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CHAPTER ONE INTRODUCTION 1.1   BACKGROUND TO THE STUDY Population Genetics of aquatic species focuses on describing the genetic differences between populations of fish, between the individuals within the same population and between fish in aquaculture. For example, a brown trout from one part of Nigeria does usually not have the same genetic fingerprint (DNA profile) as a brown trout from another part of Nigeria, just as the North Sea cod does not have the same genetic fingerprint as the Baltic Sea cod.  The genetic variation of contemporary fish populations is the result of evolutionary processes, reflecting both geographical separations of populations over thousands of years and genetic adaptation to local conditions. The genetic differences can be analyzed and described using modern DNA technologies, providing important information on the factors influencing the distribution and dynamics of fish populations. They also provide us with a technical tool for tracing individual fish and fish products back to the sea-areas or aquaculture plants from where they originated.   Population genetic analyses are used to determine the population composition of fish catches in order to avoid over exploitation of small and vulnerable fish populations. The analyses may also be used to control illegal fishing by testing whether landed fish and fish products originate from species and stocks which can legally be caught.  Genetic monitoring also plays an important role in planning the long-term management of fish resources. The work is carried out by comparing DNA from contemporary fish samples with DNA analyses of samples from historical time series.  This is done by comparing DNA from fish scales and otoliths sampled more than 100 years ago, providing insight into how wild populations have responded to stocking, fishing and environmental change. Thus, inferences from such experiment can be used to guide management in order to preserve the genetic variation, resulting in healthy and productive fish populations that can be exploited sustainably. Population genetics is the study of genetic variation among species, individuals and populations; fundamentally, it shows that distribution of genetic variability is affected by evolutionary forces of mutation, migration, selection, and random genetic drift (Hansen, 2003).