Browsing Doctoral Degrees (Genetics) by browse.metadata.advisor "Bester-van der Merwe, Aletta Elizabeth"
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- ItemThe evolutionary history of the genus Seriola and the phylogeography and genetic diversity of S. lalandi (yellowtail) across its distribution range(Stellenbosch : Stellenbosch University, 2014-04) Swart, Belinda Louisa; Roodt-Wilding, Rouvay; Bester-van der Merwe, Aletta Elizabeth; Von der Heyden, Sophie; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.ENGLISH ABSTRACT: The genus Seriola includes several important commercial fish species, yet the phylogenetic relationships between species have not been fully investigated to date. This study reports the first molecular phylogeny for this genus based on two mitochondrial (Cytb and COI) and two nuclear gene (RAG1 and Rhod) fragments for all extant Seriola species (nine species, n = 27). The phylogenetic patterns resolved three main lineages: a ((S. fasciata and S. peruana), S. carpenteri) clade, a (S. dumerili and S. rivoliana) clade and a (S. lalandi and S. quinqueradiata) clade. The closure of the Tethys Sea (12 - 20 MYA) coincides with divergence of the ((S. fasciata and S. peruana), S. carpenteri) clade from the rest of the Seriola species; while the uplifting of the Isthmus of Panama (± 3 MYA) played an important role in speciation between S. fasciata and S. peruana. The climate and water temperature fluctuation in the Pliocene played important roles during the divergence of the remainder of the Seriola species. This study is also the first to describe the evolutionary history of the commercially important species Seriola lalandi across its distribution range. Global patterns of genetic variation within S. lalandi (n = 190) were examined using three genes fragments (mitochondrial DNA COI, Cytb and nuclear RAG1). Three distinct clades were identified, corresponding to three different geographic regions (North-western Pacific - Japan, North-eastern Pacific - USA, and the southern hemisphere clade). These groupings correspond with the previously identified subspecies of S. lalandi (North-western Pacific – S. lalandi aureovittata, North-eastern Pacific – S. lalandi dorsalis, and the southern hemisphere clade - S. lalandi lalandi). AMOVA results and pairwise FST values revealed significant population differentiation between these groups. The population subdivision between these clades in all probability is maintained by biogeographic or oceanographic barriers (such as the equator and East Pacific Barrier) that disrupt gene flow. The southern hemisphere clade comprised of samples from the southern Pacific (AUS, NZL and Chile) and the southern Atlantic (SA). No haplotypes were shared between these areas in the southern hemisphere. This southern hemisphere clade was further investigated with six microsatellite markers. The analyses revealed the South African populations as genetically distinct from populations of the South Pacific oceans (AMOVA, FCA and STRUCTURE results). In summary, the South African and southern Pacific grouping could be the result of recent vicariant events during the Pleistocene glacial / interglacial periods and / or contemporary oceanographic forces acting on these populations. Further population differentiation was found within the South African samples, but not in the South Pacific. In the southern Pacific clade this lack of population structure is the result of high gene flow (analysed with MIGRATE) between the sampling localities. This is the first report on the genetic structure of this commercial important species for South African populations. Five sampling localities from the west- to the east coast of South Africa were sampled (n = 201). The microsatellite analyses revealed two potentially genetically distinct groups. AMOVA, FST and FCA results suggest small but significant differentiation between populations from the west coast and from the south- and east coast, suggesting a potential genetic break in the Cape Point region (BARRIER). However, the program STRUCTURE showed a high level of admixture along the South African coast and the migration results (MIGRATE and BAYESASS) also suggest a high degree of gene flow between these regions.
- ItemMapping of dwarf growth habit traits in apple (Malus pumila Mill.) using molecular markers and transcriptomics approaches(Stellenbosch : Stellenbosch University, 2020-03) Mbulawa, Zama Thandekile Laureen; Bester-van der Merwe, Aletta Elizabeth; Kriel, Johan; Tobutt, Kenneth R.; Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.ENGLISH ABSTRACT: Apple (Malus pumila Mill.) is one of the most important deciduous fruit crops worldwide. Apples are traditionally valued as an important dietary source of fibre and are high in antioxidants, contributing to human nutrition. In South Africa, the apple industry plays a vital role in the country's agricultural economy due to global exports. In recent years, more emphasis has been directed to dwarf trees, as they are well suited for profitable high-density orchards and sustainability of fruit production. However, dwarfism cannot always be linked to increased yield. At Bien Donné Research Farm of the Agricultural Research Council (ARC) Infruitec-Nietvoorbij’, several dwarf growth habits exist, which is related to a form of hybrid incompatibility, hybrid necrosis. One of them is associated with undesirable characteristics such as crinkled leaves and poor growth. Expression of hybrid necrosis in plants can lead to a significant reduction in productivity, due to the deleterious epistatic interactions between alleles that arose from divergent genetic backgrounds. Few, if any, genetic studies have thus far investigated crinkle dwarf growth traits in apple. This study aimed to examine the genetic basis underlying the crinkle dwarf phenotype by employing multidisciplinary approaches that included segregation pattern studies, assessment of self-incompatibility (hybrid incompatibility), molecular mapping and transcriptomic profiling of pooled samples of apical buds and young leaves from normal and from crinkle dwarf phenotypes. The genetics behind the crinkle dwarf trait was undertaken by studying the segregation patterns of the first filial generation (F1) apple progenies, where parental combinations were heterozygous. Segregation ratios of 9:7 and 3:1 were observed, for which crinkled dwarf phenotypes is expressed when one of the two genes is homozygous recessive (D-ee or ddE-). Additionally, the involvement of self-incompatibility (S) was investigated by identifying the parental S-genotypes using PCR based consensus and allele-specific primers of the apple S-RNAse gene. Eight parental S-genotypes were determined. Herein, the S-genotypes of Malling 1 (‘M.1’) (S3S9) and TSR1T187 (S7S24) were deduced for the first time. High-density SNP-based parental genetic linkage maps of ‘McIntosh’ and ‘M.1’ were constructed using the apple 20K Infinium SNP array. The crinkle dwarf trait was mapped on linkage group (LG) 8 in ‘McIntosh’ and on LG2 in ‘M.1’. In the consensus genetic map, crinkle dwarf trait also mapped on LG8. Additionally, the crinkle dwarf trait obtained for the parental genetic maps were validated using Kruskal-Wallis (KW) analysis. To gain deeper insights into the genes regulating crinkle dwarf phenotype, transcriptome profiles of pooled meristematic tissues of normal and crinkle dwarf phenotypes were generated using RNA-sequencing technology. A total of 921 significantly differentially expressed genes (DEGs), with 763 up-regulated and 158 down-regulated transcripts, were identified. Gene expression analyses revealed that defense signaling and stress-related genes were up-regulated during the expression of crinkle dwarf phenotype along with the activation of several antioxidant proteins/enzymes. The high expression of lactoperoxidase (Class III peroxidase) together with glutathione S-transferase suggests the involvement of reactive oxygen species (ROS). Genes typically encoding for pathogenesis-related proteins (chitinase and pectin), antioxidant enzymes, receptor-like protein (protein serine/threonine phosphatase), as well as alpha-linolenic acid, a precursor of the phytohormone jasmonic acid were all up-regulated during expression of crinkle dwarf phenotype. These findings support the notion that crinkle dwarf phenotype does indeed exhibit hybrid necrosis symptoms. Consequently, an autoimmune response might have been triggered by the allele incompatibilities, in this case between ‘McIntosh’ and ‘M.1’. Overall, the information generated in this study will aid in designing an in-house screening system for eliminating seedlings carrying crinkle dwarf genes from the ARC breeding material. In future, these findings will also aid in the design of crosses with predictable outcomes and in broadening a sustainable genetic base of the apple cultivars for high productivity orchards, while avoiding raising seedlings with dwarf growth habit associated with crinkled leaves.
- ItemPopulation genetics of Galeorhinus galeus, Carcharhinus brachyurus and Rhinobatos annulatus- implications for regional fisheries and elasmobranch conservation(Stellenbosch : Stellenbosch University, 2016-03) Bitalo, Daphne Nyachaki; Bester-van der Merwe, Aletta Elizabeth; Roodt-Wilding, Rouvay; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.ENGLISH ABSTRACT: Elasmobranchs (sharks, skates and rays) are highly exploited world-wide and more vulnerable than most teleosts due to their life history traits (e.g. late age at maturity, low fecundity and slow growth). Most elasmobranchs are either targeted by commercial fisheries or unintentionally taken as bycatch in mixed-species fisheries. Among these, the tope shark Galeorhinus galeus, the copper shark Carcharhinus brachyurus and the southern African endemic lesser sandshark Rhinobatos annulatus, are targeted globally and locally in demersal, pelagic and recreational fisheries. Across the Southern Hemisphere, the International Union for the Conservation of Nature (IUCN) categorizes both the tope and copper sharks as “vulnerable” while the lesser sandshark as “data deficient” within its region of endemism. Information is urgently needed on their regional genetic structure and diversity to help delineate management units (MUs) for better fisheries monitoring and conserving local biodiversity. Regional and local population genetic structure of these species was assessed using previously optimised cross-species microsatellite panels and/or the mitochondrial NADH2 and NADH4 genes. Patterns of evolutionary and demographic history were inferred using coalescent and Bayesian statistical methods. For G. galeus, the data showed a lack of contemporary gene flow and deep historical divergence across the Southern Hemisphere. Two geographically distinct mitochondrial clades were recovered, one including the Atlantic and Indo-Pacific collections (ARG, SA and AUS) and one comprising the Pacific samples (NZ and CHI) as well as single divergent haplotype restricted to South Africa. Nuclear data also revealed large population subdivisions (FST = 0.050 to 0.333, P < 0.05) indicating very limited gene flow for tope sharks across ocean basins. On a local scale, F-statistics, multivariate and clustering analyses supported gene flow with substantial admixture along the South African coastline (FST = 0.016 to 0.048, P > 0.05), with some degree of genetic structure between the Atlantic and Indian Ocean samples. The east coast samples of Port Elizabeth were significantly differentiated from the rest (FST = 0.023 to 0.091, P > 0.05). For C. brachyurus, estimates of pairwise population differentiation were significant (average FST = 0.031, P = 0.000) indicating some degree of gene flow between sampling sites while the sub-structuring observed at Strandfontein indicated the existence of a possible distinct, more admixed group of individuals. Neither AMOVA (FCT = -0.011, P = 1.000) nor Bayesian clustering analyses indicated genetic discontinuity or significant population structure across the Atlantic/Indian boundary. Although the ND4 results also alluded to historical dispersal across this boundary, the population of Mossel Bay harboured four highly divergent haplotypes, indicating that this region might be a potential nursery site for C. brachyurus. The genetic diversity and genetic connectivity of R. annulatus was inferred using cross-amplified polymorphic microsatellite loci across the Agulhas bioregion that coincides with the warm temperate biogeographical province of South Africa. Significant genetic differentiation was observed over a small sampling range (FST = 0.016 to 0.094, P < 0.050) implying that the species might be highly structured throughout its entire geographical range. Overall effective population size for R. annulatus was very low (Ne = 106) and not in accordance to the abundance proposed for the species. As this is the first regional assessment for all three of these species, the findings of this study could have immediate implications for the regional management and conservation of commercial and recreational sharks.
- ItemSignatures 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.
- ItemUnravelling the mystery of the shark genus Mustelus in southern Africa using a multidisciplinary approach(Stellenbosch : Stellenbosch University, 2017-12) Maduna, Simo Njabulo; Bester-van der Merwe, Aletta Elizabeth; Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.ENGLISH ABSTRACT: Multidisciplinary approaches have previously offered some alternative innovative ways of addressing classical ecological questions while providing novel insights into behaviour and biology of elasmobranch species. The species-rich shark genus Mustelus, or smoothhounds (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 the knowledge on the copulating and dispersal strategies of species of Mustelus is scarce. Here, a multidisciplinary approach – molecular, morphology and histology – with different methods of analysis on various spatial scales was used. First, this study investigated the evolutionary origin of the shark genus Mustelus in southern Africa using molecular phylogenetic and statistical biogeography approaches. Results gave strong support for a northern hemisphere origin of southern African Mustelus species, and that the radiation of Mustelus in this region was primarily driven by long-distance dispersal. The monophyly of expanded Mustelus indicated that southern African species of the genus arose from at least two separate colonisation events from the Northern Hemisphere. On a microevolutionary scale, a comparative population genetics approach was used to gain insight into spatial genetic structure and dispersal patterns in species of Mustelus (M. mustelus and M. palumbes) and other co-distributed demersal sharks (Galeorhinus galeus and Triakis megalopterus) characterised by assorted life histories, habitat preferences, and dispersal behaviour. Based on novel Next Generation Sequencing (NGS)-mined microsatellites, the null hypothesis of genetic homogeneity was rejected for all species investigated except for T. megalopterus. Most noteworthy is that the coalescent analysis of migration supported asymmetric gene flow from the Indian to the Atlantic Ocean, concordant with the Atlantic Ocean–Indian Ocean connection via Agulhas leakage proposed for many marine species along the South African coast. In terms of fisheries forensics, a dermal denticle identification key guide and two molecular assays (a microsatellite panel and High-resolution melting assay) were successfully developed for species identification of southern African Mustelus (M. mosis, M. mustelus and M. palumbes) and three other shark species (Galeorhinus galeus, Scylliogaleus quecketti and Triakis megalopterus) commonly confused with species of Mustelus in the region. Additionally, a SNP discovery and genotyping pipeline was optimised that could in future be used to obtain genome-wide data that will enable population genetic and demographic processes of the study species to be assessed more accurately. Lastly, evidence of sperm storage in female common smoothhound sharks was reported for the first time using a histological approach. The molecular analysis of a single common smoothhound litter also hinted at the within-species variation in the presence and frequency of multiple paternity previously reported for elasmobranchs. Overall, this study provides the most comprehensive set of conservation genetic resources for the common smoothhound shark to date. The results provide novel insights into the conservation biogeography, species identification and ecology of dispersal as well as mating behaviours in species of Mustelus. This will help inform existing and ongoing management and conservation efforts for smoothhound sharks occurring in southern Africa.