Aletta E Bester-van der Merwe

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Aletta E verified their affiliation via an institutional email.

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• PhD Molecular Genetics
• Professor (Associate) at Stellenbosch University

Mitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dynamics, and investigating how environmental pressur...

The limited standards for the rigorous and objective use of mitochondrial genomes (mitogenomes) can lead to uncertainties regarding the phylogenetic relationships of taxa under varying evolutionary constraints. The mitogenome exhibits heterogeneity in base composition, and evolutionary rates may vary across different regions, which can cause empiri...

The black soldier fly (BSF), Hermetia illucens , has the ability to efficiently bioremediate organic waste into usable bio‐compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its associat...

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains comparatively understudied compared to other members of the family Sphyrnidae, and despite its Vulnerable status, a comprehensive understanding of its genetic landscape remain...

Wedgefishes (Rhinidae) are threatened by unsustainable fishing globally, and especially in the Southwest Indian Ocean (SWIO), due to their high-value fins in the shark trade. The whitespotted wedgefish Rhynchobatus djiddensis and the bottlenose wedgefish R. australiae are both classified as Critically Endangered on the IUCN Red List of Threatened S...

Here, we present, for the first time, the Ion Torrent® next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include Galeorhinus galeus (number of bases pairs (bp) 17,487; GenBank accession number ON652874), Mustelus asterias (16,708; ON652873), Mustelus mosis (16,755; ON075077), Mustelus palumbes (16,708; ON...

The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny r...

Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non‐model species, gene–environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large c...

Complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich order, the Carcharhiniforms (groundsharks) has yielded challenges in phylogenomic reconstruction of families and genera belonging to it, particularly in the family Triakidae (houndsharks), where there are arguments for both monophyly and paraphyly. We hy...

The International Union for Conservation of Nature (IUCN) estimates that over a third of all chondrichthyan species (sharks, rays and chimaeras) are threatened with extinction, primarily by overfishing (as target or bycatch species). Owing to the wide-ranging distributions of many chondrichthyans, they are often overlooked in marine protected area...

The ability to correctly identify specimens at the species level is crucial for assessing and conserving biodiversity. Despite this, species-specific data are lacking for many of South Africa’s catsharks due to a high level of morphological stasis. As comprehensive and curated DNA reference libraries are required for the reliable identification of...

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remaine...

Due to continued overexploitation and anthropogenic change, hammerhead sharks (Carcharhiniformes: Sphyrnidae) have experienced drastic declines over most of their geographic range. Owing to the K-selected life histories of these sharks, their population resilience and persistence, remain severely strained, further compromising ecosystem stability....

Phyllosticta citricarpa is the causative agent of citrus black spot (CBS), a cosmetic fungal disease that has been reported in most of the citrus-growing regions of the world. The occurrence of CBS in orchards is predominantly controlled by the application of fungicides during the fruit susceptibility period. Benzimidazoles (benomyl and carbendazim...

We present the complete mitochondrial genomes of the Critically Endangered whitespotted wedgefish, Rhynchobatus djiddensis (Forsskål, 1775), and bottlenose wedgefish, Rhynchobatus australiae (Whitley, 1939), with the R. djiddensis mitogenome documented for the first time. The genomes for R. djiddensis and R. australiae are 16,799 and 16,805 bp in l...

This is the first report on the complete mitochondrial genome (mitogenome) of South African Thyrsites atun (Euphrasén, 1791) and its phylogenetic placement within the Gempylidae family. The complete mitogenome of snoek is 16,494 bp in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs, and one control region. Gene order is similar to t...

The micro-evolutionary forces that shape genetic diversity during domestication have been assessed in many plant and animal systems. However, the impact of these processes on gene expression, and consequent functional adaptation to artificial environments, remains under-investigated. In this study, whole-transcriptome dynamics associated with the e...

Shark-like rays (order Rhinopristiformes) are the most threatened cartilaginous fish globally. Despite this, unresolved taxonomic issues still exist within the group. To date, no studies have used complete mitochondrial genomes to assess the phylogenetic placement of Acroteriobatus within the non-monophyletic family Rhinobatidae. The current study...

Phyllosticta citricarpa is a fungal pathogen causing citrus black spot (CBS). As a regulated pest in some countries, the presence of the pathogen limits the export of fruit and is therefore of agricultural and economic importance. In this study, we used high throughput sequencing data to infer the global phylogeographic distribution of this pathoge...

In recent decades, a combination of increasing demand and economic globalisation has created a global market for elasmobranch products, especially the highly prized shark fins for Asian markets. Morphological species identification, as well as traditional cytochrome c oxidase subunit I (COI) barcoding of shark fins and other products, become challe...

The common smooth‐hound shark, Mustelus mustelus, is a widely distributed demersal shark under heavy exploitation from various fisheries throughout its distribution range. To assist in the development of appropriate management strategies, the authors evaluate stock structure, site fidelity and movement patterns along the species’ distribution in so...

Simple Summary With a growing human population, global climate change and diminishing natural resources, the need for sustainable agricultural systems is evident. Insect farming has been shown to be an envi-ronmentally friendly alternative to conventional livestock farming. The black soldier fly (BSF) is a species of interest because the larvae are...

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. Shall...

Phyllosticta citricarpa is a fungal plant pathogen that causes citrus black spot (CBS). This study is the first to use high throughput sequencing (HTS) to study the genetic diversity within a P. citricarpa population. Seventeen isolates from the United States of America were sequenced and their genomes assembled. A pairwise mapping and variant call...

Citrus Black Spot (CBS), caused by Phyllosticta citricarpa, is a disease that affects citrus worldwide. In different regions of the world where both mating types occur, reports differ as to whether asexually produced pycnidiospores play an important role in the epidemiology of CBS and fruit infections. We, therefore, investigated the potential role...

Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The...

Black Sigatoka, caused by Pseudocercospora fijiensis, is a major foliar disease of banana and plantain worldwide. There are few available data regarding the genetic diversity and population structure of the pathogen in East Africa, which are needed to design effective and durable disease management strategies. We genotyped 319 single-spore isolates...

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 s...

• 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 st...

The 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 an...

Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The...

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 juvenil...

The blacktip shark Carcharhinus limbatus is a cosmopolitan species found in warm-temperate, subtropical and tropical waters around the world. The research here aimed to assess whether multiple paternity exists in South African C. limbatus and to confirm phylogeographic patterns previously observed within the species. A minimum and maximum frequency...

The common smoothhound, Mustelus mustelus, is an epibenthic species targeted by fisheries around the world driven by the increasing demand for shark products. Given the wide-spread occurrence of this species and corresponding lack of molecular data in many areas of said distribution, baseline molecular assessments of this commercially important sha...

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 su...

Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA...

We present the complete mitochondrial genome of the common smoothhound , Mustelus mustelus,which is 16,755 bp long, contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and non-coding control region. All protein-coding genes begin with the ATG codon, except for the COI gene, which begins with GTG. Six protein-coding genes terminated with...

The non-model shark species, dusky shark Carcharhinus obscurus, is a bio-economically and recreationally important shark in many areas of its range. Despite of the fishery importance of C. obscurus few genetic resources are currently available for the species. Here, we report on the isolation of eight novel microsatellite loci from C. obscurus usin...

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-codin...

The present histological study of adult female common smoothhound shark Mustelus mustelus demonstrates that the species can store sperm in their oviducal glands. In addition, single paternity of a litter of 22 pups is reported, contributing to further knowledge regarding the genetic and behavioural mating strategy of M. mustelus.

The species-rich shark genus Mustelus (smoothhounds or smoothhound sharks) is one of the most bio-economically important groups of elasmobranchs in the world’s oceans. Despite the commercial value of Mustelus, its systematics remains largely unresolved and there is no global review or synthesis of knowledge about the conservation status and conserv...

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 A...

Regional and local sampling populations, collection site, sample numbers (N) and sampling year. (DOCX)

L (K) distributions using the “log probability of data” (Mean of LnP±1) approach prior to application of Evanno method (above) and Delta K analysis of the true number of clusters following the Evanno method (below) across the Southern Hemisphere (left) and across South African (right). (DOCX)

L (K) distributions using the “log probability of data” (Mean of LnP±1) approach prior to application of Evanno method (above) and Delta K analysis of the true number of clusters following the Evanno method (below) for the two main genetic clusters Group 1 (left) and Group 2 (right) identified using STRUCTURE. (DOCX)

Plots of the isolation-by-distance (IBD) analysis of the South African sampling populations showing regression linearized FST and geographic distance (R2 = 0.238, P = 0.1478). (DOCX)

Individual cluster membership of the Southern Hemisphere samples following hierarchical structure performed on the two main genetic clusters (Group 1 and Group 2) identified using STRUCTURE. (TIF)

The common smoothhound (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...

The South African abalone (Haliotis midae) is a gastropod mollusc of economic importance. In recent years natural populations have come under considerable pressure due to overharvesting and ecological shifts. The spatial genetic structure of H. midae has been determined; however there has not been a temporal assessment of abalone population dynamic...

The study investigated the global and regional phylogeography of the yellowtail kingfish Seriola lalandi 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 b (Cytb) and cytochrome c oxidase subunit I (COI) and o...

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/...

The South African abalone is a gastropod mollusc of economic importance. In recent years natural populations have come under considerable pressure due to natural and anthropogenic factors. The spatial genetic structure of abalone has been determined; however the degree to which adaptive evolutionary processes vs. neutral mechanisms maintain this po...

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 u...

Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua Afrikaner (NA), South African Merino (SA...

The population genetic structure and demographics of the common smoothhound shark Mustelus mustelus were investigated across 2 major oceanographic barriers along the southern African coastline: the Angola-Benguela Front and the Indian/Atlantic boundary. Population genetic structure was inferred using multilocus data generated from 8 microsatellite...

A longline survey was conducted from 2004 to 2014 to investigate the demographic population structure and seasonal abundance of the blacktip shark Carcharhinus limbatus in the Bimini Islands, the Bahamas. All individuals sampled (n = 242) were sub-adult or adults [70·1–145·1 cm pre-caudal length (LPC) range] with no neonates or YOY recorded in Bimi...

Prior knowledge of the genetic diversity, extent of linkage disequilibrium (LD) and population structure is necessary to determine the sample size and number of SNPs necessary to ensure sufficient power of detection in genome-wide association studies (GWAS) and genomic prediction. The OvineSNP50 chip was used to genotype Dorper, Namaqua Afrikaner (...

Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South Africa's chondrichthyans are threaten...

South Africa’s demersal sharks are threatened by over-exploitation, lack of species-specific catch data and non-cohesive fishing regulations. Two of the species most affected by fisheries are the common smoothhound (Mustelus mustelus) and the tope shark (Galeorhinus galeus) for which regional population structure is largely unknown. In this study,...

The abalone, Haliotis midae, is an important aquaculture species in South Africa and the largest generator of revenue for the mariculture sector. Despite domestication of this species still being in the initial stages, significant differentiation has been observed between wild and cultured populations. The genetic consequences of founder effects, i...

Overfishing has led to the collapse of many marine fish stocks along the South African coast, particularly species characterised by predictable distribution patterns and vulnerable life-history traits. Dusky kob (Argyrosomus japonicus) is an estuarine-dependent sciaenid fish that has been severely depleted by overfishing and is currently managed by...

Exploitation through direct and indirect fisheries has caused a drastic decline of shark populations over the last few decades. Similar to the rest of the world, Southern Africa's diverse chondrichthyan fauna (sharks, skates and chimeras) is experiencing high fishing pressures brought on by the current demand for shark related products. Integrated...

The abalone, Haliotis midae, is an important aquaculture species in South Africa. The species is still largely undomesticated; however there is increasing interest in the development of genetically superior strains for production traits. Abalone aquaculture, therefore, provides a model system to study the initial genetic effects of domestication on...

Hybridization between fish species can play a significant role in evolutionary processes and can influence management and conservation planning, however, this phenomenon has been widely understudied, especially in marine organisms. The distribution limits of two sciaenid species (silver kob, Argyrosomus inodorus, and dusky kob, A. japonicus) partly...

Background Similarly to the rest of the world, southern Africa’s diverse chondrichthyan fauna is currently experiencing high fishing pressures from direct and non-direct fisheries to satisfy market demands for shark products such as fins and meat. In this study, the development of microsatellite markers through cross-species amplification of primer...

A South African Merino sheep flock has been divergently selected for more than 8 generations for the ability of ewes to rear multiple offspring. Selection has resulted in a High line and a Low line that differ markedly in their reproductive output. The causative mutations and/or quantitative trait loci responsible for the difference in reproductive...

Haliotis midae is South Africa's most important aquaculture species. The reproduction cycle is currently not closed as many farms rely on wild-caught broodstock for seed production. However, there is an increasing interest in genetic improvement in commercial stocks, with a growing number of producers implementing selective breeding strategies. Hig...

The abalone, Haliotis midae, is currently the primary mariculture species of South Africa. There is increasing interest to genetically improve the species for production traits. A combination of classical breeding and molecular breeding has been advocated for a number of aquaculture species. Various methods have been developed in order to identify...

Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular...

Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in...

The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild...

The marine family Haliotidae (Mollusca: Gastropoda) includes approximately 56 extant abalone species found worldwide. None of these species are globally distributed while four areas of endemism (temperate Australia, South Africa, New Zealand and North Pacific) have been recognized. Phylogenetic relationships of 18 abalone species including five Sou...

Farming of Haliotis midae is the most lucrative aquaculture venture in South Africa. The genome of this species needs to be studied to assist in selective breeding programs aimed at increasing overall yield, and molecular markers will be required to attain this goal. We identified and characterized 82 polymorphic microsatellite loci by using repeat...

Haliotis midae is the only commercially important abalone species in South Africa with a high international demand. Since the closure of the commercial fishery, for conservational purposes, emphasis has shifted to aquaculture. Currently, abalone culture is the largest aquaculture sector in South Africa in terms of tonnage and revenue. With regards...

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 bre...

Genetic diversity within and among three ostrich populations was investigated to corroborate whether these populations can be classified genetically as three different breeds. The DNA of South African Black (SAB, n = 30), Zimbabwean Blue (ZB, n = 32) and Kenyan Redneck (KR, n = 17) birds was assessed for genetic differences using 19 microsatellite...

Haliotis midae is the only commercially important abalone species in South Africa and in recent years the demand for this species has increased steadily. Since the fishery is unable to supply this demand, emphasis has shifted to aquaculture and at present it is South Africa’s largest aquaculture sector in terms of revenue. Nonetheless, much scope 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 bre...

The South African Abalone, commonly known as perlemoen, is a marine gastropod mollusc with considerable economic value as its production is the country’s largest aquaculture sector. Abalone is in a unique position as efforts to conserve natural populations and endeavours to create a genetically superior strain for production will run concurrently....

Over the past two decades, the South African abalone (Haliotis midae), has been under serious threat mainly due to overexploitation. To assure successful management and conservation of wild stocks, the consideration of species-specific evolutionary and population dynamic aspects is critical. In this study, eight microsatellites and 12 single nucleo...

There are two recognized forms of the disease net blotch of barley: the net form caused by Pyrenophora teres f. teres (PTT) and the spot form caused by P. teres f. maculata (PTM). In this study, amplified fragment length polymorphism analysis was used to investigate the genetic diversity and population structure of 60 PTT and 64 PTM isolates collec...

Six micro satellite DNA markers were used to investigate the levels of genetic diversity and to determine parentage in a South African hatchery of the abalone Haliotis midae. Samples examined from the farm consisted of three broodstock groups and their respective F1 offspring. Additional wild samples were collected at sites on the East and West coa...

In this study, we describe the first set of SNP markers for the South African abalone, Haliotis midae. A cDNA library was constructed from which ESTs were selected for the screening of SNPs. The observed frequency of SNPs in this species was estimated at one every 185 bp. When characterized in wild-caught abalone, the minor allele frequencies and F...

The perlemoen (the local name for abalone, Haliotis midae) fishery is not the largest yielding aquaculture venture in South Africa, but it is definitely the most profitable. Perlemoen fetches prices in excess of R300 (U.S.$60) per kg in the Far East. Japan is considered the largest con- sumer in the world of abalone in any form, with mainland China...