Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range-wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region.

Cytochrome b nexus file for Gadopsisgad.cytb.with.outs.final.nexS7 sequence nexus file for Gadopsis and outgroupsgads7.with.outs.nexCombined Cytochrome b and S7 sequence data in nexus formatThe codes for each OTU are in the readme file. The first number is the population, the second is the name of the population and the third is the specific individual. Note that the readme file contains the codes for samples that are not in the nexus file.gad_cytb.s7.concat.dryad.sub.nex*beast xml file for Gadopsis (S7 and cytb)The codes for each OTU are in the readme file. The first number is the population, the second is the name of the population and the third is the specific individual.gad.relax.long.xmlGARLI configuration file for best treeSettings used to generate the best ML tree in GARLI. This example is for cytb, but the settings were the same for each of the three datasets analysed except the number of attachments (which was twice the number of OTUs), outgroup and the model of sequence evolution.garli.nobs.confGARLI configuration file for bootstrappingSettings used to generate 250 ML bootstrap replicates in GARLI. This example is for cytb, but the settings were the same for each of the three datasets analysed except the number of attachments (which was twice the number of OTUs), outgroup and the model of sequence evolution.garli.bs.conf