Since about 70% of the Earth is covered with saltwater and about 0.01% with freshwater, you would expect marine fish species to grossly outnumber their freshwater counterparts. But this is not necessarily the case...
In a study by Greta Vega and John Wiens, to be published in a forthcoming issue of the Proceedings of the Royal Society B the authors analysed the evolutionary history of ray-finned fishes and found that despite the much greater area and productivity of marine environments, the diversity of marine fishes is about the same as that of freshwater fishes (about 15,000 species each).
By reconstructing the evolutionary history of ray-finned fishes, the authors found that most marine fishes living today were descended from a freshwater ancestor.
Although evidence suggests that most marine fishes are derived from a recent radiation, while freshwater fishes comprise a mixture of ancient lineages, a major recent radiation and multiple invasions from marine environments, there is no correlation between the age of the lineage and diversity (ie. older lineages are not more diverse).
Therefore, the authors hypothesise that the relatively low diversity of marine fishes is more likely due to ancient extinction events, something that may also help explain the low diversity in other marine groups (eg. sponges).
It is also likely that some marine habitats are more homogeneous, provide fewer effective barriers to dispersal and therefore less likely to promote endemism and speciation.
For more information, see the paper: Vega, GC and JJ Wiens (2012) Why are there so few fish in the sea? Proceedings of the Royal Society B: Biological Sciences, doi:10.1098/rspb.2012.0075
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