South African Taxa Research Articles

RAD sequencing, morphometry and synecology clarify the taxonomy of the Melica ciliata (Poaceae) complex in France and Poland

AbstractMelica (Poaceae) consist of about 92 species distributed across temperate regions of the world. Within section Dalycum, Melica ciliata sensu lato forms a taxonomic complex of several species and subspecies with clinal morphological variation causing conflicting identifications. To resolve taxonomic confusion, we used three complementary approaches, through molecular, morphological, and phytoecological analyses. The double‐digest restriction‐associated DNA markers significantly support the monophyly of three taxa: (i) the Mediterranean Melica magnolii, (ii) the Eurasian Melica transsilvanica subsp. transsilvanica, and (iii) the west‐European M. ciliata subsp. glauca. This differentiation is corroborated by the analysis of 22 morphometric variables. Furthermore, phytoecological analysis of 221 floristic inventories revealed habitat distinctions among these taxa. Our approach of integrative taxonomy argues for a specific distinction for these three taxa, and we include a key to separate these forms. These new molecular data on the section Dalycum, subsection Ciliatae, call for further phylogenetic analyses including samples of M. ciliata subsp. ciliata and other East‐Mediterranean and South African taxa.

Taxonomic identity and evolutionary relationships of South African taxa related to the Spergularia media group (Caryophyllaceae)

The taxonomic identity and phylogenetic relationships of several South African perennial taxa often synonymised to the European Spergularia media are discussed. In particular, the case of Arenaria glandulosa Jacq., a species described as native to the Cape region of South Africa, was revisited. We found this taxon to be a Spergularia, endemic to salt-laden coastal (and rarely also saline inland) habitats of the Western Cape and Eastern Cape provinces of South Africa. This taxon is a prostrate to procumbent caespitose herb, densely glandulous all over, with small flowers solitary at the base of each leaf-like bract or in congested dichasial cymes, producing petals about equalling the sepals and free styles, among other characters. Further, we describe a morphologically similar species (often mistaken for S. media and S. bocconei) occurring in succulent Karoo scrub of Namaqualand, as a new species, named S. namaquensis. Both are glandulous dwarf subshrubs considerably differing from the recently discovered S. quartzicola, a soil-specialist endemic from Namaqualand quartzitic outcrops, by many notable vegetative and reproductive features. Molecular analyses of plastid (trnL–trnF region) and nuclear ribosomal (5.8S-ITS2 region) DNA sequence data support the morphological differentiation between the South African species S. glandulosa, S. namaquensis and S. quartzicola, representing an independent lineage when compared with the Northern Hemisphere members of the S. maritima group. Synonymy, new complete descriptions and ecological and distributional data are provided to facilitate further identification of species within the putative S. media group.

Resolving the taxonomic identities and genetic structure of two cryptic Platynereis Kinberg species from South Africa

The perceived cosmopolitanism of polychaete worms could be an artefact of historical factors such as poor original species descriptions, lack of type material and the European taxonomic bias, to name a few. Thus, it is possible that several cosmopolitan species hide complexes of cryptic and pseudocryptic species. Two putative cosmopolitan species, Platynereis dumerilii and Platynereis australis, collected in South Africa were investigated here (1) to determine whether the South African taxa are conspecific with the morphologically identical taxa from France and New Zealand (the respective type localities of P. dumerilii and P. australis), (2) to compare the South African species morphometrically to determine whether their morphological characters are reliable enough to separate them, and (3) to investigate whether these species have geographically structured populations along the coast of South Africa. Molecular data (COI and ITS1) confirm that P. dumerilii and P. australis do not occur in South Africa. Instead, the South African taxon formerly thought to be Platynereis dumerilii is new and is described here as Platynereis entshonae, sp. nov.; the identity of the other South African species is currently unresolved and is treated here as Platynereis sp. Surprisingly, Platynereis massiliensis (type locality: Marseilles) nested within the South African Platynereissp. clade but, since it is part of a cryptic species complex in the Mediterranean, the name is considered doubtful. Morphological characters traditionally used to define these South African Platynereis species are not reliable as predefined morphological groupings do not match phylogenetic clades and principal component scores revealed no separation in morphological characters that could distinguish between them. Haplotype networks and phylogenetic trees revealed that P. entshonae, sp. nov. and Platynereis sp. have geographically structured populations along the South African coast. http://zoobank.org/urn:lsid:zoobank.org:pub:6E36A210-9E48-430F-8A93-EDC27F0C5631

Ficinia pygmaea is not conspecific with F. limosa, and a description of a new species of Ficinia (Cyperaceae) from South Africa

The taxonomy of several species allied to Ficinia pygmaea, that are perennials of small stature (typically under 100 mm) and with a capitate inflorescence, is contentious. Recent authors have considered Ficinia pygmaea to be conspecific with F. limosa, and these South African taxa have been thought to be allied to the Ethiopian taxon F. clandestina. Examination of herbarium specimens and further field studies supports recognition of F. pygmaea and F. limosa at species rank. An additional allied species, putatively named F. echinata in several herbaria, occurring in the Cape Agulhas area, is described. Ficinia echinata is a rigid tufted plant growing at the edges of coastal salt pans and is distinguished by its sharply pointed leaves and bract apices, and its glume morphology. The interpretation of the morphology of F. echinata as intermediate between F. pygmaea and F. limosa had influenced the decision to merge the two taxa.

<p><strong>A new <em>Disperis</em> (Orchidoideae; Orchidaceae) for the flora of the Mascarenes</strong></p>

Disperis was established by Swartz (1800: 218), and there is little doubt that the genus is monophyletic in morphological and molecular (Waterman et al. 2009) terms. Kurzweil & Manning (2005) proposed two subgenera, subgenus Dryorkis (Thouars) Kurzweil & Manning (2005: 172), comprising the species in the tropics and subtropics of Africa, Madagascar and Asia, and subgenus Disperis with mostly the South African taxa. Disperis currently includes 80 species distributed in sub-Saharan Africa, Madagascar and the adjacent islands of the Indian Ocean (la Croix et al. 2002, Manning & Kurzweil 2005, Govaerts, 2019) and one widespread species in tropical Asia (Kurzweil & Manning 2005). The highest diversity is found in the humid tropics of Africa, the Cape Floristic Region and Madagascar, with little species overlap between these regions (Kuzrweil & Manning, 2005). So far, four species have been confirmed for the Mascarenes (la Croix et al. 2002). However, the presence of Disperis similis Schlechter (1924: 111) is doubtful because no picture or herbarium specimen documenting its presence on the Mascarenes is available. All four species also occur on Madagascar. Here, we report the presence of a fifth species of this genus for the Mascarenes.

Taxonomic notes on the Rhynchosia densiflora group (Phaseoleae, Fabaceae) in South Africa and its segregation from Rhynchosia section Arcyphyllum

Background: Rhynchosia section Arcyphyllum is one of the five sections of Rhynchosia as currently circumscribed. Previous studies in South Africa placed two species of Rhynchosia in this section. Some authors treated the species as a group rather than a section, to avoid phytogeographical confusion because the section is based on the North American generic name Arcyphyllum.Objectives: To formally remove the South African taxa from section Arcyphyllum and to provide diagnostic features for these taxa, a key to the subspecies, distribution maps and an illustration of their morphological features.Methods: Observations were made on herbarium specimens housed at NH, NU and PRE. Several field trips were undertaken in search of Rhynchosia connata. Morphological and anatomical features were studied and measurements of characters recorded.Results: In South Africa, the section was until now represented by two species, Rhynchosia densiflora (subsp. chrysadenia) and R. connata. These were separated primarily on stem indumentum, stipule shape, petiole length, leaflet shape and apices. However, this study revealed that there are no clear discontinuities between the two taxa apart from the lobes of the uppermost calyx lip, which are connate more than halfway in R. connata and up to halfway in R. densiflora subsp. chrysadenia. Therefore, R. connata is here relegated to varietal level as R. densiflora subsp. chrysadenia var. connata (Baker f.) Jaca & Moteetee.Conclusions: Two varieties of Rhynchosia densiflora subsp. chrysadenia occur in South Africa and are treated as part of the R. densiflora group instead of section Arcyphyllum.

Temporal changes in threatened ephemeral claypans over annual and decadal timescales in south-west Australia

The vegetation of the ephemeral claypans of south-west Australia were first described over 100 years ago. Since then they have been almost totally cleared for agriculture and urban development and are currently listed as critically endangered. These claypans have many similarities with ephemeral wetlands found in other Mediterranean climate regions with significant species turnover both within and between claypans and fine scale patterning highly correlated with micro-topography. Although annual variation in species composition was apparent there was also a consistent trend of increasing exotic taxa richness due to higher recruitment rates. This increasing exotic richness is of note, as the major threat to these communities is the invasion by a small number South African taxa, which can establish dense monocultures across these wetlands. Over the last two decades these invasive taxa have spread into 37% of the previously non-invaded quadrats. As remnant size was not a good predictor of their occurrence all remnants should be considered vulnerable. Management of these invasive taxa will be the major conservation issue in these threatened wetlands into the future.

The cervical spine of Australopithecus sediba

Cervical vertebrae are rare in the early hominin fossil record, presenting a challenge for understanding the evolution of the neck and head carriage in hominin evolution. Here, we examine the cervical vertebrae of Australopithecus sediba, which unlike other South African taxa is known from associated cervical vertebrae. The A. sediba cervical vertebrae exhibit human-like values for wedging, pedicle cross-sectional areas, and articular facet heights, indicating reduced ventral loading relative to African apes. These features combine with a pattern of vertebral body bone distribution and caudally progressive size expansion suggesting a mode of cervical lordosis, load mitigation, and head carriage similar to humans and distinct from the cantilevered mode of head carriage of the extant African great apes. Yet these derived features in A. sediba are accompanied by ape-like vertebral body and dorsal pillar sizes, articular facet orientation, and uncinate process morphology signaling reduced lateral and rotational coupled movements between vertebral elements and indicate a considerably stiffer neck than in humans. A primitively long and horizontally-oriented C7 spinous process is likely related to a prognathic viscerocranium, although the complimentary C3 spinous process is short, implying large moments emanating from scapular and shoulder elevators rather than large muscles of head stabilization. Cross-sectional spinous process shape and robust anterior tubercles similarly signal increased arm elevation consistent with climbing behavior in corroboration with arboreal signatures previously observed in the shoulder, arms, and hand of A. sediba. Spinal canal shape and size suggests that A. sediba lacked the cervical spinal cord enlargement of Homo that confers humans with enhanced motor control to the upper limbs. The cervical spine of A. sediba thus presents a mosaic of primitive and derived characters, with anatomical features relating to neck posture and head carriage mirroring humans juxtaposed with most other aspects of functional anatomy that resemble chimpanzees.

Pathogenicity of South African Hymenochaetales taxa isolated from esca-infected grapevines.

Little is known about the pathogenicity and etiology of Hymenochaetales taxa associated with esca in South Africa. Ten South African Hymenochaetales taxa associated with esca in grapevine were subjected to basic enzyme assays to determine which ligninolytic enzymes were secreted by each taxon. In addition, a field trial was undertaken to determine the pathogenicity of these taxa. Twenty-seven fungal isolates and two negative controls were inoculated into wounds made on mature grapevines of the cultivars Shiraz and Mourvedre. Inoculated vines were evaluated for white rot symptoms after 24 months. The results of the enzyme assays indicated a difference in enzyme secretion among taxa and also between isolates of the same taxa. All isolates secreted cellulase and laccase, but there was a difference in isolates’ ability to secrete manganese peroxidase and lignin peroxidase. The results of the pathogenicity trial showed that all of the isolates used were capable of causing the characteristic white rot symptom in the wood. There were clear differences in susceptibility to white rot between the two cultivars tested, namely Shiraz and Mourvedre. The cultivars also differed in which taxa proved to be more virulent. On Shiraz a specific isolate of Taxon 6 (an Inonotus sp.), Phellinus sp . and Inonotus setuloso-croceus were significantly virulent. On Mourvedre, Taxon 3 (an Inocutis sp.) was significantly virulent.

Co‐invasion of South African ecosystems by an Australian legume and its rhizobial symbionts

AbstractAimTo determine and compare the taxonomic identity and diversity of root nodule and rhizospheric microbial symbionts associated with Acacia pycnantha Benth. in its native (Australian) and invasive (South African) ranges, and to establish whether these associations are general or host specific.LocationThe native range of A. pycnantha in Australia and invasive ranges in South Africa and Western Australia.MethodsBacteria were isolated from root nodules collected from 18 populations of A. pycnantha. Repetitive element polymerase chain reaction (REP‐PCR) fingerprinting was used to assess overall bacterial diversity and clustering. Molecular phylogenies for a subset of isolates representing major REP‐PCR clades were reconstructed using maximum parsimony and Bayesian phylogenetic analyses of the nuclear 16S–23S rRNA intergenic spacer (IGS), 16S rRNA, and the symbiotic nodA genes.ResultsTwelve clusters were identified from the REP‐PCR analysis; 11 included isolates from both the native range in Australia and invasive range in South Africa, while one cluster comprised only Australian isolates. Six rhizobial species were found in association with A. pycnantha: Bradyrhizobium japonicum, Rhizobium gallicum, R. lusitanum, R. miluonense, R. multihospitium and R. tropici. We also identified three plant‐growth promoting bacteria isolated from root nodules of A. pycnantha: Burkholderia caledonica, B. graminis and B. phytofirmans. Phylogenetic analysis of the IGS gene retrieved clades containing symbionts from both Australia and South Africa while others comprised only South African taxa, suggesting the introduction of bacterial lineages from Australia to South Africa. Our phylogeographic analysis of the nodA gene confirmed that A. pycnantha was co‐introduced with its symbionts to South Africa.Main conclusionsAcacia pycnantha is a promiscuous legume, associated with at least six different rhizobial symbionts, and forms associations with plant‐growth promoting rhizosphere bacteria from the genus Burkholderia. In the invasive range of A. pycnantha in South Africa, nodules contained some symbionts of South African origin while other symbionts appear to have been co‐introduced from Australia. Acacia pycnantha is associated with a wider suite of symbionts in its invasive than native range.

Revision of Sarcocornia (Chenopodiaceae) in South Africa, Namibia and Mozambique

Abstract Sarcocornia comprises ca. 20–24 perennial, halophytic herb and shrub species. The genus is distinct from other genera in the Salicornioideae in having flowers that are more or less equal in size, arranged in a row, and with seeds that have a membranous hairy testa and lack perisperm. Sarcocornia is distributed worldwide, mainly in regions characterized by warm-temperate and, to a lesser extent, subtropical climates. The representatives of this genus are found in habitats such as estuarine salt marshes, tidal mud flats, coastal cliffs, inland salt pans, and salt-laden alluvia of intermittent semi-desert and desert streams. Some South African taxa also occur in inland (semi-desert) quartz patches while some South American species occur on saline soils of dry, continental high plateaus in the Andes. The genus reaches its highest species diversity in the Greater Cape Floristic Region of South Africa, where twelve species and one subspecies are known. This revision of southern African (South Africa, N...

Generic Circumscription in Menyanthaceae: A Phylogenetic Evaluation

Menyanthaceae consist of five genera of aquatic and wetland plants distributed worldwide. The three monotypic genera (Liparophyllum, Menyanthes, and Nephrophyllidium) are clearly differentiated morphologically, but the two larger genera (Nymphoides and Villarsia) contain several taxa of uncertain affinity. We undertook a phylogenetic analysis, using a combination of morphological and molecular data, to resolve relationships among species and to evaluate the current circumscription of genera. DNA sequence data for nuclear (ITS) and chloroplast (rbcL and trnK/matK) gene regions were largely congruent (by partition-homogeneity test), and a combined data phylogeny revealed several strongly supported relationships. Analyses using asterid outgroup taxa supported the monophyly of Menyanthaceae. Menyanthes trifoliata and Nephrophyllidium crista-galli comprised a clade sister to the remainder of the family. Species of Nymphoides, except N. exigua, resolved to a single, deeply-nested clade, indicating that the floating-leaved habit is derived evolutionarily within the family. The genus Villarsia comprised a paraphyletic grade toward Nymphoides, wherein the species resolved to three assemblages: (1) a shallowly nested clade containing V. albiflora, V. calthifolia, V. marchantii, V. parnassifolia, V. reniformis, and V. umbricola; (2) an isolated South African clade including V. manningiana and the type species, V. capensis; and (3) a heterogeneous clade of taxa from three genera, including V. exaltata, V. lasiosperma, and V. latifolia, plus the anomalous species V. capitata, V. congestiflora, Liparophyllum gunnii, and Nymphoides exigua. Our results indicate that the genera Menyanthes, Nephrophyllidium, and Nymphoides should be retained as circumscribed, with the exception that Nymphoides exigua should be restored to Villarsia. The genus Villarsia, however, eventually should be subdivided among monophyletic lineages, whereby in the strict sense Villarsia would contain only South African taxa.

The cranial osteology of Belebey vegrandis (Parareptilia: Bolosauridae), from the Middle Permian of Russia, and its bearing on reptilian evolution

The redescription of the cranial anatomy of Belebey vegrandis, a Permian bolosaurid reptile from southern Russia, provides valuable new information for determining the phylogenetic relationships of this enigmatic group of early amniotes. As exemplified by the superbly preserved skulls and mandibles of Belebey, bolosaurids are characterized by the following attributes: the presence of a unique, heterodont marginal dentition; a slender, anteroposteriorly elongate lower temporal fenestra that is bound mainly by the quadratojugal and squamosal bones; a large coronoid process formed by three bones; a splenial that is restricted to the ventral surface of the mandible; and a long anterior process of the prearticular that covers much of the medial surface of the dentary bone. The palate of Belebey appears to be greatly modified in the region of the snout, indicating the presence of a functional secondary palate. Phylogenetic analysis of Palaeozoic amniotes indicates that bolosaurids are parareptiles and the sister taxon to the clade comprised of Macroleter, Procolophonia, and Pareiasauria. This position, which is high within Parareptilia, necessitates long ghost lineages for several Late Permian Russian and South African taxa, because the oldest known bolosaurids have been found close to the Permo–Carboniferous boundary in New Mexico. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 151, 191–214.

Molecular phylogeny of the endemic East African flightless grasshoppers Altiusambilla Jago, Usambilla (Sjöstedt) and Rhainopomma Jago (Orthoptera: Acridoidea: Lentulidae)

A molecular phylogeny of endemic flightless grasshoppers is presented for the three Lentulidae genera Altiusambilla Jago, 1981, Usambilla Sjostedt, 1909 and Rhainopomma Jago, 1981 based on DNA sequences (16S rRNA locus). Parsimony, distance and likelihood reconstructions were performed using different assumptions on sequence evolution. The generated phylogenies agree in almost all parts of the calculated trees and support the monophyly of the observed genera. It was shown that Usambilla and Rhainopomma are more closely related to each other, Altiusambilla being a separate clade. However, the investigated East African lentulid genera are clearly separated from South African taxa, underlining the monophyly of East African genera. Usambilla olivacea is re-established. Popula- tions of Rhainopomma montanum from the Taita Hills of Kenya and from the West Usambara mountains of Tanzania are two separate species not closely related to each other. Rhainopomma samples from the North Pare mountains of Tanzania belong to a hitherto undescribed species.

Phylogenetic diversity in South African Porphyra (Bangiales, Rhodophyta) determined by nuclear SSU sequence analyses

Specimens of Porphyra were collected at 10 sites along the western, southern and eastern Cape coasts of South Africa during late January to early February 2001. Sequence data from the variable V9 region of the nuclear small subunit rDNA (nSSU) locus were determined for 45 specimens. These data identified 11 distinct entities each with unique V9 sequences. Phylogenetic analyses incorporating sequences of Porphyra and Bangia from throughout the world revealed that eight of the entities examined in this study form a monophyletic group, apparently endemic to the southern African region. The other three entities exhibited no close phylogenetic relationship either with each other or with the other South African taxa. This survey indicates that the southern African coast is a repository of greater taxonomic diversity for this genus than has been previously reported.

Relative influence of biological versus historical factors on isozyme variation of the genus Androcymbium (Colchicaceae) in Africa

We carried out isozyme electrophoresis in the South African taxa of Androcymbium to compare their levels of genetic variation with those reported for their North African congeners and to evaluate the influence of reproductive traits, phylogenetic relationships and environmental histories on the evolutionary dynamics of this disjunction between arid zones of North and South Africa. One possible factor to explain the higher number of alleles detected in South Africa is that diversification in this area started within the early Oligocene, whereas the ancestor of the North African species is more recent and corresponds to the late Miocene. Strong environmental selection and habitat specialization in South Africa probably fostered genetic differentiation between species further in this area. In South African taxa, isozymic variation levels were significantly correlated to breeding systems but not to lineage circumscription (i.e. phylogenetic closeness). The assessment of the relative influence of diverse biotic and abiotic factors on isozyme variation shows that, on a short geological time scale, breeding system is the most reliable predictor of levels of genetic variation. On a longer time frame, represented by the splitting that gave rise to the south–north disjunction of the genus in the late Miocene, the influence of environmental histories of North and South Africa on genetic variation overrides that of breeding systems.

The Genus Eugenia L. (Myrtaceae) in East Africa

Summary. The genus Eugenia is revised for East Africa. Four new species, E. toxanatolica, E. mujindiensis, E. tanaensis, and E. thikaensis, and one new subspecies, E. capernsis subsp. multiflora, are described. Preparation of an account of the family Myrtaceae for the Flora of Tropical East Africa is made difficult not only by the presence in the area of some two hundred introduced species of the family (mainly from Australia), many so widely grown or even naturalized that they must be included, but also by the intrinsic complexity of the two indigenous genera Eugenia and the ecologically very important Syzygium Gaertn. No revision of the African species of Eugenia as a whole has been carried out although Engler (1921) gave a brief conspectus in key form of the 50 species then recognized. G. J. H. Amshoff wrote accounts for Angola (1970), French Equatorial Africa (1958) and Gabon (1966). I have found the annotations of material she examined during work on these accounts often very helpful. F. White (1977, 1978) after an admittedly lengthy study of the southern African species considered many taxa previously always treated as valid species no more than subspecies of Eugenia capensis (Eckl. & Zeyh.) Harv. ex Sond.; his approach was, despite examination of a great deal of material, highly theoretical and preconceived ideas were not dislodged by the abundance of available specimens. In this genus specific differences are indeed slight but correlated with habit and habitats. Neither Van Wyk (1979) nor Arnold & De Wet (1993) mention White's work and it is clear that it is not accepted in South Africa. A study of the South African taxa confirms that this is justified. In only one case is White's treatment relevant to East Africa and that is in relation to E. capensis being widespread up the east coast of Africa; even here it is disturbingly variable. The situation is rather worse in the Flora Zambesiaca area. At least in South Africa there had been previous revisions and accounts of the genus to fall back on but further north little had been done. Once again White has considered very disparate material over a wide area to be subspecies of E. capensis; e.g., the name E. nyassensis Engl., based on an unlocalised specimen at Kew from Malawi, has been used for many specimens not one of which shows the characteristic calyx and stem indumentum. None of the inland populations appear to me sufficiently related to the coastal ones to allow them to be treated as subspecies. It has seemed to me

South African Fungi 8. Three new species of Hymenagaricus from South Africa, with a revised key to South African taxa

Three new species of Hymenagaricus Heinem. from South Africa are described, of these, two viz. H. ochraceoluteus and H. rufomarginatus belong in Hymenagaricus subgen. Xanthagaricus Heinem, while H. fuscobrunneus belongs in Hymenagaricus subgen. Hymenagaricus. Accounts of these new taxa and a revised key to the species of Hymenagaricus known to occur in South Africa are provided.

New combinations and a new species in Habenaria (Orchidaceae) from South Africa

The following changes to the status of three South African taxa in Habenaria are made: H. caffra Schltr. is reduced to a subspecies of H. falcicornis (Lindl.) H. Bol.; H. lithophila Schltr. subsp. mossi Williamson is raised to specific status; and H. rehmanni H. Bol. is regarded as a synonym of H. humitior Reichb. f. A new species, H. pseudociliosa Schelpe ex Manning, is described: it is closely allied to H. ciliosa Lindl., with which it has been confused in the past, but differs in the smaller flowers with longer spur and shorter lip lateral lobes, and lobed rostellum arms.