Advances in the molecular analysis of fish population structure

The characteristics of high population and species biodiversity, taken together with the major anthropogenic threats arising from exploitation, introductions and habitat alterations, have ensured that fishes have received major attention from molecular biologists in the study of wild populations. Foremost among the various challenges has been the development of techniques to estimate population discreteness and associated patterns of dispersal and gene flow, so-called stock structure analysis. Here, we review some recent developments in molecular technology, especially microsatellite analysis, and consider critically how such markers can be employed to estimate genetic differentiation in species exhibiting high mobility in open waters. Comparisons are made between microsatellites and other genetic markers (protein and DNA) in their ability to detect population structuring. Particular emphasis is placed on the need to design sampling programmes that rake account of aspects of the biology of the species under study, and the scale and nature of sample collection. Recent novel applications of PCR-based technology in the analysis of population structure are considered including the detection of microgeographic differentiation, the analysis of historical fish populations using recovered DNA, and the molecular characterization of allelic variants among populations in relation to function.