BackgroundWorldwide, the genus Haliotis is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, Haliotis midae is the only aquacultured species. Despite its economic importance, genomic sequence resources for H. midae, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance.ResultsMore than 25 million short reads generated by the Illumina Genome Analyzer were de novo assembled in 22,761 contigs with an average size of 260 bp. With a stringent E-value threshold of 10-10, 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed.ConclusionThis data represents the most comprehensive genomic resource for the South African abalone H. midae to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in H. midae and in other abalone species.

AimThe formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units.LocationContinental Africa.TaxonClarias gariepinus sl.MethodsWe investigated mitochondrial cytb sequences of 443 individuals from 97 localities, using a haplotype network and a genetic landscape analysis. We inferred a dated phylogeny using maximum likelihood and Bayesian inference approaches and reconstructed ancestral areas with S‐DEC and S‐DIVA models. Microsatellite genotyping complemented the mitochondrial approach in the Congo basin, where the latter revealed complex patterns.ResultsLimited differentiation is found in northern and south‐western Africa, and sharp genetic differentiation in the continent's east and centre. Populations with affinities to neighbouring basins occur at the edges of the Congo province. High diversity exists in the south of the Congo basin. The Zambezi province is partitioned into eastern, central and western sectors. In the east, specimens were related to those from the Congo. In the west, they were similar to Southern representatives. Phylogenetic inference placed the origin of C. gariepinus in the East Coast, with intraspecific diversification starting around the Great Lakes. These events occurred ca. 4.8–1.65 and 2.3–0.8 MYA respectively.Main conclusionsClades of C. gariepinus sl. show a clear geographical signature. The origin of C. gariepinus in the East Coast and diversification around the Great Lakes coincided with the periods of increased aridity. Low genetic differentiation in northern and southern Africa may result from connectivity during recent periods of higher rainfall. In contrast to other widespread African freshwater fish, colonization rather than extinction seemed to mediate distribution patterns. This can be explained by a high ecological tolerance. We highlight the species’ suitability to study landscape and climate evolution at various scales.

BackgroundSimilarly 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 sets previously developed for closely related species is reported as an alternative approach to de novo marker development. This included the design of four microsatellite multiplex assays and their cross-species utility in genetic diversity analysis of southern African elasmobranchs. As this study forms part of a larger project on the development of genetic resources for commercially important and endemic southern African species, Mustelus mustelus was used as a candidate species for testing these multiplex assays in down-stream applications.ResultsThirty five microsatellite primer sets previously developed for five elasmobranch species were selected from literature for testing cross-species amplification in 16 elasmobranch species occurring in southern Africa. Cross-species amplification success rates ranged from 28.6%-71.4%. From the successfully amplified microsatellites, 22 loci were selected and evaluated for levels of polymorphism, and four multiplex assays comprising of the 22 microsatellites were successfully constructed, optimised and characterised in a panel of 87 Mustelus mustelus individuals. A total of 125 alleles were observed across all loci, with the number of alleles ranging from 3–12 alleles. Cross-species amplification of the four optimised multiplex assays was further tested on 11 commercially important and endemic southern African elasmobranch species. Percentage of polymorphism ranged from 31.8%-95.5% in these species with polymorphic information content decreasing exponentially with evolutionary distance from the source species.ConclusionsCross-species amplification of the 35 microsatellites proved to be a time- and cost-effective approach to marker development in elasmobranchs and enabled the construction of four novel multiplex assays for characterising genetic diversity in a number of southern African elasmobranch species. This study successfully demonstrated the usefulness of these markers in down-stream applications such as genetic diversity assessment and species identification which could potentially aid in a more integrative, multidisciplinary approach to management and conservation of commercially important cosmopolitan and endemic elasmobranch species occurring in southern Africa.

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.

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