ABSTRACT
Science, by its very nature, relies upon the comparison and contrast of observations and measurements and thus is always ‘comparative’ in approach. The hierarchical level of possible comparisons that can be examined using a hypothesis-testing framework is restricted to some extent by imagination but more profoundly by the tools that are available to record and test the very attributes under investigation. The field of genomics is becoming increasingly more amenable to larger scale comparisons that were previously restricted to within-individual or at specific timepoints to examine environmental impact on a trait. For population geneticists studying the processes which mediate long term molecular evolutionary patterns, the development of new comparative approaches facilitiates an unprecedented opportunity to examine finerscale interactions between genotype frequency and phenotypic variation. For functional genomicists searching for mutations in genes that have the greatest impact on target phenotypes, comparative genomics unveils an amazing tool to test hypotheses generated by single-taxon observations in other species that examine consistency in most probable associations between phenotype and genotype. This list could continue, however the bottom line is that comparative genomics approaches
utilizing the evolutionary genetics framework are emerging as powerful tools directly impacting both theoretical knowledge and practical applications. In this chapter, we discuss how to establish the evolutionary context. We then discuss inter-genic and regional genome dynamics as well as intra-genic dynamics of different temporal sensitivities and then describe key points in parameter estimation. In the final section, we discuss how the combination of these approaches is being used to investigate co-expression networks and building towards a larger ecogenomics effort.
