Marianne M. le Roux

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Phylogenetic Relationships of Tribe Crotalarieae (Fabaceae) Inferred from DNA Sequences and Morphology

Abstract Tribe Crotalarieae is a large and diverse group of papilionoid legumes that largely occur in Africa. A systematic study of generic relationships within the tribe was undertaken using nucleotide sequences from the internal transcribed spacer (ITS) of nuclear ribosomal DNA, the plastid gene rbcL, and morphological data. The Crotalarieae are supported strongly as monophyletic and sister to the tribe Genisteae. Lebeckia, Lotononis, and Wiborgia are all paraphyletic in the molecular analyses and morphological data support the division of Lebeckia into three more natural genera (one of which includes the monotypic North African Spartidium). Four major lineages were identified within the tribe based on sequence data: the “Cape” group, comprising Aspalathus, Lebeckia, Rafnia, Spartidium, and Wiborgia; the Lotononis group, comprising Lotononis pro parte, Pearsonia, Robynsiophyton, and Rothia; a group comprising Lotononis section Leptis, L. section Listia, and allies; and the Crotalaria group, comprising Bolusia, Crotalaria, and Lotononis hirsuta (Lotononis section Euchlora). Morphological analysis yields a similar topology, except that Lotononis is monophyletic if L. hirsuta were excluded. When the molecular and morphological data sets are combined, the same major clades are retrieved as in the molecular analysis, with the notable exception that Lotononis and Lebeckia senso stricto are supported as monophyletic. The results from this study have important implications for the classification of the tribe Crotalarieae and present an important step towards a natural and phylogenetic generic classification for the tribe.

A global infrageneric classification system for the genus Crotalaria (Leguminosae) based on molecular and morphological evidence.

Crotalaria is a large genus of 702 species with its centre of diversity in tropical Africa and Madagascar and secondary radiations in other parts of the world. The current infrageneric classification system is based on morphological and morphometric studies of the African taxa only and is here re-evaluated using a phylogenetic approach. DNA sequences derived from the nuclear ITS and the plastid matK, psbA-trnH and rbcLa markers were analyzed using parsimony and model-based (Bayesian) approaches. The resultant molecular phylogeny allowed for a new interpretation of diagnostically important morphological characters, including specialisations of the calyx, keel, standard petal and style, which are variously convergent in several unrelated infrageneric groups. Of particular interest is the congruence between the new phylogeny and the distribution of standard petal callosity types. A sectional classification system for the entire genus is proposed for the first time. The new system that is formalised here comprises eleven sections: Amphitrichae, Calycinae, Crotalaria, Geniculatae, Glaucae, Grandiflorae, Hedriocarpae, Incanae, Schizostigma, Borealigeniculatae and Stipulosae. Sectional limits of the Geniculatae, Calycinae and Crotalaria are modified. The subsections Stipulosae, Glaucae and Incanae are raised to sectional level, while some groups previously recognized as subsections are abandoned due to non-monophyly (subsections Chrysocalycinae, Hedriocarpae, Macrostachyae and Tetralobocalyx). Two new sections are recognized, Amphitrichae and Borealigeniculatae.

Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci.

The genus Bradyrhizobium contains predominantly nitrogen-fixing legume symbionts. Phylogenetic analysis of the genes responsible for their symbiotic abilities (i.e., those encoded on the nodulation [nod] and nitrogen-fixation [nif] loci) has facilitated the development of an extensive phylogeographic framework for the genus. This framework however contains only a few nodulating isolates from Africa. Here we focused on nodulating Bradyrhizobium isolates associated with native southern African legumes in the tribes Genisteae and Crotalarieae found along the Great Escarpment in the Mpumalanga Province of South Africa. The aims of this study were to: (1) obtain rhizobial isolates from legumes in the Genisteae and Crotalarieae; (2) verify their nodulation ability; (3) characterize them to species level based on phylogenetic analyses of several protein coding gene regions (atpD, dnaK, glnII, recA, rpoB and gyrB) and (4) determine their placement in the phylogeographic framework inferred from the sequences of the symbiotic loci nodA and nifD. Twenty of the 21 Bradyrhizobium isolates belonged to six novel species, while one was conspecific with the recently described B. arachidis. Among these isolates, the nodA phylogeny revealed several new clades, with 18 of our isolates found in Clades XIV and XV, and only three forming part of the cosmopolitan Clade III. These strains formed predominantly the same groups in the nifD phylogeny although with slight differences; indicating that both vertical and horizontal inheritance of the symbiotic loci occurred. These findings suggest that the largely unexplored diversity of indigenous African rhizobia are characterized by unique ancestries that might mirror the distribution of their hosts and the environmental factors driving their evolution.

Creating an Online World Flora by 2020: a perspective from South Africa

At the 10th Conference of the Parties of the Convention on Biodiversity (CBD), which was held in Nagoya, Japan, in October 2010, an updated Global Strategy for Plant Conservation (GSPC) was adopted as part of the plan of work of the CBD. Target 1 of the GSPC aims to produce an online Flora for all the plants of the world by 2020. Governments that have ratified the CBD will have to report over the next several years on progress towards achieving this challenging target. Floras are still widely regarded as a means of providing descriptive information and identification tools for the plants that occur in a specified region. Historically, Floras have included identification keys; scientific names with authorship for all taxa known to occur in the area; synonymy; descriptions; distributions within the region in question; specimen citations; habitat; literature references; and illustrations. Of these, nomenclature, descriptions, identification tools, illustrations and distributions are critical components. The approach being taken by South Africa, a biodiversity-rich country, in working towards achieving Target 1 of the GSPC by 2020 is presented and discussed, outlining a methodology that may be of practical use to other countries. We hope this will urge other countries to consider how they might meet this challenging conservation target.

Producing a plant diversity portal for South Africa

The National Research Foundation (grant reference number: UID92629) and Royal Society (grant reference number: SA140038) are thanked for the funding that was awarded to host an e-Flora workshop in South Africa.

A Taxonomic Revision of Amphitrichae, a New Section of Crotalaria (Fabaceae)

Abstract Crotalaria sect. Amphitrichae is described as new to give formal recognition to a strongly supported clade revealed by a recent molecular systematic study. The five known species are restricted to the arid western parts of southern Africa (C. colorata, C. excisa, C. humilis, C. meyeriana, and C. pearsonii). Species of the section are morphologically distinct in having (1) hairs distributed all around the distal part of the style; (2) ridge callosities on the standard petal blade and claw; (3) a rounded keel; (4) a twisted keel beak; and (5) a rounded style. A cladistic analysis of 18 morphological characters resulted in a well-resolved cladogram that recovers relationships within the section. The study revealed that two new species should be recognised, described here as C. giessii and C. kolbergii. A taxonomic revision of the section is presented, with descriptions, diagnostic characters, distribution maps, and illustrations of all seven recognised species.