor differences in the mode of dehiscence of the fruits (a craspedium separating into one-seeded endocarp segments in Entada versus a craspedium with the whole fruit valve breaking away from the persistent replum in Elephantorrhiza) and the craspedial fruit type itself provides a shared synapomorphy for the re-circumscribed Entada. Here, we provide a synopsis of Entada, including 11 new combinations in total, for the eight species, one subspecies and one variety previously placed in Elephantorrhiza, as well as a new combination for a subspecies of Entada rheedei Spreng. not previously dealt with when Entada pursaetha DC. was placed in synonymy. These new combinations are: Entada burkei (Benth.) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada elephantina (Burch.) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada goetzei (Harms) S.A. O’Donnell and G.P. Lewis, comb. nov.; Entada goetzei subsp. lata (Brenan & Brummitt) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada obliqua (Burtt Davy) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada praetermissa (J.H. Ross) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada rangei (Harms) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada rheedei subsp. sinohimalensis (Grierson & D.G. Long) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada schinziana (Dinter) S.A. O’Donnell & G.P. Lewis, comb. nov.; Entada woodii (E. Phillips) S.A. O’Donnell & G.P. Lewis, comb. nov.; and Entada woodii var. pubescens (E. Phillips) S.A. O’Donnell & G.P. Lewis, comb. nov. We provide a revised circumscription of the genus Entada which now comprises 40 species distributed pantropically, with the greatest diversity of species in tropical Africa. We present a complete taxonomic synopsis, including a map showing the global distribution of the genus and photographs showing variation amongst species in habit, foliage, flowers and fruits. A short discussion about extrafloral nectaries, mainly observed in the Madagascan species, is presented

Boliviadendron, a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the interior Andean valleys of Bolivia

Phylogenetic analyses of DNA sequence data sampling all species of Leucochloron alongside representatives of genera of the Inga and Albizia clades of the larger ingoid clade of mimosoid legumes (sensu Koenen et al. 2020) confirm the non-monophyly of the genus Leucochloron. We show that Leucochloron bolivianum is placed in the Albizia clade, while the remaining four species of Leucochloron are placed in the Inga clade, in line with previous results. To rectify this non-monophyly, L. bolivianum is segregated as the new genus, Boliviadendron, with a single species, Boliviadendron bolivianum, narrowly endemic to the interior Andean valleys of Bolivia. We illustrate this new segregate genus, present a map of its distribution and discuss the striking lack of morphological distinctions between Boliviadendron and Leucochloron, as well as the phylogenetic and morphological affinities of Boliviadendron to the genera Enterolobium and Albizia

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

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the “tree of life” are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species‐rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low‐copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well‐supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation

A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses

Background : Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene. Results: This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity. Conclusions: The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses

Botanical Monography in the Anthropocene

Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs — comprehensive systematic treatments of a family or genus — have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.Fil: Grace, Olwen M.. Royal Botanic Gardens, Kew; Reino UnidoFil: Pérez-Escobar, Oscar A.. Royal Botanic Gardens, Kew; Reino UnidoFil: Lucas, Eve J.. Royal Botanic Gardens, Kew; Reino UnidoFil: Vorontsova, Maria S.. Royal Botanic Gardens, Kew; Reino UnidoFil: Lewis, Gwilym P.. Royal Botanic Gardens, Kew; Reino UnidoFil: Walker, Barnaby E.. Royal Botanic Gardens, Kew; Reino UnidoFil: Lohmann, Lúcia G.. Universidade de Sao Paulo; BrasilFil: Knapp, Sandra. Natural History Museum; Reino UnidoFil: Wilkie, Peter. Royal Botanic Gardens; Reino UnidoFil: Sarkinen, Tiina. Royal Botanic Gardens; Reino UnidoFil: Darbyshire, Iain. Royal Botanic Gardens; Reino UnidoFil: Lughadha, Eimear Nic. Royal Botanic Gardens; Reino UnidoFil: Monro, Alexandre. Royal Botanic Gardens; Reino UnidoFil: Woudstra, Yannick. Universidad de Copenhagen; Dinamarca. Royal Botanic Gardens; Reino UnidoFil: Demissew, Sebsebe. Addis Ababa University; EtiopíaFil: Muasya, A. Muthama. University Of Cape Town; SudáfricaFil: Díaz, Sandra Myrna. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Baker, William J.. Royal Botanic Gardens, Kew; Reino UnidoFil: Antonelli, Alexandre. University of Oxford; Reino Unido. University Goteborg; Sueci