Browsing by Author "Macdonald, Angus Hector Harold."

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Connectivity of two scleractinian corals in the south west Indian Ocean.
(2010) Macdonald, Angus Hector Harold.; Schleyer, Michael H.; Lamb, Jennifer Margaret.
Generations of hard corals have built the complex reef ecosystems that harbour a huge diversity of sea-life in the world’s shallow tropical oceans. These undergo both sexual and clonal reproduction, and may contain signatures in their genomes which help to decipher the riddles of past population dynamics and evolutionary history. Two species of coral, Acropora austera and Platygyra daedalea, were collected from sites along the east African coastline from Kenya in the north to Maputaland, South Africa in the south, and from the Chagos Archipelago. Sequences of two different DNA regions were tested, in a preliminary study, for their potential ability to elucidate connectivity and differentiation among these coral populations. These were the nuclear ribosomal ITS region of P. daedalea populations, and a previously-unused marker, the carbonic anhydrase 3/550 nuclear intron of A. austera. These molecular markers indicated high levels of connectivity amongst populations in a preliminary study based on limited sample sizes and a subset of populations. It was decided to further explore the variability of the carbonic anhydrase 3/550 intron, which showed evidence of subdivision and structuring within Mozambique populations relative to South African populations, in a study in which both the sample size per site and the number and range of sampled sites were increased. ITS sequences, although highly variable, revealed no population differentiation in P. daedalea; STR markers were used in subsequent studies of population differentiation in this species. Populations of both A. austera and P. daedalea showed signs of high connectivity along the region of the coastline sampled in this study. However, there appeared to be a disjunction in ecological connectivity between reefs in Maputaland, South Africa and those in southern Mozambique, between Durban and Maputo where the Agulhas Current originates. This was reinforced in A. austera populations which displayed a region of genetic discontinuity between Inhaca Island and Maputaland reefs of the central reef complex, in the region of Rabbit Rock. Northern reef complexes also harboured unique haplotypes in contrast to southern reefs which shared all haplotypes with those in the north, an indication that northern reefs have seeded the southern (Maputaland) reefs. P. daedalea populations appeared evolutionarily panmictic over scales relevant to this study. Evidence for fine-scale structure indicated that populations were separated from one another over ecologically relevant time-scales. These populations were defined by both their habitats and their sampling location. There was a possibility that the Platygyra species complex included cryptic species that were not distinguishable from P. daedalea. However, the disjunction in the connectivity between northern and southern population groups was also evident in the population structure of P. daedalea. There was a net immigration of propagules of both P. daedalea and A. austera into populations north of the disjunction between groups, where the prevailing current regime is dictated by the Mozambique Channel eddies. In contrast populations to the south of the disjunction (the southern population group) which are subject to the swiftly flowing Agulhas Current, showed a net emigration of propagules from Maputaland reefs. These emigrants were likely to be lost to inhospitable habitat south of the marginal Maputaland region. Although there was evidence for migration of both Platygyra and Acropora propagules between the Bazaruto Archipelago reefs and certain Maputaland reefs, genetic exchange between Mozambique and Maputaland reefs appeared to be limited and may have occurred primarily at evolutionary rather than demographic levels. Managers may need to treat the regional Maputaland reefs as separate stocks and manage them accordingly, as the relative isolation of these corals in the central and southern reef complexes in Maputaland, South Africa, means that they are at risk to losing species to evolutionary extinction. It is also important that reef health in northern Mozambique and Tanzania is maintained as, despite evidence of a break in demographic connectivity, between reefs in these regions and those in Maputaland, there was evidence to suggest that reefs were connected at evolutionary scales, thus maintaining levels of genetic diversity on southern African reefs.
Decadal changes in rocky shore communities in KwaZulu-Natal and survey methods for future monitoring.
(2020) Mvula, Philile Emelda.; Macdonald, Angus Hector Harold.; Pfaff, Maya Catherine.
Intertidal rocky shores form part of the sea during high tides and part of the land during low tides. They are therefore subjected to diverse anthropogenic pressures, including climate change, pollution, coastal erosion and harvesting. Due to their accessibility, rocky shores are among the most heavily exploited marine ecosystems. The rocky shores of the East and the South coasts of South Africa have been exploited for thousands of years. With growing coastal populations, they require management practices that ensure their ecological integrity and function. Rocky shore community structure along the KwaZulu-Natal (KZN) coast has been well studied between the years 1996 and 2000 when surveys were conducted at 39 sites. A monitoring Programme has since been established by Ezemvelo KwaZulu-Natal Wildlife in partnership with the Department of Environmental Affairs, Forestry and Fisheries (DEAFF) to inform the management of these heavily impacted ecosystems. This study aimed to contribute to the monitoring Programme in two ways: Firstly, by characterising and evaluating changes in rocky shore communities that have occurred since 2000, which was done by resurveying historical sites and comparing community structure and diversity between decades. Secondly, by comparing and evaluating different rocky shore sampling methods to identify the most suitable sampling protocol for a long-term monitoring programme of KZN rocky shores. This required statistical analyses of parallel surveys conducted using different methods. Significant changes in the community structure were observed with increased species richness and evenness. A decline in the abundance of harvested mussels was also noted, coupled with an increase in coralline algae and the arrival of two species of alien barnacles. Even though more long-term studies will be required to determine the status of the intertidal communities under anthropogenically induced change, the current study can be used to initiate better managementpractices in order to maintain species diversity and distribution.
Ecological genetic connectivity between and within southeast African marginal coral reefs.
(2014) Montoya-Maya, Phanor H.; Schleyer, Michael H.; Macdonald, Angus Hector Harold.
Marine protected areas (MPAs) have been established along the East African coast to protect coral communities from human and natural disturbance. Their success is dependent on the degree to which resource populations are self-seeding or otherwise connected. Estimates of contemporary gene flow on or between south-east African reefs are thus required to reveal the interdependence of the South African coral communities and those to the north. Accordingly, the ecologically relevant (1 or 2 generations) connectivity of two broadcast-spawning corals, Acropora austera and Platygyra daedalea, was assessed on reefs in the region, from the Chagos Archipelago to Bazaruto Island in Mozambique and Sodwana Bay in South Africa, using hyper-variable genetic markers. Analysis of genetic diversity and differentiation provided evidence for the existence of four discrete genetic populations of A. austera and five of P. daedalea in the sampled area. Higher genetic diversity was found on northern South African reefs (Nine-mile Reef and Rabbit Rock) and migration patterns inferred from assignment tests suggested that, at ecological time scales, South African reefs are disconnected from those in Mozambique and might originate from a source of gene flow that was not sampled. The analysis of fine-scale genetic connectivity conducted on Two-mile Reef (TMR) demonstrated the existence of significant spatial genetic structure at the reefal scale that might be related to the non-random dispersal of coral larvae, putatively explaining the genetic discontinuity observed in the region. Altogether, the results are consistent with the isolation observed in other studies using less variable markers, and support the hypothesis that there is demographic discontinuity between the coral populations along the south-east African coast. More importantly, Acropora austera and P. daedalea represent different life strategies in the South African reef communities yet manifested similar genetic patterns, suggesting that these corals are responding similarly to forces that are driving genetic connectivity in the region. For management purposes, the genetically distinct populations identified at each of the spatial scales analysed in this study may correspond to management units, or evolutionarily significant units. Furthermore, since some reefs appear to act as “landing-sites” for migrants (Nine-mile Reef) and there is evidence of significant within-reef genetic structure (TMR), an adaptive management framework would be the best option for the MPA in the region.
Genetic analyses of a Southern African millipede (Bicoxidens Attems 1928)
(2014) Tinago, Tawanda.; Mwabvu, Tarombera.; Macdonald, Angus Hector Harold.
Bicoxidens Attems, 1928 is an afrotropical millipede in the family Spirostreptidae which constitutes nine species. Based on the analysis of the male copulatory organs known as gonopods, Bicoxidens is monophyletic. However, gonopod morphology is central to millipede taxonomy, examination of gonopod morphology alone may not elucidate hidden genetic diversity thereby underestimating species richness in Bicoxidens. Analysis of genetic data as an additional source of taxonomic data has been noted to reveal genetic variation and flagged hidden species within millipedes. Hence there is a need to revise the morphological species definitions and phylogeny of Bicoxidens using both mitochondrial and nuclear DNA sequences. Furthermore, low vagility and habitat discontinuity may limit gene flow among Bicoxidens populations resulting differentiation and high genetic variation. In this regard, the sequences of the mitochondrial cytochrome oxidase 1 (COI) and 16S rRNA genes were used to delimit species, unravel hidden species and test the monophyly of Bicoxidens. In addition, the phylogeography and population genetic structure of B. flavicollis was investigated based on COI and 16S rRNA sequences. Genetic distances were computed using COI. Phylogenetic inferences were done based on Maximum likelihood and Bayesian inference analyses of the COI and 16S rRNA sequences individually and with the combined data set (COI+16S rRNA). The phylogeography and population genetic structure of B. flavicollis was inferred based on genetic diversity indices, population genetic differentiation estimate PhiPT, haplotype network analyses and maximum likelihood analyses of both COI and 16S rRNA. Bayesian population structure analyses was done using the COI data set only. Furthermore, Mantel’s isolation by distance among B. flavicollis specimens was tested. Interspecific genetic distances (> 0.075) based on the Juke-Cantor model supported the morphological species definitions in Bicoxidens. However, high intraspecific sequence differences in B. flavicollis (> 0.14), B. friendi (0.084) and B. brincki (> 0.188) suggest the presence of cryptic species. The possible presence of cryptic species was supported by the phylogenic analyses which recovered a paraphyletic Bicoxidens phylogram with B. flavicollis, B. brincki and B. friendi exhibiting divergent lineages. Bicoxidens flavicollis populations exhibited high genetic diversity and strong population differentiation which suggests restricted gene flow. Haplotype network and Maximum likelihood analyses revealed limited sharing of haplotypes and cryptic species in populations at Mazowe and Nyanga, respectively. Bicoxidens flavicollis populations were grouped in two four genetic clusters. Isolation by distance was insignificant among B. flavicollis specimens. The results support the utility of both COI and 16S rRNA in species delimitation in Bicoxidens. There is a growing body of evidence which also suggests presence of hidden species in B. flavicollis, B brincki and B friendi. Furthermore effort to uncover more hidden species should be made to elucidate the species richness before conservation strategies can be implemented.
A genetic approach to the biodiversity of shallow water alcyonacea in South Africa.
(2018) Etsebeth, Kerry-Lee.; Macdonald, Angus Hector Harold.
The cnidarian order Alcyonacea (Octocorallia) represents a diverse group of marine invertebrates that are dominant taxa on shallow and deep reefs. These organisms constitute sensitive indicators of climate change and have bioprospecting potential. In South Africa, alcyonacean soft corals form the dominant faunal component of the high latitude marginal reefs on the east coast, an understudied region of interest that forms some of the southernmost distribution limits for key taxa in this order. Globally, soft corals are understudied whereby systematic, ecological, and biochemical studies are challenged by inconclusive taxonomy. This is in contrast to the growing understanding of the necessity for genetics in the systematics of Scleractinia, where large scale reclassification has been successful in reconstructing more accurate phylogenies of the order. The knowledge deficit in the systematics and evolution of Alcyonacea is paralleled in South African taxa. An integrative assessment using morphological classification in combination with phylogenetics of Alcyonacea is the most promising approach to assess their biodiversity in South Africa. Accordingly, the aims of these studies were to advance the taxonomic knowledge of soft corals in South Africa; assess species richness and provide a national checklist; and investigate evolutionary relationships between taxa. In so doing, this thesis also aimed to support the global taxonomy of Alcyonacea. Particular attention was given to Alcyonacea that dominate the reef biota in the UNESCO world heritage site, the iSimangaliso Wetland Park (iSWP). Three genetic markers, cytochrome c oxidase I (COI), bacterial MutS homolog (MutS) and nuclear 28S ribosomal RNA (28S rRNA) were used to determine genus and species boundaries in the closely related Alcyoniidae genera; Cladiella, Aldersladum and Klyxum. The use of these genes corroborated taxonomic analyses and demonstrated that morphologically aberrant members of the genus Cladiella should be reassigned to another as yet undescribed genus. The undescribed genus, Beta6, is characterised by an absence of platelet sclerites in the polyp region, features that demonstrate major distinctions from the genera Cladiella, Aldersladum and Klyxum. The species richness of 67 Sinularia specimens in the iSWP was estimated 6 Beta was selected as a placeholder name until the full taxonomic descriptions of this new genus and any of its associated species are published. using DNA barcoding (MutS and concatenated MutS+28S respectively). Phylogenetics and species delimitation methods were used to infer identifications for 63% of the specimens in the study, including a new record for Sinularia grandilobata. In addition, 16 putative species of Sinularia were discovered that are considered potentially undescribed or new records that require further taxonomic investigation by an octocoral expert. Furthermore, S. brassica exhibited two distinct morphotypes that were genetically differentiated and indicative of two distinct species. Taxonomic boundaries were investigated using integrative taxonomic approaches for 239 specimens of Alcyonacea from the iSWP. Specimens were assigned to ~61 putative species that were inferred from phylogenies, divergence estimates, colony photographs and sclerite characters for taxa in this study. Molecular evidence supported the reassignment of non-S. brassica congeners of Sinularia to an undescribed genus due to significant large scale polyphyly. Furthermore, this study reported new records for three genera; Scleronephthya, Paraplexaura, and Chironephthya and an undescribed species of Lobophytum. The results of this study, in conjunction with previously published records, contributed towards revised species estimates for the iSWP that increased from 37 to 81 species (with 12% endemism), 11 to 47 genera and 4 to 17 families. An updated checklist of the Alcyonacea across South Africa was compiled using records from chapters 2 to 4 in this thesis and published records. Two hundred and twenty-six different species from among 89 genera and within 25 families of Alcyonacea were reported. Seventy-five of these species are endemic to South Africa (33%). This represents a substantial increase from the last published estimates in South Africa of 130 species of Alcyonacea. This body of research represents a significant advancement in the knowledge of the biodiversity of an important group of marine invertebrates in South Africa. It provides resolution within some problematic identification assignations (Cladiella, Sinularia brassica). Sinularia, Beta and the Lobophytum-Sarcophyton complex require further taxonomic work for a better perspective on the diversity of this complex, marginal and neglected aspect of South Africa’s marine heritage.
The genetic connectivity of diplodus capensis (blacktail) and neoscorpis lithophilus (stonebream) fish populations in the Southwest Indian Ocean.
(2016) Cele, Lindile Venencia.; Macdonald, Angus Hector Harold.; Gouws, Gavin.; Fennessy, Sean Thomas.
Abstract available in PDF file.
Genetic population structure of deep-water prawns Haliporoides triarthrus and langoustines Metanephrops mozambicus in the South West Indian Ocean : use of mitochondrial DNA to investigate metapopulation structure.
(2013) Zacarias, Lourenco Domingos.; Macdonald, Angus Hector Harold.; Groeneveld, Johan Conrad.
Deep-water prawns Haliporoides triarthrus and langoustines Metanephrops mozambicus are endemic to the South West Indian Ocean (SWIO) region and make up the largest proportion of deep-water crustacean trawl catches in Mozambique and South Africa. Despite their economic importance to these fisheries, little is known about their distribution, biology and genetic population structure. The metapopulation genetic variation of H. triarthrus and M. mozambicus was assessed from 220 specimens per species collected from three sites in Mozambique (Bazaruto A, Boa Paz and Inhaca), two sites in western Madagascar (Morombe and Tulear) and one site in eastern South Africa (Durban). Two fragments of the mitochondrial region were amplified using universal primers ribosomal 16S subunit (16S) and mitochondrial cytochrome oxidase subunit I (COI). From H. triarthrus, fragments of 569 base pair (bp) (16S) and 1300 bp (COI) were amplified. A total of 207 sequences (16S) and 151 sequences (COI) were recovered, and 69 and 78 haplotypes identified, respectively. Metanephrops mozambicus 16S and COI genes produced similar fragment lengths, and 112 (16S) and 127 haplotypes (COI) were recovered. Both species demonstrated high genetic diversity and significant population differentiation in the SWIO region. Two sister-species (or subspecies) of H. triarthrus were identified, one occurring along the African continental shelf and the other off western Madagascar. Furthermore, individual populations making up each lineage were genetically structured, as indicated by the absence of shared haplotypes, and should be recognized as demographically distinct subspecies. Both species have undergone recent population expansions, likely since the late Pleistocene. The large anti-cyclonic and cyclonic eddies prevalent in the Mozambique Channel, and the boundary area between these eddies and upper Agulhas Current are likely factors driving larval retention or return process, thus giving rise to the observed genetically structured populations. The findings from this study are unique for the SWIO region, and may lead to a paradigm shift in the way that deep-water crustacean stocks are perceived by fisheries managers – instead of single shared stocks, they comprise of many isolated ones, in spite of the dispersal potential of larvae in strong ocean current regimes. Thus stocks should be managed as small independent units.
An investigation of the population connectivity of sardines (Sardinops sagax) of the KZN sardine run using meristic, morphological and genetic data.
(2014) Chiazzari, Brent.; Macdonald, Angus Hector Harold.; O'Donoghue, Sean Henry.
The Sardine run occurs annually when large schools of sardine (Sardinops sagax) move from the Agulhas Bank towards KwaZulu-Natal, and has significant ecological and anthropogenic importance. Recent investigation has highlighted the nature and mechanisms resulting in the sardine run, however, critical questions about why the sardine run occurs remain unanswered. Therefore, the aim of this project was to elucidate the population diversity, connectivity and structure of sardines undertaking the sardine run. Sardines were sampled at four sites along the South African coast, and their morphology assessed using meristic data, multivariate, and geometric morphometrics. Nine exon-primed, intron-crossing (EPIC) DNA markers and the mitochondrially encoded cytochrome oxidase I (mtCOI) region of DNA were used for population and phylogeographic genetic analyses. Morphological analyses revealed significant differences between head size and shape of sardine run stock compared with other regions, and supports the delineation of a western, southern and eastern South African stock. Phylogeographic analysis using cytochrome oxidase I data, supported the idea that the Sardinops genus is monotypic. Genetic analyses using EPIC data confirmed low levels of segregation between sardines from the sardine run and the Western Cape stock. However, larvae spawned in KwaZulu-Natal demonstrated moderate levels of isolation from the Western Cape stock. The results reveal that there is successful recruitment of KwaZulu-Natal juveniles to the adult stock undertaking the sardine run. KwaZulu-Natal juveniles also recruit to the Western Cape population, although, to a lower degree. Results suggest sardines from the West Coast and Agulhas Bank partake in the sardine run. However genetic evidence suggests a certain subpopulation of the Agulhas Bank and a sub-stock of the Western Cape stock spawn successfully in KwaZulu-Natal. These results support the hypothesis that the sardine run represents a subpopulation spawning migration of Sardinops sagax in South Africa.
Metagenomics assessment of Anthropogenic impact on coral reef-associated microorganisms on the Kenyan Indian Ocean.
(2020) Wambua, Sammy Musee.; Macdonald, Angus Hector Harold.; De Villiers, Santie.
The Western Indian Ocean (WIO) is the world’s second richest marine biodiversity hotspot. It is characterized by a diverse range of ecologically and nutritionally rich marine ecosystems that are increasingly under pressure from the impacts of human population growth and coastal development. A comprehensive understanding of variations of marine microbial community composition with environmental conditions is key to understanding and predicting responses to human and climate pressures because microorganisms are the main drivers of biogeographical processes, and they respond and adapt fast to climatic patterns. Also, because unique environments harbour unique microorganisms with unique properties, genomic exploration of marine microorganisms may lead to discovery of novel metabolic processes, and bioactive products with potential for novel biotechnological applications. This project aimed to assess the effect of local anthropogenic impacts on the community structure and the functional potential of microorganisms inhabiting the WIO coral reefs along the Kenyan coast by metagenomics. Reasons for low application of genomics specifically in marine research in the WIO region were examined through literature review and in-depth interviews with scientists in the region. Coral reef seawater and sediment samples were collected, for microbial assessments, along gradients of human impacts and protection regimes. Environmental variables were estimated, and microbial taxonomic and functional diversity analysed by metagenomic approaches. Comparisons were done between sites with differential human impacts, and with oceanic metagenomes from Tara Oceans expedition. Compartmentalised training of marine scientists and lack of collaboration with molecular scientists are key reasons highlighted for poor uptake of genomics in marine research. Significant differences in taxonomic and functional composition were observed between the coral reef and Tara Oceans datasets. Coral reef metagenomes had more diverse and even microbial taxa and gene groups. Tara Oceans metagenomes were enriched with groups of genes of functions in keeping with oligotrophic conditions, and reefs metagenomes with genes for functions related to adaptations to heterogenous environments. E. coli density decreased with increasing degree of protection, but physicochemical and nutrient variables did not differ across coral reefs in the protected coral reefs. Variations in relative abundances of copiotrophic bacteria and coliphages were observed in coral reefs corresponding to magnitude of the neighbouring human impacts. Malindi and Mombasa marine parks, the coral reef sites experiencing degradative human impacts, were significantly enriched with genes for functions suggestive of mitigation of environment perturbations e.g. capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. This study establishes essential baselines for microbiome studies in the WIO region and provides insights to anthropogenic impact on microbial structure and functions, and potential indicators of health status coral reef ecosystems.
Molecular phylogeny and population genetic structure of the shallow-water spiny lobster Panulirus homarus in the South West Indian Ocean region : implications for management.
(2013) Reddy, Mageshnee Mayshree.; Macdonald, Angus Hector Harold.; Schleyer, Michael H.
The scalloped spiny lobster, Panulirus homarus has a subspecies trio that are widely distributed in shallow-water habitats in the South West Indian Ocean. Subspecies are defined by differences in colour and abdominal sculptural pattern. A red variety with the megasculptural carapace pattern, P. h. rubellus is distributed along the south east coast of Africa and Madagascar, where they are endemic. Along the African coast P. h. rubellus stocks traverse political boundaries, Mozambique and South Africa. This project aimed to facilitate regional fisheries management of shared stocks by employing genetic tools to determine whether stocks (or populations) are indeed shared between countries. Lobster samples were collected from seven localities throughout the east African coast. The mitochondrial cyctochrome c oxidase subunit 1 region was sequenced to assess the genetic diversity 1) between different subspecies, P. h. homarus and P. h. rubellus and 2) between populations of P. h. rubellus across its African distribution range. Using DNA barcoding methods, genetic diversity was also found between morphologically distinct subspecies, Panulirus homarus homarus and P. h. rubellus which differed genetically by ca. 2-3% in sequence divergence. Both subspecies were monophyletic relative to the out-group taxa and formed well supported sister clades (BI: 1.00, ML: 93%, P: 100%, NJ: 100%). The distribution of P. h. rubellus along the African coast occurs adjacent to different current regimes and therefore varied larval transport modes (i.e. Agulhas Current and inshore countercurrents along the Eastern Cape). This may have driven the formation of subpopulations (ΦPT = 0.104, p = 0.010) which differ by ca. 1.7% in sequence difference. The pattern of gene flow of populations of P. h. rubellus lends support to the Agulhas Current being a major mode of larval transport as well as corroborates previous abundance and distribution records. Time since population expansion estimates for the P. h. homarus and P. h. rubellus subspecies as well as for the P. h. rubellus subpopulations dated back to the mid-Holocene Epoch in accordance with a warmer, more stable marine environment. Genetically distinct subspecies of P. homarus as well as differentiated subpopulations of P. h. rubellus calls for a re-visit of the current collective management of P. homarus as well as P. h. rubellus as a single genetic stock along the south east African coast.
Molecular revision of Zoantharia (Anthozoa Hexacorallia) on the east coast of South Africa.
(2014) Risi, Michelle Megan.; Macdonald, Angus Hector Harold.
The order Zoantharia (Cnidaria: Anthozoa) is ubiquitous on the east coast of South Africa, and despite their widespread distribution they are poorly represented in literature. 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 initial aim in this study was to examine the molecular characteristics of three Zoanthus species; Z. sansibaricus, Z. durbanensis Carlgren, 1938 and Z. natalensis Carlgren, 1938, to determine whether they are three separate species or merely morphotypes of one another. Following on from this research, the aim was to conduct a molecular revision of all zoanthids found in the intertidal zone along the east coast of South Africa, and to identify the Symbiodinium spp. within zoanthids for comparisons with conspecifics elsewhere. Samples were collected at sites along the coast from Umgazana (31.7024° S, 29.4175° E) to Sodwana (27.6594° S, 32.6477° E) and at one site in Libanona, Madagascar (25.0421° S, 46.9952° E). Sequences of cytochrome oxidase subunit one (COI), mitochondrial 16S ribosomal DNA (mt 16S rDNA), the nuclear internal transcribed spacer region of ribosomal DNA (ITS rDNA) for zoanthids and ITS-rDNA region for Symbiodinium spp. were used in this study to run phylogenetic analyses and examine the molecular characteristics for comparisons with zoanthids elsewhere using GenBank. Seven species were identified; Isaurus tuberculatus, Palythoa nelliae, Palythoa tuberculosa, Z. durbanensis, Z. gigantus, Z. natalensis and Z. sansibaricus. The COI sequences (for Z. sansibaricus, Z. natalensis and Z. durbanensis) had little variation between species groups, while the mt 16S rDNA tree showed that Z. sansibaricus matched with sequences of previously reported Z. sansibaricus from the Pacific. Zoanthus natalensis was identical to Z. kuroshio Reimer & Ono, 2006 and Z. durbanensis was identical to Z. vietnamensis Pax & Müller, 1957. The ITS rDNA sequences were very similar for these four species; Z. natalensis, Z. kuroshio, Z. durbanensis and Z. vietnamensis. Palythoa nelliae Pax, 1935 appears to match with Pacific species Palythoa mutuki Haddon & Shackleton, 1891, and this is supported by the mt 16S and ITS rDNA markers. Symbiodinium subclade A1 was most often found with Z. natalensis and subclade C15/C91 was most often found with Z. durbanensis. Subclade C1 sensu LaJeunesse (2002) was found with all Isaurus and Palythoa samples, and most of Z. sansibaricus samples. The results of this study indicate that Z. natalensis is likely conspecific to Z. kuroshio, Z. durbanensis is likely conspecific to Z. vietnamensis, and P. nelliae is likely conspecific to P. mutuki, however, this is only a tentative hypothesis as no formal morphological analyses were done on proposed conspecifics.This work highlights the importance for similar studies in the clarification of zoanthid taxonomy
A phylogeny of South African east coast intertidal rocky-shore Polychaete worms (Annelida) and the genetic structure and demographic history of an example, Marphysa corallina.
(2015) Kara, Jyothi Ashok.; Macdonald, Angus Hector Harold.
The Annelida is an evolutionarily ancient invertebrate taxon. Recent studies have found that the formerly described sister taxon of the Polychaeta, Clitellata, is a derived Polychaete group thus making Polychaeta a paraphyletic group. Polychaete worms represent one of the most diverse invertebrate groups and are well represented in a variety of environments such as temporary freshwater puddles, rocky intertidal shores, estuaries and the abyssal plain. Polychaetes are fundamentally important in their environments as many are regarded as ecosystem engineers. Phylogenetic relationships within the Polychaeta are poorly understood and some species level classifications are uncertain due to the large number of polychaete worms present. In Chapter two, the phylogenetic relationships within the commonly found polychaete families (Nereididae and Eunicidae) were analysed using the universal mitochondrial cytochrome oxidase subunit 1 (COI). Within Eunicidae, analyses supported a polyphyletic Marphysa and Eunice which is consistent with previous results as individuals from both genera are nested among one another. Within Nereididae, relationships between genera and species were poorly supported and complex. Genera did not form exclusive clades but instead grouped with one another. A large degree of homoplasy has been recorded for the family which could have attributed to the convoluted groupings. Thus it has been suggested that genera from both Eunicidae and Nereididae be revised. Marphysa corallina is a poorly studied Eunicid polychaete which has a tropical indo-west distribution. It was observed to be a common worm among others on the intertidal rocky shores of KwaZulu-Natal and the Eastern Cape. In Chapter three, the population genetic structure and demographic history of M. corallina was investigated using two genes: universal mitochondrial cytochrome oxidase subunit 1 (COI) and the nuclear intron spacer region (ITS1). Diagnostic taxonomic characters were used to identify and validate the specimens as Marphysa corallina. The COI marker revealed that populations were highly connected to one another and formed a large panmictic population whereas ITS1 showed shallow genetic structuring of populations. Family Eunicidae individuals are known to lack a long lived planktonic larval stage which could not have contributed to panmixia as demostrated by the COI marker. Demographic results indicated that populations had recently undergone sudden expansions which could have falsely resembled highly connected populations. Estimation of divergence times places the expansions in the mid to late Pleistocene. Populations had not reached migration-drift equilibrium thus contemporary population distributions of Marphysa corallina along the east coast of South Africa are largely shaped by past climatic events such as in the Pleistocene.
Population connectivity of stylophora pistillata and sinularia brassica between KwaZulu-Natal marine protected areas.
(2021) Gilmore, Jessica Rose.; Pearton, David James.; Macdonald, Angus Hector Harold.
Marine Protected Areas are a valuable tool for ecosystem protection and to enhance resilience in the face of global stressors such as global warming and ocean acidification. There is currently an incomplete understanding regarding the level to which MPAs in KwaZulu-Natal protect existing biodiversity and provide benefits beyond their boundaries. The focus of this study was to determine the extent to which the current MPA network acts to facilitate connectivity of sessile benthic species, the role of oceanographic processes, and whether these processes will persist under global change. The population connectivity of two coral species, a hard coral (Scleractinia), Stylophora pistillata, and a soft coral (Alcyonacea), Sinularia brassica, within and between the MPA network on the east coast of South Africa was studied using both traditional markers and RADSeq, a reduced representation genomic sequencing technique. Sampling locations were selected in three existing MPAs and on a representative reef located in the “gap” in between. These MPAs span the tropical Delagoa and subtropical Natal Bioregions. Stylophora pistillata in South Africa is split into two non-hybridizing clades with clear differences in distribution. Clade 2 was confined to the subtropical Delagoa bioregion whereas clade 3 was found throughout the study region from the tropical Delagoa bioregion down to the southern boundary of the warm temperate Natal bioregion. ITS data indicated that there is a complex population structure of the clade 2 potentially driven by a combination of currents, ecological selection, and distance. A subset of Stylophora clade 2 samples was analysed using a RADSeq approach which clarified the structure suggested by the ITS data and clearly identified three distinct populations across four reefs (Leadsman Shoal, Blood Reef, Aliwal Shoal and Aliwal Deep) spanning the Delagoa/Natal biogeographic break. These populations did not appear to be structured solely by geographic distance, with one population comprising samples from two sites (Blood Reef and Aliwal Deep) that were non-adjacent and at different depths (12-18 m vs >30 m), while a geographically adjacent population (Aliwal Shallow) at 12-18 m constituted a distinct population. This suggests that ecological selection might be involved in structuring the population over short distances for this coral. Sinularia brassica was not found south of the iSimangaliso Wetland Park in this study, despite it being recorded in the southern sites in previous surveys. Analyses of COI and mtMutS sequences revealed that there are potentially multiple clades present in the IWP population and that there is a poleward decrease in genetic diversity. Neither of these clades showed any clear geographical or genetic population structure between the reef complexes but additional studies using RADSeq may help to clarify the situation.
Population connectivity of Stylophorum pistillata and sinularia brassica between KwaZulu-Natal marine protected areas.
(2021) Gilmore, Jessica Rose.; Macdonald, Angus Hector Harold.
Marine Protected Areas are a valuable tool for ecosystem protection and to enhance resilience in the face of global stressors such as global warming and ocean acidification. There is currently an incomplete understanding regarding the level to which MPAs in KwaZulu-Natal protect existing biodiversity and provide benefits beyond their boundaries. The focus of this study was to determine the extent to which the current MPA network acts to facilitate connectivity of sessile benthic species, the role of oceanographic processes, and whether these processes will persist under global change. The population connectivity of two coral species, a hard coral (Scleractinia), Stylophora pistillata, and a soft coral (Alcyonacea), Sinularia brassica, within and between the MPA network on the east coast of South Africa was studied using both traditional markers and RADSeq, a reduced representation genomic sequencing technique. Sampling locations were selected in three existing MPAs and on a representative reef located in the “gap” in between. These MPAs span the tropical Delagoa and subtropical Natal Bioregions. Stylophora pistillata in South Africa is split into two non-hybridizing clades with clear differences in distribution. Clade 2 was confined to the subtropical Delagoa bioregion whereas clade 3 was found throughout the study region from the tropical Delagoa bioregion down to the southern boundary of the warm temperate Natal bioregion. ITS data indicated that there is a complex population structure of the clade 2 potentially driven by a combination of currents, ecological selection, and distance. A subset of Stylophora clade 2 samples was analysed using a RADSeq approach which clarified the structure suggested by the ITS data and clearly identified three distinct populations across four reefs (Leadsman Shoal, Blood Reef, Aliwal Shoal and Aliwal Deep) spanning the Delagoa/Natal biogeographic break. These populations did not appear to be structured solely by geographic distance, with one population comprising samples from two sites (Blood Reef and Aliwal Deep) that were non-adjacent and at different depths (12-18 m vs >30 m), while a geographically adjacent population (Aliwal Shallow) at 12-18 m constituted a distinct population. This suggests that ecological selection might be involved in structuring the population over short distances for this coral. Sinularia brassica was not found south of the iSimangaliso Wetland Park in this study, despite it being recorded in the southern sites in previous surveys. Analyses of COI and mtMutS sequences revealed that there are potentially multiple clades present in the IWP population and that there is a poleward decrease in genetic diversity. Neither of these clades showed any clear geographical or genetic population structure between the reef complexes but additional studies using RADSeq may help to clarify the situation.
A re-appraisal of the holothuroid genera Pseudocnus Panning, 1949 and Pseudocnella Thandar, 1987 based on morphological and, for the latter, also molecular evidence (Echinodermata : Holothuroidea : Dendrochirotida : Cucumariidae)
Mjobo, Sifiso.; Thandar, Ahmed Suleman.; Macdonald, Angus Hector Harold.
After the erection of the genus Pseudocnella by Thandar (1987) to accommodate three southern African Cucumariids and a Mediterranean form, then classified in Pseudocnus, certain problems still remained. In addition to this the recent revision of the Antarctic-Subantarctic species of Pseudocnus by O’Loughlin et al. (2014) left the remaining world species unattended to. Due to the above, both these genera (Pseudocnus and Pseudocnella) were looked at critically in order to determine whether all species assigned to them are congeneric. As far as the genus Pseudocnus is concerned those species excluded from O’Loughlin et al (2014) revision are looked at only morphologically by examining available materials and literature. Species belonging to the genus Pseudocnella are examined from both morphological and molecular aspects. O’Loughlin et al. (2014) restriction of the genus Pseudocnus was accepted and hence two new genera Panningocnus and Thandarocnus are diagnosed for those species with unequal tentacles and body wall deposits respectively made up of a single or more than a single layer of calcareous material. On this basis only three species now remain in Pseudocnus, with Cucumaria koellikeri Semper, 1868 as type species, nine species are transferred to Panningocnus, with Cucumaria dubiosa Semper, 1868 as type species and the remaining six species transferred to Thandarocnus with Pseudocnus sentus O’Loughlin & Alcock, 2000 as type species. A new genus Hemiocnus is erected for Cladodactyla syracusana Grube, 1840 (=Pseudocnella syracusana) as type species and to this is also transferred Pseudocnella insolens (Théel, 1886). The genus Pseudocnella now appears to accommodate only two South African nominal species with Cucumaria sinorbis Cherbonnier, 1952 remaining as type species. All species dealt with are diagnosed, keyed and their geographical distributions mapped, except those dealt with by O’Loughlin et al. (2014) and Thandar (1987).
The marine aquarium trade in South Africa: a vector for alien invasive species?
(2019) Wehr, Gitte Kirsten.; Macdonald, Angus Hector Harold.; Sink, Kerry.
Biological invasions are increasingly recognized as a primary threat to biodiversity. Global transport and trade play an important role in the movement of alien species around the world, and as transport and trade have intensified over the decades, so too has the number of alien species introductions. As preventing the introduction of harmful species is a more cost-effective and efficient method to managing biological invasions, it is imperative that scientific studies are aimed at identifying the pathways responsible for introductions. The marine aquarium trade is an ever-growing business globally and only up until recently has been identified as a major pathway for the introduction of alien species. Except for the notorious cases of the invasive lionfish, Pterois volitans, and seaweed, Caulerpa taxifolia, the role of the aquarium trade towards the introduction of alien marine organisms has been largely unevaluated. With popularity rising for the marine aquarium hobby in South Africa, it is of concern that the trade remains predominantly unregulated. This study aims to investigate the risk posed by the marine aquarium trade as a pathway for the introduction of alien invasive species in South Africa. One such vector examined in this study is live rock: any type of rock or dead coral skeleton encrusted with, and containing within its crevices, a wide variety of marine organisms, including colourful sessile invertebrates and encrusting algae. A combination of morphological and DNA barcoding molecular identifications, based on the phylogenetic inference of mitochondrial cytochrome c oxidase subunit 1 (COI) and internal transcribed spacer region (ITS) sequence data, was used to assign identifications to 174 taxa harvested from imported Indonesian and Kenyan live rock. Of the 6 diverse phyla identified, one alien species was flagged as harmful due to its successful invasion of other ecosystems in the world: the glass sea anemone Aiptasia pulchella. Non-target DNA amplification of live rock associated taxa exposed the coral pathogenic bacteria Vibrio spp., further suggesting that the marine aquarium trade is also a pathway for the introduction of pathogens. A second component of the study involved the assessment, via formal survey, of the role that pet stores and hobbyists play in the introduction and transmission of marine organisms around South Africa. Irresponsible aquarium pest disposal methods and informal trading pathways were revealed highlighting the need for an education intervention to promote responsible aquarium ownership skills. The third part of the study entailed a national stock inventory of marine aquarium traded fish and revealed that the number of species traded is vast (n = 228) and that 60 % are alien to South African waters. Although the strength of this vector was not defined, this study confirms that the marine aquarium trade is a pathway for the introduction of alien and potentially invasive organisms and serves as the foundation for future research into marine aquarium trade vectors in South Africa. The findings and conclusions presented here should be considered by biosecurity monitoring and management initiatives.