Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and 'abundance' compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out.

North-western North America has been repeatedly glaciated over most of the past two million years, with the most recent glaciation occurring between 60 000 and 10 000 years ago. Intraspecific genetic variation in many species has been shaped by where they survived glaciation and what postglacial recolonization routes were used. In this study, molecular techniques were used to investigate biogeographical, taxonomic and conservation issues in rainbow trout, Oncorhynchus mykiss. Mitochondrial DNA (mtDNA) variation was assessed using a restriction fragment length polymorphism (RFLP) analysis, focusing mainly on the previously understudied northern extent of the species' range. Two phylogenetically distinct mitochondrial lineages were found that differed from each other by up to 1.8% in sequence. Although the geographical distributions of the two clades overlap extensively, diversity and distributional analyses strongly suggest that trout survived glaciation in both coastal and inland refugia followed by postglacial gene flow and secondary contact. Postglacial dispersal into British Columbia most likely occurred from the Queen Charlotte Islands and the Columbia River. Although trout most likely also survived glaciation along the coast of Washington, Oregon and California, as well as near the Bering Strait, evidence suggests that dispersal into British Columbia from these areas was limited. Sequence analysis of mitochondrial haplotypes revealed higher diversity in California than in the northern part of the species' range, indicating an ancient presence of the species in the south. Phylogeographic divergence probably predates adaptive variation in the species as suggested by evidence for parallel evolution of life history types across the range of O. mykiss.

Marine fishes from the northwest Atlantic Ocean were analysed to determine whether barcoding was effective at identifying species. Our data included 177 species, 136 genera, 81 families and 28 orders. Overall, 88% of nominal species formed monophyletic clusters based on >500 bp of the CO1 region, and the average bootstrap value for these species was 98%. Although clearly effective, the percentage of species that were distinguishable with barcoding based on the criterion of reciprocal monophyletic clusters was slightly lower than has been documented in other studies of marine fishes. Eelpouts, sculpins and rocklings proved to be among the most challenging groups for barcoding, although we suspect that difficult identifications based on traditional (morphology based) taxonomy played a role. Within several taxa, speciation may have occurred too recently for barcoding to be effective (e.g. within Sebastes, Thunnus and Ammodytes) or the designation of distinct species may have been erroneous (e.g. within Antimora and Macrourus). Results were consistent with previous work recognizing particularly high levels of divergence within certain taxa, some of which have been recognized as distinct species (e.g. Osmerus mordax and Osmerus dentex; and Liparis gibbus and Liparis bathyarcticus), and some of which have not (e.g. within Halargyreus johnsonii and within Mallotus villosus). The results from this study suggest that morphology-based identification and taxonomy can be challenging in marine fishes, even within a region as well characterized as Atlantic Canada. Barcoding proved to be a very useful tool for species identification that will likely find a wide range of applications, including the fisheries trade, studies of range expansion, ecological analyses and population assessments.