Comparison of population genetic estimates amongst wild,F1 and F2 cultured abalone (Haliotis midae)

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. High throughput commercial production and mass spawning make it difficult to maintain breeding records; therefore, mostly mass selection is practised. The high fecundity and unequal parental contributions also often lead to increased levels of inbreeding. This study therefore aimed to assess the genetic effects of such breeding practices on commercial populations of H. midae. Using microsatellite loci, the genetic properties of a wild, an F1 and an F2 population were estimated and compared. Although there was no significant loss of genetic diversity amongst the cultured populations in comparison with the wild progenitor population, there was low‐to‐moderate genetic differentiation between populations. Relatedness amongst the F2 population was significant, and the rate of inbreeding was high. The effective population size for the F2 (±50) was also comparatively small with respect to the wild (∞) and F1 (±470) populations. These results suggest that farms need to give caution to breeding practices beyond the first (F1) generation and aim to increase effective population sizes and minimise inbreeding to ensure long‐term genetic gain and productivity. This study also confirms the usefulness of population genetic analyses for commercial breeding and stock management in the absence of extensive pedigree records.     

Development of an experimental laboratory fertilization protocol for the South African abalone,Haliotis midae (Linnaeus 1758)

In this study, effective gamete concentrations, egg viability, and fertilization volumes were evaluated for Haliotis midae (L.). Sperm concentrations between 5?×?10³ and 5?×?10⁴?mL^?1 (p?>?0.05) consistently resulted in high hatch-out rates (96?±?1%). At concentrations higher than 5?×?10⁵?mL^?1, hatch-out rates decreased to 69?±?7% (p??1 resulted in high fertilization rates, with 50?eggs?mL^?1 being the ideal concentration for fertilization in H. midae. Egg viability was consistently high up to 100?min post-spawning, with a decrease in hatch-out success, when eggs were fertilized 120?min post-spawning. Fertilization volumes did not affect successful hatch-out. The results from this study can be implemented by South African abalone farms to increase hatch-out rates and subsequent culture. It can also be used as basis for the development of fertilization protocols in other marine invertebrate species.     

Preliminary investigation to determine the cytotoxicity of various cryoprotectants on southern African abalone (Haliotis midae) embryos

Cryopreservation could provide stock quantities of embryos for transgenic research. This study aimed to determine the least toxic cryoprotective agent for Haliotis midae embryos. They were exposed for 30 min to concentrations varying from 5% to 20% of the following cryopreservatives: methanol (MET), polyethylene glycol (PEG), dimethyl sulfoxide (ME₂SO) and glycerol (GLY). In contrast to cryopreservation studies done in other molluscs, PEG showed the least toxicity to H. midae embryos in concentrations ranging from 5% to 15%. MET was also less toxic than ME₂SO and GLY at correlating concentrations. GLY showed the most toxic effects with most embryos dead or abnormal at concentrations above 15%.     

An assessment of spatio-temporal genetic variation in the South African abalone (<Emphasis Type="Italic">Haliotis midae</Emphasis>), using SNPs: implications for conservation management

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 dynamics around the South African coast. Using a population genomics approach this study aimed to assess fluctuations in genetic diversity among wild and cultured South African abalone populations through time and space. Various estimates of genetic diversity and population differentiation were calculated using EST-derived SNP markers. All populations had comparable levels of genetic diversity and the long-term effective population size appears to be sufficiently large for the wild populations, despite evidence of recent bottlenecks. Population differentiation was for the most part geographically correlated, with spatial genetic structure maintained across temporal samples. Significant genetic differentiation was, however, detected among temporal samples taken from the same locality. There was evidence for comparatively small short-term effective population sizes that could explain large changes in allele frequencies due to stochastic effects. Temporal heterogeneity could also be explained by changes in selection pressures over time. H. midae populations could, therefore, be more dynamic than previously estimated and this could have implications for effective conservation and fisheries management.     

Historical isolation and hydrodynamically constrained gene flow in declining populations of the South-African abalone, Haliotis midae

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 nucleotide polymorphic loci (SNPs) were applied to determine genetic structure in nine populations sampled throughout the species?? natural distribution range. It spans along three biogeographical regions of the South African coastline: temperate in the West coast, warm temperate in the South coast and subtropical in the East coast. Data analysis applying frequentist and Bayesian-based clustering methods indicated weak genetic differentiation between populations of the West, South and East coast. Spatial Bayesian inference further revealed clinal variation along a longitudinal gradient and a transitional zone in the South coast. Coalescent analysis of long-term migration showed restricted interchange among the sampling locations of the South coast while estimates of effective population size were comparable between coastal regions. Furthermore demographic analysis of microsatellite data suggested population expansion, probably reflecting range expansion that occurred following glacial retreat during the Pleistocene. Overall, population structure analysis suggested contemporary (hydrographical conditions) as well as historical (Pleistocene contraction of habitat) restrictions to gene flow. This study provides the foundation for the establishment of an integrated management policy for preserving the natural diversity and adaptive potential of H. midae.     

Phylogenetic relationships in Southern African chloridoid grasses (Poaceae) based on nuclear and chloroplast sequence data

Phylogenetic relationships in southern African members of chloridoid grasses were investigated using DNA sequences from the chloroplast trnL (UAA) 5’ exon‐ trnF (GAA) region and the nuclear ribosomal internal transcribed spacer regions. The two datasets were analysed separately before being combined into a matrix of 50 specimens, representing 38 species. The congruence between the individual data sets was assessed in a conditional combination approach and the congruent data sets were then combined into a single data set. In this analysis, the chloridoid grasses were monophyletic and two large groups, corresponding to the tribes Eragrostideae and Cynodonteae, were polyphyletic; Eragrostis, the largest genus in the subfamily, was polyphyletic. Otherwise, high support levels were found at species and generic level.     

Bioinformatic survey of Haliotis midae microsatellites reveals a non-random distribution of repeat motifs

Recent studies have shown the non-random distribution of microsatellite motifs between genomic regions within a particular species. This study investigates such microsatellite distributions in the genome of the economically important abalone Haliotis midae, via a bioinformatic survey. In particular, the association of specific repeat motifs to coding regions and transposable elements is investigated. An understanding of microsatellite genomic distribution will facilitate more efficient use and development of this popular molecular marker. A bias toward di- and tetranucleotide repeats was found in the H. midae genome. CA microsatellite units were the most abundant repeat motif, but were notably underrepresented in genic regions where GAGT repeats predominate. Approximately 17.5% and 21% of the microsatellites showed gene and/or transposable element associations, respectively. This could explain the high genomic frequencies of particular motifs across the genome and may allude to a possible functional role. The data presented in this study are the first to demonstrate such non-random dispersal of microsatellites in abalone and support previous findings arguing in favor of non-random distribution of repeat motifs.