Testing and validating a modified CTAB DNA extraction method to enable molecular parentage analysis of fertilized eggs and larvae of an emerging South African aquaculture species, the dusky kob Argyrosomus japonicus.

This study describes the successful implementation of a modified cetyltrimethyl ammonium bromide (CTAB) protocol to isolate genomic DNA and amplify 14 microsatellite markers from fertilized eggs and larvae of an emerging South African farmed marine fish species, the dusky kob Argyrosomus japonicus. To test and validate the efficiency of this method, genetic data were utilized to resolve parentage and kinship of first-generation (F1) offspring produced in mass-spawning events of wild broodstock fish in a commercial hatchery.

Identification of naturally occurring hybrids between two overexploited sciaenid species along the South African coast.

Hybridisation 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 overlap along the South African coast, where both species have undergone severe depletion due to overfishing. Following the identification of a number of possible cases of species misidentification or hybridisation (21 out of 422 individuals), nuclear and mitochondrial DNA data (12microsatellite loci and 562bp of the COI gene) were analysed to investigate the genetic composition of these individuals. Results indicated a field-based species misidentification rate of approximately 2.8% and a rate of natural hybridisation of 0.7%. Interestingly, all hybrid fish resulted from first-generation (F1) hybridisation events, which occurred exclusively between silver kob females and dusky kob males. Whether hybridisation is the result of natural events (such as secondary contact following a shift in distribution range), or anthropogenic activities (size-selective pressure due to overfishing), these findings have important implications for critical recovery and future management of these species in the wild.

Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua.

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

A quick, least-invasive, inexpensive and reliable method for sampling Gadus morhua postlarvae for genetic analysis.

The present study describes the successful design and testing of a quick, least-invasive, reliable and inexpensive sampling procedure for Atlantic cod Gadus morhua. This protocol can be easily applied to postlarval fish following a simple three-step procedure, without availing of commercial DNA extraction kits, while ensuring survival of sampled individuals.

Trace elements, PCBs and organochlorine pesticides in New Zealand common dolphins (Delphinus sp.).

Trace elements, polychlorinated biphenyls (PCBs) and organochlorine (OC) pesticide levels were determined in tissues collected from stranded and bycaught common dolphins (Delphinus sp.) from New Zealand waters between 1999 and 2005. The concentrations of mercury (Hg), selenium (Se), chromium (Cr), zinc (Zn), nickel (Ni), cadmium (Cd), cobalt (Co), manganese (Mn), iron (Fe), copper (Cu), tin (Sn), lead (Pb), arsenic (As) and silver (Ag) were determined in blubber, liver and kidney tissue. PCBs (45 congeners) and a range of OC pesticides including dieldrin, hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT) and its metabolites DDE and DDD were determined in blubber samples. Cr and Ni were not detected in any of the samples and concentrations of Co, Sn and Pb were generally low. Concentrations of Hg ranged from 0.17 to 110 mg/kg wet weight. Organochlorine pesticides dieldrin, HCB, o,p'-DDT and p,p'-DDE were present at the highest concentrations. Sum DDT concentrations in the blubber ranged from 17 to 337 and 654 to 4430 microg/kg wet weight in females and males, respectively. Similarly, Sigma45CB concentrations ranged from 49 to 386 and 268 to 1634 microg/kg wet weight in females and males, respectively. The mean transmission of SigmaDDTs and ICES7CBs between a genetically determined mother-offspring pair was calculated at 46% and 42%, respectively. Concentrations of organochlorine pesticides determined in the present study are within similar range to those reported for Hector's dolphins (Cephalorhyncus hectori) from inshore New Zealand waters.