Phylogenetic Implications of a Unique 5.8S nrDNA Insertion in Cyperaceae

The purpose of this study was to assess the phylogenetic utility of a large insertion (3 bp) in the 5.8S gene of nuclear ribosomal DNA (nrDNA) in Cyperaceae and selected Juncaceae. This was done by reconstructing the character evolution of the insertion on a phylogeny derived from rbcL sequences. Results suggest that the insertion was gained once at the base of Cyperaceae followed by multiple losses in its most-derived taxa. Despite several homoplastic losses (CI = 0.20), the pattern of insertion loss (RI = 0.88), and base pair variation within the insertion were useful for defining sedge clades at various taxonomic levels. For example, whereas a loss of the insertion appeared to characterize a major terminal clade within Cyperaceae, both an insertion loss and sequence variation were consistent with infrageneric clades previously discovered in an ITS phylogeny of Eleocharis. The presence/absence of the insertion also supported previous conclusions based on morphological and molecular data that tribe Scirpeae and Scirpus s.l. are polyphyletic. In the context of our current understanding of Cyperaceae relationships, evolutionary patterns related to this insertion provide additional support for groups defined in prior phylogenetic analyses. The present analysis also suggests that the controversial position of Oxychloe andina (Juncaceae) in previous rbcL analyses, as sister to Cyperaceae (Y12978) or as nested within Cyperaceae (U49222), is due to the fact that Y12978 is a Juncaceae/Cyperaceae chimera, whereas U49222 is the sequence of a Cyperaceae contaminant. When U49222 is excluded from analyses and the Cyperaceae portion of Y12978 is removed, Juncaceae and Cyperaceae are monophyletic with Oxychloe positioned within a Juncaceae clade of single-flowered genera

Revision of the Afro-Madagascan genus Costularia (Schoeneae, Cyperaceae) : infrageneric relationships and species delimitation

A recent molecular phylogenetic study revealed four distinct evolutionary lineages in the genus Costularia s.l. (Schoeneae, Cyperaceae, Poales). Two lineages are part of the Oreobolus Glade of tribe Schoeneae: the first being a much-reduced genus Costularia s.s., and the second a lineage endemic to New Caledonia for which a new genus Chamaedendron was erected. The other two lineages were shown to be part of the Tricostularia Glade of tribe Schoeneae. Based on morphological and molecular data, the genus Costularia is here redelimited to represent a monophyletic entity including 15 species, which is restricted in distribution to southeastern Africa (Malawi, Mozambique, South Africa, Swaziland, Zimbabwe), Madagascar, the Mascarenes (La Reunion, Mauritius), and the Seychelles (Mahe). Molecular phylogenetic data based on two nuclear markers (ETS, ITS) and a chloroplast marker (trnL-F) resolve the studied taxa as monophyletic where multiple accessions could be included (except for Costularia laxa and Costularia purpurea, which are now considered conspecific), and indicate that the genus dispersed once to Africa, twice to the Mascarenes, and once to the Seychelles. Two endemic species from Madagascar are here described and illustrated as new to science, as is one additional species endemic to La Reunion. Two taxa previously accepted as varieties of Costularia pantopoda are here recognised at species level (Costularia baronii and Costularia robusta). We provide a taxonomic revision including an identification key, species descriptions and illustrations, distribution maps and assessments of conservation status for all species

Biogeographical patterns of legume-nodulating <i>Burkholderia </i>spp.:from African Fynbos to continental scales

UNLABELLED: Rhizobia of the genus Burkholderia have large-scale distribution ranges and are usually associated with South African papilionoid and South American mimosoid legumes, yet little is known about their genetic structuring at either local or global geographic scales. To understand variation at different spatial scales, from individual legumes in the fynbos (South Africa) to a global context, we analyzed chromosomal (16S rRNA, recA) and symbiosis (nifH, nodA, nodC) gene sequences. We showed that the global diversity of nodulation genes is generally grouped according to the South African papilionoid or South American mimosoid subfamilies, whereas chromosomal sequence data were unrelated to biogeography. While nodulation genes are structured on a continental scale, a geographic or host-specific distribution pattern was not detected in the fynbos region. In host range experiments, symbiotic promiscuity of Burkholderia tuberum STM678(T) and B phymatum STM815(T) was discovered in selected fynbos species. Finally, a greenhouse experiment was undertaken to assess the ability of mimosoid (Mimosa pudica) and papilionoid (Dipogon lignosus, Indigofera filifolia, Macroptilium atropurpureum, and Podalyria calyptrata) species to nodulate in South African (fynbos) and Malawian (savanna) soils. While the Burkholderia-philous fynbos legumes (D lignosus, I filifolia, and P calyptrata) nodulated only in their native soils, the invasive neotropical species M pudica did not develop nodules in the African soils. The fynbos soil, notably rich in Burkholderia, seems to retain nodulation genes compatible with the local papilionoid legume flora but is incapable of nodulating mimosoid legumes that have their center of diversity in South America. IMPORTANCE: This study is the most comprehensive phylogenetic assessment of root-nodulating Burkholderia and investigated biogeographic and host-related patterns of the legume-rhizobial symbiosis in the South African fynbos biome, as well as at global scales, including native species from the South American Caatinga and Cerrado biomes. While a global investigation of the rhizobial diversity revealed distinct nodulation and nitrogen fixation genes among South African and South American legumes, regionally distributed species in the Cape region were unrelated to geographic and host factors.status: publishe

DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera

Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK + rbcLa) dataset as a better barcode than single regions. We found a high score (100%) of correct identification of individuals to their respective genera but very low score (<50%) in identifying them to species. We found a considerable match (54%) between genetic species and morphologicallydelimited species. We also found that different lineages showed a weak but significant phylogenetic conservatism in their response to fire as reseeders or resprouters, with more clustering of resprouters than would be expected by chance. These novel microevolutionary patterns might be acting continuously over time to produce multi-scale regularities of biodiversity. This study provides the first insight into the DNA barcoding campaign of land plants in species identification and detection of phylogenetic signal in recently diverged lineages of the CFR.The South African National Research Foundation (NRF; AMM); Nigeria Tertiary Education Trust Fund (NTETF) / Umaru Musa Yar’adua University Katsina, Nigeria (Fellowship Grant; A. Bello); and University of Cape Town, J. W. Jagger Centenary Gift Scholarship (to A. Bello).http://aobpla.oxfordjournals.orgam2016Physiotherap

First molecular phylogenetic insights into the evolution of Eriocaulon (Eriocaulaceae, Poales)

Eriocaulon is a genus of c. 470 aquatic and wetland species of the monocot plant family Eriocaulaceae. It is widely distributed in Africa, Asia and America, with centres of species richness in the tropics. Most species of Eriocaulon grow in wetlands although some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. In a previous molecular phylogenetic hypothesis, Eriocaulon was recovered as sister of the African endemic genus Mesanthemum. Several regional infrageneric classifications have been proposed for Eriocaulon. This study aims to critically assess the existing infrageneric classifications through phylogenetic reconstruction of infrageneric relationships, based on DNA sequence data of four chloroplast markers and one nuclear marker. There is little congruence between our molecular results and previous morphology-based infrageneric classifications. However, some similarities can be found, including Fyson’s sect. Leucantherae and Zhang’s sect. Apoda. Further phylogenetic studies, particularly focusing on less well sampled regions such as the Neotropics, will help provide a more global overview of the relationships in Eriocaulon and may enable suggesting the first global infrageneric classification