Browsing by Author "Rhode, Clint"

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    A population genetic analysis of abalone domestication events in South Africa: Implications for the management of the abalone resource
    (2012) Rhode, Clint; Hepple J.-A.; Jansen S.; Davis T.; Vervalle J.; Bester-van der Merwe A.E.; Roodt-Wilding R.
    Abalone culture is South Africa's largest aquaculture sector in terms of revenue. Nonetheless, the industry is in its formative years and much scope remains for refinement and regulation of production practices. It is important to manage genetic diversity in terms of the particular breeding objectives pursued by respective facilities: selective breeding vs. ranching; whilst conserving the genetic integrity of wild populations remains a national imperative. The present study found no significant decrease in genetic diversity between wild and cultured populations as based on heterozygosity and allelic content of genomic- and EST-microsatellite loci. However, estimates for pairwise genotypic differentiation, F st, AMOVA and Factorial correspondence analysis suggest the genetic heterogeneity of cultured populations and their significant differentiation from the wild progenitor populations. As expected, the cultured population showed reduced effective population sizes, but relatedness remained low. It is postulated that both neutral and selective evolutionary forces are responsible for the observed patterns of genetic variability within and amongst populations. The implications of the results are discussed in terms of broad managerial objectives for the South African abalone and continued monitoring is advised. © 2012 Elsevier B.V.
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    The complete mitochondrial genome and phylogenetic position of the leopard catshark, Poroderma pantherinum
    (Taylor & Francis Open, 2018) Van Staden, Michaela; Gledhill, Katie S.; Rhode, Clint; Bester-Van Der Merwe, Aletta E.
    We present the first mitochondrial genome of a South African endemic catshark, Poroderma pantherinum. The complete mitogenome is 16,686 bp in length, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding control region. Similar to other shark mitogenomes, it is AT rich (61.1%), with a GC content of 38.9%. Protein-coding genes used one of two start codons (ATG and GTG) and one stop codon (TAA/TA-/T-). Phylogenetic analysis of the leopard catshark and 34 carcharhinid species showed that it clusters with two other scyliorhinid species (Cephaloscyllium umbratile and Scyliorhinus canicula) with 100% support.
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    Development of gene-linked molecular markers in South African abalone (Haliotis midae) using an in silico mining approach
    (Stellenbosch : University of Stellenbosch, 2010-03) Rhode, Clint; Roodt-Wilding, R.; University of Stellenbosch. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is the only endemic species of commercial value. Aquaculture remains the only avenue for expanding the industry, since the closure of the fishery. The current focus is on implementing a molecular breeding programme; thus the development of molecular markers for linkage mapping and QTL analysis is a priority. Various markers, mainly anonymous, have been developed for H. midae; however emphasis is being placed on the development of gene-linked type I molecular markers. The present study investigates and demonstrates the use of public sequence collections to develop type I markers for a species with limited genomic resources, via three strategies: Surveying anonymous H. midae microsatellite markers’ flanking regions to find homology to gene sequences in public databases, cross-species marker transfer of anonymous markers from H. rubra and H. discus hannai demonstrating putative gene associations and lastly EST marker mining (SNP and microsatellites) from various Haliotids and testing transfer to the target species. Approximately 17% of H. midae anonymous markers showed significant similarity to genes. The current study also reports higher cross-species transferability from both H. rubra and H. discus hannai to H. midae (39% and 20.5%, respectively) than previously demonstrated and 15 EST-microsatellites and 16 EST-SNPs were successfully mined. Furthermore, the non-random distribution of microsatellites and high nucleotide diversity in the H. midae genome was confirmed. This is a low cost and time effective method for marker development and presents a continuous and dynamic resource that could be used for future marker development and characterisation as sequence information in public databases grow exponentially.
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    Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens
    (BMC, 2021-05-05) Kaya, Cengiz; Generalovic, Tomas N.; Ståhls, Gunilla; Hauser, Martin; Samayoa, Ana C.; Nunes-Silva, Carlos G.; Roxburgh, Heather; Wohlfahrt, Jens; Ewusie, Ebenezer A.; Kenis, Marc; Hanboonsong, Yupa; Orozco, Jesus; Carrejo, Nancy; Nakamura, Satoshi; Gasco, Laura; Rojo, Santos; Tanga, Chrysantus M.; Meier, Rudolf; Rhode, Clint; Picard, Christine J.; Jiggins, Chris D.; Leiber, Florian; Tomberlin, Jeffery K.; Hasselmann, Martin; Blanckenhorn, Wolf U.; Kapun, Martin; Sandrock, Christoph
    Background: The black soldier fly (Hermetia illucens) is the most promising insect candidate for nutrient-recycling through bioconversion of organic waste into biomass, thereby improving sustainability of protein supplies for animal feed and facilitating transition to a circular economy. Contrary to conventional livestock, genetic resources of farmed insects remain poorly characterised. We present the first comprehensive population genetic characterisation of H. illucens. Based on 15 novel microsatellite markers, we genotyped and analysed 2862 individuals from 150 wild and captive populations originating from 57 countries on seven subcontinents. Results: We identified 16 well-distinguished genetic clusters indicating substantial global population structure. The data revealed genetic hotspots in central South America and successive northwards range expansions within the indigenous ranges of the Americas. Colonisations and naturalisations of largely unique genetic profiles occurred on all non-native continents, either preceded by demographically independent founder events from various single sources or involving admixture scenarios. A decisive primarily admixed Polynesian bridgehead population serially colonised the entire Australasian region and its secondarily admixed descendants successively mediated invasions into Africa and Europe. Conversely, captive populations from several continents traced back to a single North American origin and exhibit considerably reduced genetic diversity, although some farmed strains carry distinct genetic signatures. We highlight genetic footprints characteristic of progressing domestication due to increasing socio-economic importance of H. illucens, and ongoing introgression between domesticated strains globally traded for large-scale farming and wild populations in some regions. Conclusions: We document the dynamic population genetic history of a cosmopolitan dipteran of South American origin shaped by striking geographic patterns. These reflect both ancient dispersal routes, and stochastic and heterogeneous anthropogenic introductions during the last century leading to pronounced diversification of worldwide structure of H. illucens. Upon the recent advent of its agronomic commercialisation, however, current human-mediated translocations of the black soldier fly largely involve genetically highly uniform domesticated strains, which meanwhile threaten the genetic integrity of differentiated unique local resources through introgression. Our in-depth reconstruction of the contemporary and historical demographic trajectories of H. illucens emphasises benchmarking potential for applied future research on this emerging model of the prospering insectlivestock sector.
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    Integrated linkage map of Haliotis midae Linnaeus based on microsatellite and snp markers.
    (NATL SHELLFISHERIES ASSOC, C/O DR. SANDRA E. SHUMWAY, NATURAL SCIENCEDIVISION, SOUTHAMPTON COLLEGE, SOUTHAMPTON, USA, NY, 11968, 2013) Vervalle J; Hepple J; Jansen S; Du Plessis J; Wang P; Rhode, Clint; Roodt-Wilding R
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    New mitochondrial gene rearrangement in psyttalia concolor, p. humilis and p. lounsburyi (hymenoptera: braconidae), three parasitoid species of economic interest
    (MDPI, 2020-12-02) Powell, Chante; Caleca, Virgilio; Rhode, Clint; Da Costa, Luis Teixeira; Van Asch, Barbara
    The family Braconidae consists mostly of specialized parasitoids, some of which hold potential in biocontrol of agricultural pests. Psyttalia concolor, Psyttalia humilis and Psyttalia lounsburyi are parasitoids associated with Bactrocera oleae, a major pest of cultivated olives. The native range of Psyttalia concolor is the Mediterranean, and P. humilis and P. lounsburyi are native to sub-Saharan Africa. This study reports the mitochondrial genomes of the three species, thus laying the foundation for mitogenomic analyses in the genus Psyttalia. Comparative mitogenomics within Braconidae showed a novel gene arrangement in Psyttalia in involving translocation and inversion of transfer RNA genes. The placement of Psyttalia in the subfamily Opiinae was well-supported, and the divergence between Psyttalia and its closest relative (Diachasmimorpha longicaudata) was at ~55 MYA [95% highest posterior density (HPD): 34–83 MYA]. Psyttalia lounsburyi occupied the most basal position among the three Psyttalia, having diverged from the other two species ~11 MYA (95% HPD: 6–17 MYA). Psyttalia concolor and P. humilis were recovered as sister species diverged at ~2 MYA (95% HPD: 1.1–3.6 MYA). This phylogeny combining new sequences and a set of 31 other cyclostomes and non-cyclostomes highlights the importance of a comprehensive taxonomic coverage of Braconidae mitogenomes to overcome the lack of robustness in the placement of several subfamilies.
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    Phylogeography, genetic diversity, and population structure of Nile crocodile populations at the fringes of the southern African distribution
    (Public Library of Science, 2018) Van Asch, Barbara; Versfeld, William F.; Hull, Kelvin L.; Leslie, Alison J.; Matheus, Timoteus I.; Beytell, Petrus C.; Du Preez, Pierre; Slabbert, Ruhan; Rhode, Clint
    Nile crocodiles are apex predators widely distributed in sub-Saharan Africa that have been viewed and managed as a single species. A complex picture of broad and fine-scale phylogeographic patterns that includes the recognition of two species (Crocodylus niloticus and Crocodylus suchus), and the structuring of populations according to river basins has started to emerge. However, previous studies surveyed a limited number of samples and geographical regions, and large areas of the continent remained unstudied. This work aimed at a fine scale portrait of Nile crocodile populations at the fringes of their geographic distribution in southern Africa. Wild and captive individuals were sampled across four major river systems (Okavango, Lower Kunene, Lower Shire and Limpopo) and the KwaZulu-Natal region. A multi-marker approach was used to infer phylogeographic and genetic diversity patterns, including new and public mitochondrial data, and a panel of 11 nuclear microsatellites. All individuals belonged to a phylogenetic clade previously associated with the C. niloticus species, thus suggesting the absence of C. suchus in southern Africa. The distribution of mitochondrial haplotypes indicated ancestral genetic connectivity across large areas, with loss of diversity along the north-south axis. Genetic variation partitioned the populations primarily into western and eastern regions of southern Africa, and secondarily into the major river systems. Populations were partitioned into five main groups corresponding to the Lower Kunene, the Okavango, the Lower Shire, and the Limpopo rivers, and the KwaZulu-Natal coastal region. All groups show evidence of recent bottlenecks and small effective population sizes. Long-term genetic diversity is likely to be compromised, raising conservation concern. These results emphasize the need for local genetic assessment of wild populations of Nile crocodiles to inform strategies for management of the species in southern Africa.
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    Population genetic analysis for the identification of loci associated to abalone domestication in South Africa.
    (Aquaculture Association of South Africa, 2013) Rhode, Clint; Vervalle J; van der Merwe AE; Roodt-Wilding R
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    Signatures of selection in natural and cultured Abalone (Haliotis midae) : a population genomics study
    (Stellenbosch : Stellenbosch University, 2013-03) Rhode, Clint; Roodt-Wilding, R.; Bester-van der Merwe, Aletta Elizabeth; Stellenbosch University. Faculty of Science. Dept. of Genetics.
    ENGLISH ABSTRACT: The South African abalone, Haliotis midae, commonly known as perlemoen, is an economically important gastropod mollusc. Historically, this species maintained a lucrative fisheries sector; however with increasingly lower landings there has now been a shift to aquaculture. Efforts to conserve natural populations and to improve abalone aquaculture production are thus running in parallel. Previous studies reported significant disparities in parental contributions in aquaculture populations that could explain the rapid divergence of commercial stocks from wild populations. Furthermore, subtle, but significant, population differentiation has also been reported for wild populations on the west-, south-, and east coast of the South African coastline. This study therefore aimed to investigate the evolutionary forces, in particularly selection, facilitating population divergence in wild and cultured H. midae populations using a population genomics approach. By using both microsatellite- and single nucleotide polymorphism (SNP) markers it was found that approximately 10% to 27% of the H. midae genome may be influenced by selection. When incorporating these loci into analyses of population differentiation (e.g. AMOVA, factorial correspondence analysis and estimates of genetic distance) there was a marked increase in genetic divergence between wild and cultured populations (especially when using microsatellite loci) and amongst populations from different geographic regions (particularly supported by the SNP loci). The differences in population clustering as highlighted by microsatellite- and SNP markers can most likely be attributed to the genomic distribution of the respective loci: The SNP markers were developed from EST sequences and therefore mostly represents protein structural variation; whereas the microsatellite markers, found to be putatively under selection, were mainly located in regulatory motifs. The results of this study therefore confirmed previous observations of divergence amongst wild- and cultured populations, but more importantly demonstrated that selection is an important factor driving this divergence. In wild populations selection probably facilitates adaptation to local environmental conditions, whilst amongst aquaculture population adaptation to captivity, husbandry practices and artificial selection may be important determinants. There is evidence for population bottlenecks in wild- and cultured populations; nonetheless long-term effective population sizes seem to be large. Amongst the wild populations, however, short-term population sizes appear to be small most likely due to differential spawning rates amongst reproductively active animals leading to temporal fluctuation in genetic diversity. The results indicate that contact between wild and cultured abalone should be minimised to prevent any adverse effects due to outbreeding depression. With regards to conservation, an emphasis on maintaining adaptive diversity of the wild stocks might be warranted. Continued genetic monitoring is advisable for both wild and cultured abalone populations as to optimally manage the abalone resource for both conservation and commercial viability and sustainability.
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    Strategies for managing complex social-ecological systems in the face of uncertainty : examples from South Africa and beyond
    (Resilience Alliance, 2015) Biggs, Reinette, 1979-; Rhode, Clint; Archibald, Sally; Kunene, Lucky Makhosini; Mutanga, Shingirirai S.; Nkuna, Nghamula; Ocholla, Peter Omondi; Phadima, Lehlohonolo Joe
    Improving our ability to manage complex, rapidly changing social-ecological systems is one of the defining challenges of the 21st century. This is particularly crucial if large-scale poverty alleviation is to be secured without undermining the capacity of the environment to support future generations. To address this challenge, strategies that enable judicious management of socialecological systems in the face of substantive uncertainty are needed. Several such strategies are emerging from the developing body of work on complexity and resilience. We identify and discuss four strategies, providing practical examples of how each strategy has been applied in innovative ways to manage turbulent social-ecological change in South Africa and the broader region: (1) employ adaptive management or comanagement, (2) engage and integrate different perspectives, (3) facilitate self-organization, and (4) set safe boundaries to avoid system thresholds. Through these examples we aim to contribute a basis for further theoretical development, new teaching examples, and inspiration for developing innovative new management strategies in other regions that can help address the considerable sustainability challenges facing society globally.