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

Mezcala – a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the Balsas Depression in Mexico

Recent results have demonstrated that the genus Desmanthus is non-monophyletic because the genus Kanaloa is nested within it, with a single species, Desmanthus balsensis placed as sister to the clade comprising Kanaloa plus the remaining species of Desmanthus. Here we transfer D. balsensis to a new segregate genus Mezcala, discuss the morphological features supporting this new genus, present a key to distinguish Mezcala from closely related genera in the Leucaena subclade, and provide a distribution map of M. balsensis

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

Extrafloral nectaries in Leguminosae: phylogenetic distribution, morphological diversity and evolution

Extrafloral nectaries (EFNs) mediating ecologically important ant-plant protection mutualisms are especially common and unusually diverse in the Leguminosae. We present the first comprehensively curated list of legume genera with EFNs, detailing and illustrating their systematic and phylogenetic distributions, locations on the plant, morphology and anatomy, based on a unified classification of EFN categories and a time-calibrated phylogeny incorporating 710 of the 768 genera. This new synthesis, the first since McKey (1989)?s seminal paper, increases the number of genera with EFNs to 152 (20% of legumes), distributed across subfamilies Cercidoideae (1), Detarioideae (19), Caesalpinioideae (87) and Papilionoideae (45). EFNs occur at nine locations, and are most prevalent on vegetative plant parts, especially leaves (74%) and inflorescence axes (26%). Four main categories (with eight subcategories) are recognized: formless, trichomatic (exposed, hollow), parenchymatic (embedded, pit, flat, elevated) and abscission zone EFNs (non-differentiated, swollen scars). Phylogenetic reconstruction of EFNs suggests independent evolutionary trajectories of different EFN types, with elevated EFNs restricted almost exclusively to Caesalpinioideae (where they underwent spectacular morphological disparification), flat EFNs in Detarioideae, swollen scar EFNs in Papilionoideae, and Cercidoideae is the only subfamily bearing intrastipular EFNs. We discuss the complex evolutionary history of EFNs and highlight future research directions.Fil: Marazzi, Brigitte. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina. Natural History Museum Of Canton Ticino; SuizaFil: González, Ana María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Delgado Salinas, Alfonso. Universidad Nacional Autónoma de México; MéxicoFil: Luckow, Melissa A.. Cornell University; Estados UnidosFil: Ringelberg, Jens J.. Universitat Zurich; SuizaFil: Hughes, Colin E.. Universitat Zurich; Suiz

Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider ingoid clade (Leguminosae, Caesalpinioideae)

The Indo-Pacific legume genus Serianthes was recently placed in the Archidendron clade (sensu Koenen et al. 2020), a subclade of the mimosoid clade in subfamily Caesalpinioideae, which also includes Acacia, Archidendron, Archidendropsis, Falcataria, Pararchidendron, Paraserianthes and Wallaceodendron. Serianthes comprises ca. 18 species, five subspecies and two varieties that are characterised by bipinnately compound leaves with alternate sessile leaflets, branched axillary corymbiform panicles and woody indehiscent pods. Generic relationships, as well as species relationships within genera in the Archidendron clade, remain uncertain. While the sister relationship between Serianthes and the genus Falcataria is strongly supported by molecular data, the distinction between Serianthes and the monotypic genus Wallaceodendron has been questioned, based on their similar flower and fruit morphologies. We combined three gene-enriched hybrid capture DNA sequence datasets (generated from the 964 mimobaits v1 probe set, the expanded 997 mimobaits v2 probe set and the GoFlag angiosperm 408 probe set) and used their overlapping markers (77 loci of the target exonic and flanking regions) to test the monophyly of Serianthes and to investigate generic relationships within the Archidendron clade using 55 ingoid plus two outgroup taxa. We show that Serianthes is monophyletic, confirm the Serianthes + Falcataria sister relationship to Wallaceodendron and recognise this combined clade as the Serianthes clade within the Archidendron clade. We also evaluated the use of overlapping loci across datasets in combination with concordance analyses to test generic relationships and further investigate previously unresolved relationships across the wider ingoid clade. Concordance analysis revealed limited gene tree conflicts near the tips of the Archidendron clade, but increased discordance at the base of the clade, which could be attributed to rapid lineage divergence (radiation) and/or incomplete lineage sorting

Dilemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy?

Senegalia comprises 219 species distributed in tropical and subtropical regions of North and South America, Africa, Asia and Australia. Two sections are currently recognised within Senegalia and these are most readily distinguished by the differences in disposition of their cauline prickles, i.e. sect. Senegalia with prickles at or near leaf nodes and sect. Monacanthea with mostly internodal prickles. Previous phylogenetic studies, based primarily on small numbers of plastid DNA loci, found Senegalia to be monophyletic with two large subclades corresponding to the sections. Here, we present new phylogenomic evidence from 997 single-copy nuclear gene sequences for a small, but representative set of species. These new analyses show that Senegalia is non-monophyletic, but instead, forms a grade that is paraphyletic with respect to the remainder of the ingoid clade (i.e. Ingeae + Acacia s.s. + Acaciella), comprising two well-supported subclades most likely representing the same clades as found in previous phylogenetic studies of the genus and, interspersed between these, a third, moderately supported clade, comprising the genera Mariosousa, Pseudosenegalia and Parasenegalia. In marked contrast to the nuclear phylogeny, the two Senegalia clades are sister groups in the plastid phylogeny, based on analyses of 72 chloroplast genes, rendering the genus monophyletic, based on plastid data alone. We discuss this new evidence that Senegalia is non-monophyletic in relation to the marked cytonuclear discordance, high gene tree conflict and lack of resolution across this senegalioid grade and review the consistency of the key morphological characters distinguishing the two sections of Senegalia. We conclude that it is likely that Senegalia will need to be split into two (or possibly more) genera: a re-circumscribed Senegalia s.s. that corresponds to the existing Senegalia sect. Senegalia plus the S. ataxacantha group (Senegalia sect. Monacanthea s.s.; future studies may show that this group warrants generic status) and a new genus corresponding to the remainder of sect. Monacanthea (here designated as Senegalia sect. Monacanthea p.p.). However, re-delimiting Senegalia now would be premature given that the key morphological characters are not fully congruent with the two sections and pending denser phylogenetic sampling of taxa. A judiciously selected list of critical taxa is presented to facilitate future phylogenomic studies. Finally, we discuss the identity of Albizia leonardii, which is also placed in this senegalioid grade in these new phylogenomic analyses and place it in synonymy with Parasenegalia vogeliana

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

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

Early natural historians – Compte de Buffon, von Humboldt and De Candolle – established ecology 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, an pantropical plant clade of 3,400 species, we show that the water availability gradient from deserts to rainforests 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.Fil: Ringelberg, Jens J. University of Zurich. Department of Systematic and Evolutionary Botany; SuizaFil: Koenen, Erik J.M. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza. Université Libre de Bruxelles. Faculté des Sciences. Evolutionary Biology & Ecology; BélgicaFil: Sauter, Benjamín. University of Zurich. Department of Systematic and Evolutionary Botany; SuizaFil: Aebli, Anahita. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza. Abteling Umweltschutz und Energie. Departement Bau und Umwelt; SuizaFil: Rando, Juliana G. Universidade Federal do Oeste da Bahia. Centro das Ciências Biológicas e da Saúde. Programa de Pós Graduação em Ciências Ambientais; BrasilFil: Iganci, João R. Universidade Federal de Pelotas. Campus Universitário Capão do Leão. Instituto de Biologia; Brasil. Universidade Federal do Rio Grande do Sul. Programa de Pós-Graduação em Botânica; BrasilFil: de Queiroz, Luciano P. Universidade Estadual de Feira de Santana. Departamento Ciências Biológicas; BrasilFil: Murphy, Daniel J. Royal Botanic Gardens Victoria: AustraliaFil: Gaudeul, Myriam. Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA: FranciaFil: Bruneau, Anne. Université de Montréal. Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques; CanadáFil: Luckow, Melissa. Cornell University. School of Integrative Plant Science. Plant Biology Section; Estados UnidosFil: Morales, Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentin

New segregates from the Neotropical genus Stryphnodendron (Leguminosae, Caesalpinioideae, mimosoid clade)

Non-monophyly is a prominent issue in mimosoid legumes, even in some of the less speciose genera such as the neotropical genus Stryphnodendron. This genus includes 35 species occurring from Nicaragua to Southern Brazil mostly in humid forests and savannas. Previous taxonomic studies of Stryphnodendron have highlighted morphologically distinct groups within the genus, recognized by differences on leaves (number of pinnae and size of leaflets), inflorescences (a simple or compound thyrse), and fruit types (legume, nucoid legume or follicle). Recent phylogenetic analyses have confirmed the non-monophyly of Stryphnodendron, supporting the recognition of three independent and morphologically well-delimited genera. Here we re-circumscribe Stryphnodendron and propose the two new genera Gwilymia and Naiadendron. In addition, we also provide an updated taxonomic account of the closely related genus Microlobius, including the proposal of a lectotype for the single species in the genus