Freshwater fishes are the world’s most speciose vertebrates and their variety staggers the imagination. There are species with suction-cap oral disks, saw-like rostrums, flamboyant barbels, poisonous spines and even lungs. Some lack eyes and scales; some have fins better adapted to climbing than swimming. Others guard their eggs or young; some keep them in their mouths, in a pouch, or even attached to their heads! Flashes of colour are a feature of many species, but even dull or camouflaged species can have spectacular nuptial displays. Movements can be local sorties, regular forays between fresh water and sea water or opportunistic journeys over thousands of kilometres during floods, and might include burrowing into sediments to survive dry times. Within and between populations there are likely to be variations in such biological traits as appearance, habitat use, diet, spawning, disease resistance, movements and behaviour. The remarkable variability of fishes contributes to ecologically diverse aquatic ecosystems and to diversity in populations, families, genera, species and individuals, collectively ‘biological diversity’ or simply ‘biodiversity’ (Fig. 3.1).

This chapter is a primer on genetics for fish ecologists, recognising that advances in genetics are playing an increasing role in our understanding of patterns of biodiversity and underlying evolutionary processes. It describes approaches that (a) document biodiversity, relationships and identity, (b) explore processes such as dispersal and population dynamics and (c) provide data on species, populations and individuals to inform management and conservation planning of Australian freshwater fishes. These approaches are readily translated into questions. When did these species diverge? Are these two forms members of the same species? Is this species diadromous? How many subpopulations, stocks or conservation units are present? Is there evidence of current or historical dispersal between these populations or regions? What larva is that, and what are these fish remains in the gut contents? Is there a different way to tag fish? Did the colourful or the subordinate male sire these offspring? Which broodstock should we spawn? Genetic data can help to answer questions like these.