Angus H. H. Macdonald

DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.

PHYLOGEOGRAPHY OF THE SCALLOPED SPINY-LOBSTER PANULIRUS HOMARUS RUBELLUS IN THE SOUTHWEST INDIAN OCEAN

The Mozambique Channel between south-east Africa and Madagascar potentially forms a barrier to larval dispersal and thus gene flow across the channel, even in species with long larval lifespans such as spiny lobsters. The DNA of 181 specimens of Panulirus homarus rubellus Berry, 1974, collected from six sites along the African coast and a site in Madagascar, was sequenced (591 base pairs) to investigate gene flow along the coast and across the channel. Bayesian methods were implemented to infer genetic structure and relatedness. A total of 112 haplotypes were recovered, of which 78% were unique. Samples from Africa and Madagascar did not share any haplotypes and differed by 78 mutations and 3% DNA divergence. These distinct lineages suggest an absence of contemporary gene flow across the Mozambique Channel. Shallow genetic structure along approximately 1000 km of African coastline comprised combinations of seven distinct lineages but did not correspond to known biogeographic provinces. The African lineage appeared to be ancestral, and the source population for the Madagascan clade. Genetic isolation in refuges during glacial periods, followed by subsequent range expansions and secondary contact, may account for the high diversity in the African lineages.

Possible synonymies of Zoanthus (Anthozoa: Hexacorallia) species on the east coast of South Africa with Pacific congeners

Zoanthids cover large patches on the rocky shores of KwaZulu-Natal and northern parts of the Eastern Cape, South Africa. No molecular identification has been carried out on these organisms on the South African shoreline. Zoanthus sansibaricus Carlgren, 1900 has a global distribution and has been reported having numerous morphotypes in terms of polyp shape, size, colour and oral disk colour. The molecular characteristics of three Zoanthus species, Z. sansibaricus, Zoanthus durbanensis Carlgren, 1938 and Zoanthus natalensis Carlgren, 1938, were investigated to determine whether they are three separate species or merely morphotypes of one another. Samples were collected between May 2012 and July 2013, ranging from Umgazana (31.7024°S, 29.4175°E) to Ballito (29.5451°S, 31.2160°E) on the east coast of South Africa and at one site in Libanona, Madagascar (25.0421°S, 46.9952°E). Cytochrome oxidase subunit one (COI), mitochondrial 16S ribosomal DNA (mt 16S rDNA) and the nuclear internal transcribed spacer region of ribosomal DNA (ITS rDNA) were used in this study. The COI sequences had little variation between species groups, while the mt 16S rDNA tree showed that Z. sansibaricus matched with sequences of Z. sansibaricus from the Pacific. Zoanthus natalensis formed a haplotype with Zoanthus kuroshio Reimer & Ono, 2006 and Z. durbanensis formed a haplotype with Zoanthus vietnamensis Pax & Müller, 1957. The ITS rDNA sequences were very similar for these four species: Z. natalensis, Z. kuroshio, Z. durbanensis and Z. vietnamensis. The results of this study indicate that Z. natalensis is likely conspecific to Z. kuroshio and Z. durbanensis is likely conspecific to Z. vietnamensis. This is only a tentative hypothesis as no formal morphological analyses were done on proposed conspecifics. This work highlights the potential of synonymies that can be found globally when investigating new areas.

Molecular examination of rocky shore brachycnemic zoantharians (Anthozoa: Hexacorallia) and their Symbiodinium symbionts (Dinophyceae) in the southwest Indian Ocean

The order Zoantharia is ubiquitous on the east coast of South Africa, but despite its widespread distribution its species are poorly represented in recent literature from the region. A previous study in this region has shown that Zoanthus natalensis Carlgren, 1938 and Z. durbanensis Carlgren, 1938 are most likely conspecific to the Pacific Z. kuroshio Reimer & Ono, 2006 and Z. vietnamensis Pax & Müller, 1957, respectively. The aims of the present study were to expand on the previous one by conducting a molecular examination of zoantharians found in the intertidal zone along the east coast of South Africa as well as to identify their Symbiodinium symbionts for comparison with conspecifics elsewhere. Symbiodinium identification can be a useful tool when dealing with species that are synonymous as they are likely to share Symbiodinium spp. from the same subclade. The molecular markers mitochondrial 16S ribosomal DNA (mt 16S rDNA), the nuclear internal transcribed spacer region of ribosomal DNA (ITS rDNA), and for the first time on South African zoantharians, the ITS rDNA region for Symbiodinium spp. were used. Seven species were identified. They were Isaurus tuberculatus, Palythoa nelliae, P. tuberculosa, Z. durbanensis, Z. gigantus, Z. natalensis, and Z. sansibaricus. A possible synonymy was found as Palythoa nelliae Pax, 1935 appears to match with the Pacific P. mutuki (Haddon & Shackleton, 1891). Symbiodinium subclade A1 was most often found with Z. natalensis and subclade C15/C91 was most frequently observed in Z. durbanensis. Subclade C1 was found with all Isaurus and Palythoa samples, and with most of Z. sansibaricus samples. Symbiodinium subclades in this study were generally the same as those reported from Indo-Pacific conspecifics.

What can South African reefs tell us about the future of high-latitude coral systems?

Coral communities are found at high latitude on the East Coast subtropical reefs of South Africa. They are biodiverse, economically important, and afforded World Heritage Site status in the iSimangaliso Wetland Park where some are subjected to recreational use. While the Parks unique coral reefs have, to date, suffered little bleaching from climate change, they are susceptible to the phenomenon and provide a natural laboratory for the study of its effects at high latitude. This review covers recent advances in the regional oceanography; coral community dynamics and the underpinning reef processes, including minor bleaching events; the incidence of coral disease; and coral genetic connectivity. The effects of human activity (SCUBA diving, recreational fishing, pesticide use) were assessed, as well as the nursery benefits of Acropora austera, a coral which provides the reefs with much structure and is vulnerable to damage and climate change. The reefs were valued in terms of human use as well as services such as sediment generation and retention. The results have provided valuable information on relatively pristine, high-latitude reefs, their socio-economic benefits, and the anticipated effects of climate change.

Uncovering the basis of viability loss in desiccation sensitive Trichilia dregeana seeds using differential quantitative protein expression profiling by iTRAQ

Recalcitrant seeds, unlike orthodox types, are desiccation sensitive and hence, cannot be stored using conventional seed storage methods In this study, relative changes of protein expression in T. dregeana seeds during desiccation and hydrated storage (a short- to medium-term storage method) were analysed to understand the basis of their desiccation- and storage-induced viability loss. Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) were used to compare (selected) protein expression levels across fresh, partially dehydrated and stored seeds. A total of 114 proteins were significantly differentially expressed in embryonic axes of fresh seeds and those seeds exposed to dehydration and hydrated storage (which exposed seeds to a mild dehydration stress). Proteins involved in protein synthesis were up-regulated in stored and dehydrated seeds, possibly in response to dehydration-induced repair processes and/or germinative development. A range of proteins related to antioxidant protection were variably up- and down-regulated in stored and dehydrated seeds, respectively. Additionally, a class I heat shock protein was down-regulated in dehydrated and stored seeds; no late embryogenesis abundant proteins were identified in both stored and dehydrated seeds; and storage and dehydration up-regulated proteins involved in the provision of energy for cell survival. The results suggest that dehydration- and storage-induced viability loss in recalcitrant seeds may be based on proteomic changes that lead to cellular redox imbalance and increased cell energy demands. This, together with the absence/down-regulation of proteins associated with desiccation tolerance in plant tissues may form part of the proteomic footprint for desiccation sensitivity in seeds.

Evidence of Multiple Divergent Mitochondrial Lineages within the Southern African Diplopod Genus Bicoxidens Attems, 1928 (Spirostreptida)

Two recent studies have suggested that divergent mitochondrial lineages may be present within spirostreptid genera such as Bicoxidens Attems, 1928. Bicoxidens, similar to many other endemic soil invertebrates, exhibits low dispersal capabilities and strict microclimate habitat preferences, attributes that often lead to geographic isolation. Given that prolonged geographic isolation often lays the foundation for population genetic differentiation, genetic divergence and possibly speciation, there was good reason to suspect that Bicoxidens may consist of several distinct lineages. On this basis, the mitochondrial cytochrome c oxidase subunit 1 (COI) was used to reconstruct the phylogeny of Bicoxidens and reveal divergent lineages within the genus. Maximum likelihood and Bayesian inference analyses recovered a paraphyletic Bicoxidens phylogram with divergent lineages present in three species — B. friendi, B. flavicollis and B. brincki — suggesting high genetic diversity within the genus. Bayesian genetic cluster analyses suggested the presence of multiple distinct mitochondrial lineages within the genus with four identified in B. flavicollis alone. It was therefore concluded that the divergent lineages observed among Bicoxidens populations may suggest the presence of hidden species.