The field of Genomics has essentially been fuelled by medical research with developments in human gene therapy, such as the Human Genome Project. This major international undertaking resulted in a significantly increased sequencing capacity, a dramatic decrease in the time and cost of sequencing and also the computational effort required for the analysis. Marine biologists are taking advantage of this high throughput technology, hence, the tools are now available to answer questions that would have not been possible even five years ago. Genomics, in terms of studying DNA, can effectively define the genetic structure of populations and as a consequence the mapping of species boundaries, approximate drift in populations and accurately measure biodiversity. Studying transcribed sequences (RNA) enables the identification of changes at the cellular level associated with the adaptation of species to particular habitats and now, in our changing environment, predicts their ability to survive perturbation. \ud The aim of this chapter is to familiarize the reader with the most commonly used genomic techniques that are available for population and adaptation studies. These encompass both DNA based methodologies for population studies and RNA based techniques for expression studies. Which technique is used largely depends on the species under study and the resources available. In environmental research it is important to understand that “resources” does not just refer to money for sequencing and library production, but also access to starting material and the ability to store the material successfully, often under difficult conditions. For example, a cruise to investigate a particular hydrothermal vent may only happen once in a researcher’s lifetime and so material will be scarce, numbers will be limited and it may not be possible to store the material at a low enough temperature to prevent RNA degradation (thereby excluding expression studies). Also species availability tends to be on what is there at the time, rather than being able to perform a calculated choice for which species is the best to study. In other studies such as aquaculture or invasive species, a means has to be found to work on a particular species even if the material is intractable as there is a defined requirement for work in that area. So having outlined the techniques, the question is how to use them? \ud In this chapter specific examples will be used to demonstrate how such techniques are being used to address these important ecological issues in the marine environment, concentrating on lower vertebrates (fish) and invertebrates. These encompass both population analyses and gene expression (functional) studies to understand how populations have adapted to and interact with, their environment. \ud Ultimately, the challenge for the marine biologist is to utilize the tools produced for the study of model organisms, where significant amounts of sequence data exist (i.e. resource rich) and to develop these for non-model species, essentially from a zero base-line. It is not an easy task. \u
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