The Indo-West Paci¢c is characterized by extraordinary marine species diversity. The evolutionary mechanisms responsible for generating this diversity remain puzzling, but are often linked to Pleistocene sea level £uctuations. The impact of these sea level changes on the population genetic architecture of the estuarine ¢sh Lates calcarifer are investigated via a natural experiment in a region of the Indo-West Paci¢c known to have undergone considerable change during the Pleistocene. L. calcarifer, a coastline-restricted catadromous teleost, provides an excellent model for studying the e¡ects of sea level change as its habitat requirements potentially make it sensitive to the region's physical history. Evidence was found for a large phylogenetic break (4% mtDNA control region; 0.47% ATPase 6 and 8) either side of the Torres Strait, which separates the Western Paci¢c and Indian Oceans, although some mixing of the clades was evident. This suggests clinal secondary introgression of the clades via contemporary gene £ow. Further, populations on Australia's east coast appear to have passed through a bottleneck. This was linked to the historical drying of the Great Barrier Reef coastal lagoon, which resulted in a signi¢cant loss of habitat and forced retreat into isolated refugia. These results suggest that historical eustatic changes have left a signi¢cant imprint on the molecular diversity within marine species as well as among them in the Indo-West Paci¢c.

New and previously published genetic data from 6000 barramundi comprising 50 collections across tropical Australia were analysed for evidence of population subdivision. Sixteen discrete populations were identified, including four populations that were identified from new collections. Duplicate collections from two localities were statistically homogeneous after seven years between collections. Environmental and genetic factors that yielded the observed genetic pattern were investigated. Geological evidence of sea-level changes, when compared with bathymetry data for the region, reveals that barramundi must have recently recolonized many of the coastal estuaries of tropical Australia. This recolonization resulted from the inundation of the Gulf of Carpentaria and Torres Strait by a rapid rise in sea level of at least 130 m between 18 000 and 6000 years ago. The genetic data clearly indicate that, as the population spread into new habitats, there was a corresponding decrease in genetic diversity. This observed decrease has been maintained despite continued migration between populations. The 'onedimensional stepping stone' migration model, which most closely fits the observed population structure, predicts that the observed level of population subdivision (FST = 0.064) is maintained against substantial gene flow between adjacent populations. This contrasts with the predictions of the often-used 'island model' which gives estimates of Nem at least two orders of magnitude lower than those from the onedimensional stepping-stone model.

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Patterns of population subdivision and the relationship between gene flow and geographical distance in the tropical estuarine fish Lates calcarifer (Centropomidae) were investigated using mtDNA control region sequences. Sixty-three putative haplotypes were resolved from a total of 270 individuals from nine localities within three geographical regions spanning the north Australian coastline. Despite a continuous estuarine distribution throughout the sampled range, no haplotypes were shared among regions. However, within regions, common haplotypes were often shared among localities. Both sequence-based (average ST = 0.328) and haplotype-based (average ST = 0.182) population subdivision analyses indicated strong geographical structuring. Depending on the method of calculation, geographical distance explained either 79 per cent (sequence-based) or 23 per cent (haplotype-based) of the variation in mitochondrial gene flow. Such relationships suggest that genetic differentiation of L. calcarifer has been generated via isolation-by-distance, possibly in a stepping-stone fashion. This pattern of genetic structure is concordant with expectations based on the life history of L. calcarifer and direct studies of its dispersal patterns. Mitochondrial DNA variation, although generally in agreement with patterns of allozyme variation, detected population subdivision at smaller spatial scales. Our analysis of mtDNA variation in L. calcarifer confirms that population genetic models can detect population structure of not only evolutionary significance but also of demographic significance. Further, it demonstrates the power of inferring such structure from hypervariable markers, which correspond to small effective population sizes.

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