Papers by Aletta E Bester-van der Merwe
Local adaptation with gene flow in a highly dispersive shark
Evolutionary Applications, Dec 19, 2023
African Journal of Marine Science, Jan 2, 2019
Selected microsatellite primers were modified by adding an M13 sequence (TGTAAAACGACGGCCAGT) to t... more Selected microsatellite primers were modified by adding an M13 sequence (TGTAAAACGACGGCCAGT) to the forward primer for amplification, using the three-primer amplification protocol of , and by adding a PIG-tail (GTTT; to the reverse primer. Each 10-µl PCR reaction contained 5 µl of KAPA2G
Characterization of the complete mitochondrial genomes of two Critically Endangered wedgefishes: Rhynchobatus djiddensis and Rhynchobatus australiae
Mitochondrial DNA Part B
Gene expression differentials driven by mass rearing and artificial selection in black soldier fly colonies
Insect Molecular Biology
The study investigated the global and regional phylogeography of the yellowtail kingfish <i>... more The study investigated the global and regional phylogeography of the yellowtail kingfish <i>Seriola lalandi</i> by examining genetic diversity and population genetic structure of this species at inter-and intra-ocean level and on a regional scale. DNA fragments of two mitochondrial genes, cytochrome <i>b</i> (Cytb) and cytochrome <i>c</i> oxidase subunit I (COI) and one nuclear gene, recombination activating gene 1 (RAG1), were sequenced to investigate the global-scale phylogeography of this species. The population genetic structure within the South Pacific, as well as along the South African coastline, was examined further using six microsatellite markers. Three distinct clades were identified for <i>S. lalandi</i>, which correspond with previously described subspecies of the North-East Pacific, North-West Pacific and the Southern Hemisphere. Within the latter, additional divergence was observed between the South Pacific and the South...
Insects, 2021
The black soldier fly (BSF), Hermetia illucens, is a promising candidate for the emerging insect ... more The black soldier fly (BSF), Hermetia illucens, is a promising candidate for the emerging insect farming industry with favourable characteristics for both bioremediation and production of animal delivered nutritive and industrial compounds. The genetic management of commercial colonies will become increasingly important for the sustainability of the industry. However, r-selected life history traits of insects pose challenges to conventional animal husbandry and breeding approaches. In this study, the long-term genetic effects of mass-rearing were evaluated as well as mating systems in the species to establish factors that might influence genetic diversity, and by implication fitness and productivity in commercial colonies. Population genetic parameters, based on microsatellite markers, were estimated and compared amongst two temporal wild sampling populations and four generations (F28, F48, F52, and F62) of a mass-reared colony. Furthermore, genetic relationships amongst mate pairs ...
Scientific Reports, 2021
Phenotypic plasticity in life-history traits in response to heterogeneous environments has been o... more Phenotypic plasticity in life-history traits in response to heterogeneous environments has been observed in a number of fishes. Conversely, genetic structure has recently been detected in even the most wide ranging pelagic teleost fish and shark species with massive dispersal potential, putting into question previous expectations of panmixia. Shallow oceanic seamounts are known aggregation sites for pelagic species, but their role in genetic structuring of widely distributed species remains poorly understood. The yellowtail kingfish (Seriola lalandi), a commercially valuable, circumglobal, epipelagic fish species occurs in two genetically distinct Southern Hemisphere populations (South Pacific and southern Africa) with low levels of gene-flow between the regions. Two shallow oceanic seamounts exist in the ocean basins around southern Africa; Vema and Walters Shoal in the Atlantic and Indian oceans, respectively. We analysed rare samples from these remote locations and from the South...
南アフリカ産Venturia inaequalis(リンゴ黒星病)の4種類の群集の遺伝多様性と遺伝子流
Phytopathology, 2017
Microsatellite development and detection of admixture among three sympatric Haploblepharus species (Carcharhiniformes: Scyliorhinidae)
Aquatic Conservation: Marine and Freshwater Ecosystems, 2020
Haploblepharus is an understudied genus comprising four recognized scyliorhinid species that are ... more Haploblepharus is an understudied genus comprising four recognized scyliorhinid species that are endemic to southern Africa. Species identification within this group has historically been problematic due to a high degree of morphological conservatism among congeners, further complicated by the possibility of interspecific hybridization. This study describes the development of two microsatellite panels comprising 10 polymorphic markers for the puffadder shyshark, Haploblepharus edwardsii. The markers were characterized in 35 H. edwardsii specimens and tested for cross‐species utility in Haploblepharus fuscus, Haploblepharus pictus, and the more distantly related scyliorhinid Halaelurus natalensis. Genetic diversity statistics were estimated for each species, and the presence of population differentiation was tested for in H. edwardsii and H. pictus. Furthermore, interspecific genetic differentiation was examined to infer the potential use of these markers for species identification a...
Historical biogeography of smoothhound sharks (genus Mustelus) of Southern Africa reveals multiple dispersal events from the Northern Hemisphere
Systematics and Biodiversity, 2020
Members of the smoothhound shark genus Mustelus display a widespread distribution pattern across ... more Members of the smoothhound shark genus Mustelus display a widespread distribution pattern across ocean basins with a high degree of sub-regional endemism. The patterns and processes that resulted in smoothhound biodiversity and present-day distribution remain largely unknown. We infer the phylogenetic relationships of the genus Mustelus, based on sequence data (3474 bp) from three mitochondrial genes (CR, NADH-2 and 12S-16SrRNA) and a nuclear gene (KBTBD2) from seven species of Mustelus distributed across the eastern Atlantic- and Indo-Pacific oceans. Using the CR and KBTBD2 dataset, we infer the phylogeographic placement of Old World Mustelus, with particular reference to species from southern Africa. Using a near-complete phylogeny of the genus including Old World and New World species of Mustelus and publicly available sequences of the NADH-2 gene, we found supporting evidence indicating a major cladogenic event separating placental and aplacental species. Biogeographical analyses further revealed that the radiation of Mustelus in the southern African region was driven primarily by long-distance dispersal during the upper Miocene to lower Pleistocene. The placement of the placental blackspotted smoothhound Mustelus punctulatus at the base of the placental non-spotted clade suggests the secondary loss of black spots in the genus, and this was also supported by the ancestral state reconstruction. The results furthermore suggest that the Southern Hemisphere species of the genus arose from multiple separate dispersal events from the Northern Hemisphere which is in line with the earliest record of Mustelus in the Northern Hemisphere.
Genetic and phenotypic consequences of early domestication in black soldier flies (Hermetia illucens)
Animal Genetics, 2020
SummaryThe black soldier fly, Hermetia illucens, is an emerging biotechnological agent with its l... more SummaryThe black soldier fly, Hermetia illucens, is an emerging biotechnological agent with its larvae being effective converters of organic waste into usable bio‐products including protein and lipids. To date, most operations use unimproved commercial populations produced by mass rearing, without cognisance of specific breeding strategies. The genetic and phenotypic consequences of these commercial practices remain unknown and could have a significant impact on long‐term population viability and productivity. The aim of this study was thus to assess the genetic and phenotypic changes during the early phases of colony establishment and domestication in the black soldier fly. An experimental colony was established from wild founder flies and a new microsatellite marker panel was developed to assess population genetic parameters along with the phenotypic characteristics of each generational cohort under captive breeding. The experimental colony was characterised by a small effective p...
Spatio-temporal genetic variation of juvenile smooth hammerhead sharks in South Africa
Marine Biology Research, 2019
ABSTRACT The smooth hammerhead shark Sphyrna zygaena is known to display a high degree of site fi... more ABSTRACT The smooth hammerhead shark Sphyrna zygaena is known to display a high degree of site fidelity to specific areas along the South African coastline. This species is vulnerable to overfishing and steep declines have been noted globally. In this study, a dual marker approach was used to investigate the spatial and temporal genetic variation of juvenile S. zygaena across the south and east coast of South Africa. Kinship of individuals was determined within and across cohorts from juvenile S. zygaena sampled in Mossel Bay, a putative pupping ground. Significant genetic differentiation (supported by F-statistics, multivariate analysis and Bayesian clustering) was evident between individuals sampled from the warm temperate south coast and the subtropical east coast, with asymmetric gene flow between regions. Distinct genetic composition was also revealed between sampling years, with different levels of relatedness within and among cohorts, indicating different temporal populations utilizing Mossel Bay annually. Based on these results, further investigation of S. zygaena populations across a wider region is warranted in order to make recommendations regarding conservation management of this vulnerable coastal shark.
Molecular research on the systematically challenging smoothhound shark genusMustelus: a synthesis of the past 30 years
African Journal of Marine Science, 2017
The species-rich genus Mustelus (smoothhounds) of the shark family Triakidae is one of the most b... more The species-rich genus Mustelus (smoothhounds) of the shark family Triakidae is one of the most bio-economically important groups of elasmobranchs in the world’s oceans. Despite the commercial value of Mustelus, the systematics of the group remains largely unresolved and there is no global review or synthesis of knowledge about the conservation status and conservation genetics of smoothhounds across all oceanic regions. Here, we analysed published studies as well as grey literature to gain insight into the biogeographic, ecological and behavioural factors that shape genetic diversity in smoothhounds, and we identify critical knowledge gaps. From a series of molecular phylogenetic studies it can be inferred that the genus Mustelus is paraphyletic and that the aplacental species evolved secondarily from the placental species of the genus. The increasing availability of genetic data aids in disentangling systematic issues, such that more meaningful morphological characters can be chosen for use in practical field-identification keys for co-occurring smoothhounds. An integrative taxonomic approach to the genus Mustelus may offer the best chance of recording and protecting the biodiversity of these sharks. Furthermore, it is evident that different smoothhound species exhibit unique gene-flow patterns, suggesting varying rates within species and hence that species-level conservation approaches would be most appropriate. Molecular studies have advanced our understanding of smoothhound biology (including reproductive traits), ecology and evolution. While many knowledge gaps remain, a crucial lesson from this review is that, when doing assessments on a molecular level, it is important to place genetic results in a broader context, by assimilating biological and ecological data, if definitive conclusions are to be drawn.
Hydrobiologia, 2019
Following the kind invitation of the organizers Christian Laforsch and Max Rabus, the 11th Intern... more Following the kind invitation of the organizers Christian Laforsch and Max Rabus, the 11th International Symposium on Cladocera gathered scientists from all over the world working on multi-disciplinary aspects of Cladoceran biology. The meeting is renowned to house Cladoceran research from multiple disciplines including evolutionary history, host-parasite and predator-prey interactions, phylogeny, environmental genomics, population genetics, biogeography, systematics, and taxonomy. First being held in 1986 in Hungary, this meeting recurs every 3 years. The 11th meeting was held in Kulmbach, Germany, from September the 24th to the 29th, 2017, in the wonderful Plassenburg Castle in the margravial city of Kulmbach, Germany. During this 1 week, scientists from all around the globe coming from Austria,
African Journal of Marine Science, 2019
Selected microsatellite primers were modified by adding an M13 sequence (TGTAAAACGACGGCCAGT) to t... more Selected microsatellite primers were modified by adding an M13 sequence (TGTAAAACGACGGCCAGT) to the forward primer for amplification, using the three-primer amplification protocol of , and by adding a PIG-tail (GTTT; to the reverse primer. Each 10-µl PCR reaction contained 5 µl of KAPA2G
Reproductive philopatry in a coastal shark drives age-related population structure
Marine Biology, 2019
The cosmopolitan lamniform shark Carcharias taurus (commonly known as the ragged-tooth, grey nurs... more The cosmopolitan lamniform shark Carcharias taurus (commonly known as the ragged-tooth, grey nurse or sand tiger shark) is threatened by overexploitation in parts of its range. Return migrations of females to specific nursery areas suggest that females exhibit reproductive philopatry, a behaviour that over time might lead to genetically isolated subpopulations over various spatial scales. To investigate genetic evidence for reproductive philopatry, genetic data from mitochondrial and microsatellite markers were generated for 104 young-of-the-year and juvenile sharks. Comparing the smallest versus the largest young sharks revealed a pattern of size-related differentiation between nurseries that was only found in the smaller size class. This not only confirms reproductive philopatry of their mothers, but is also in line with previous observations of larger juvenile sharks increasing their migration range and moving between sites. Our results highlight the need to target young-of-the-year sharks when investigating reproductive philopatry to exclude roaming individuals that obscure size-related signals of genetic differentiation. Given the species’ high susceptibility to overexploitation, the evidence for reproductive philopatry is of direct importance to the management and conservation of C. taurus worldwide. As many nursery areas as possible should be protected to ensure that the number of locally resident juveniles and the pool of the returning females remain stable in the long term. This may warrant protected areas, or time-area closures, prohibiting exploitation in the nursery areas during pupping season.
Assessing multiple paternity in three commercially exploited shark species: Mustelus mustelus, Carcharhinus obscurus and Sphyrna lewini
Journal of Fish Biology, 2016
In this study, multiple paternity (MP) was investigated in three commercially important shark spe... more In this study, multiple paternity (MP) was investigated in three commercially important shark species, common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and scalloped hammerhead Sphyrna lewini occurring in southern Africa. Reduced marker panels of between five and six microsatellite loci were constructed for each species and used to genotype and assess the presence of MP in a total of 60 M. mustelus individuals from six litters, 90 C. obscurus individuals from 14 litters and 54 S. lewini individuals from 13 litters. Analysis in GERUD and COLONY revealed the presence of MP in all three species. Multiple paternities were observed in 67, 35 and 46% of the litters of M. mustelus, C. obscurus and S. lewini, with corresponding average sire size of 1·6, 1·4 and 2·0, respectively. The variation in the rate of MP among the three species is in accordance with previous studies whilst the comparatively high frequency of MP observed for M. mustelus, matches what has previou...
Phytopathology®, 2017
Venturia inaequalis isolates were collected during the 2012/13 and 2013/14 seasons from the four ... more Venturia inaequalis isolates were collected during the 2012/13 and 2013/14 seasons from the four principal apple growing regions of South Africa, Elgin (n = 114), Koue Bokkeveld (n = 126), Lower Langkloof (n = 92), and Upper Langkloof (n = 103). Sequence analysis of the ribosomal internal transcribed spacer (ITS) gene regions and genotyping with six (2012/13) and seven (2013/14) microsatellite (SSR) markers was conducted. A subset of 12 isolates from the individual ITS haplotype groups were sequenced for the translation elongation factor-1 alpha (TEF1) and the large subunit of the RNA polymerases II (RPB1) gene regions. Four haplotypes were found for ITS, whereas all isolates were identical for the TEF1 and RPB1 gene regions. The SSR markers revealed considerable variation with an average gene diversity (H) of 0.675. Multivariate analysis (discriminant analysis of principal components [DAPC]) revealed that the two Langkloof populations clustered together with the Koue Bokkeveld popu...
PloS one, 2017
The tope shark (Galeorhinus galeus Linnaeus, 1758) is a temperate, coastal hound shark found in t... more The tope shark (Galeorhinus galeus Linnaeus, 1758) is a temperate, coastal hound shark found in the Atlantic and Indo-Pacific oceans. In this study, the population structure of Galeorhinus galeus was determined across the entire Southern Hemisphere, where the species is heavily targeted by commercial fisheries, as well as locally, along the South African coastline. Analysis was conducted on a total of 185 samples using 19 microsatellite markers and a 671 bp fragment of the NADH dehydrogenase subunit 2 (ND2) gene. Across the Southern Hemisphere, three geographically distinct clades were recovered, including one from South America (Argentina, Chile), one from Africa (all the South African collections) and an Australia-New Zealand clade. Nuclear data revealed significant population subdivisions (FST = 0.192 to 0.376, p<0.05) indicating limited gene flow for tope sharks across ocean basins. Marked population connectivity was however evident across the Indian Ocean based on Bayesian c...
Ecology and Evolution, 2017
The common smooth-hound (Mustelus mustelus) is the topmost bio-economically and recreationally im... more The common smooth-hound (Mustelus mustelus) is the topmost bio-economically and recreationally important shark species in southern Africa, western Africa, and Mediterranean Sea. Here, we used the Illumina HiSeq™ 2000 next-generation sequencing (NGS) technology to develop novel microsatellite markers for Mustelus mustelus. Two microsatellite multiplex panels were constructed from 11 polymorphic loci and characterized in two populations of Mustelus mustelus representative of its South African distribution. The markers were then tested for cross-species utility in Galeorhinus galeus, Mustelus palumbes, and Triakis megalopterus, three other demersal coastal sharks also subjected to recreational and/or commercial fishery pressures in South Africa. We assessed genetic diversity (N A , A R , H O , H E, and PIC) and differentiation (F ST and D est ) for each species and also examined the potential use of these markers in species assignment. In each of the four species, all 11 microsatellites were variable with up to a mean N A of 8, A R up to 7.5, H E and PIC as high as 0.842. We were able to reject genetic homogeneity for all species investigated here except for T. megalopterus. We found that the panel of the microsatellite markers developed in this study could discriminate between the study species, particularly for those that are morphologically very similar. Our study provides molecular tools to address ecological and evolutionary questions vital to the conservation and management of these locally and globally exploited shark species.
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Papers by Aletta E Bester-van der Merwe