Development of microsatellite markers in the Sparidae and their application in population genetics of the Hottentot seabream Pachymetopon blochii (Valenciennes, 1830) along the coast of South Africa

Abstract

The marine environment is vast and is one of the last natural habitats that provides’ a major source of protein through fisheries. This has led to a massive overexploitation of this resource because in the past marine fish populations were perceived as inexhaustible. Recently it has been observed that this is not the case, with many fish populations collapsing which has initiated further investigation of these populations. By combining different aspects of research (species biology, movement and genetics) more complete management and conservation plans may be implemented. Marine studies have greatly benefited from the advancement of molecular tools that allow for inferences to be made about gene flow and connectivity between habitats which could not previously be made as it is not easy to monitor marine species within their environment. South Africa has a wide range of marine fish species due to the diverse geological and oceanographic features which provide a number of habitats along the coast. One of the most prevalent and diverse fish families along the South African coast is the Sparidae. This family is of economic importance to the line fishery and many of these species are considered vulnerable or endangered due to a combination of overfishing and life-history traits. Two species of particular interest are the hottentot seabream (Pachymetopon blochii) and white steenbras (Lithognathus lithognathus). Both species are endemic to southern Africa and are considered vulnerable to overexploitation. This study reports the development of microsatellite markers for both the above mentioned species using the FIASCO protocol and next generation 454 sequencing. Nine polymorphic markers were identified in each of these species. Nineteen markers (fifteen newly developed and four from other sparids) were used as a panel on eleven economically important sparids, to test microsatellite cross-species amplification. From this study, I was able to identify twelve adequate polymorphic loci for the white steenbras (applied in a population genetic study by a PhD student associated with SAIAB) and fourteen in the hottentot seabream which were applied in this dissertation. We were also able to identify a number of polymorphic loci for the other sparids. It was concluded that the sparids do not show a negative correlation between genetic distance and microsatellite amplification success and polymorphism. The study further investigated the population genetic structure of the hottentot seabream. This species is thought to have sedentary adults and a relatively patchy habitat distribution. Using the above mentioned markers on individuals sampled in 2001 and 2009, we were able to identify a weak spatial and temporal variation. It was concluded that the observations of weak population structure were likely due to variation in reproductive success and environmental patchiness which led to changes observed between sampling years.