across generations and the development of techniques to determine DNA sequence have allowed theory and data to combine elegantly in phylogenetic analyses to describe the evolution of organisms and their component parts, including metabolic, sensory, and developmental pathways, by comparing the DNA sequences of the relevant genes. While much is known about how genetic information is gained and lost through mutation, recombination, conversion, duplication, translocation, selection, and other processes that alter genetic material in individuals and populations, much remains to be learned about the expression and regulation of genome activity that depends on inherited genetic information. The promise of classical genetic theory was the theoretical ability to predict the form and capabilities of an organism by knowing the DNA sequence of its protein-coding genes. A comprehensive understanding of the regulation and interaction of these protein products would explain the process of development, allow prediction of the connection of genotype to phenotype (including, for example, the linking of genetic variation to disease susceptibility), and serve as the palette upon which natural selection could act. Research based on this theoretical framework has indeed contributed to the success of biological research in the last few decades and enabled the development of a vibrant biotechnology industry.
At a number of levels, observational and experimental data are accumulating that suggest that this enormously successful classical framework is ripe for further expansion. This chapter discusses some of the ways in which it is becoming clear that the characteristics of offspring cannot be fully explained by the genes acquired from their parents. First, an understanding of the roles of noncoding DNA, which makes up the bulk of the genomes of many higher organisms’ genomes, will be required to link genotype to phenotype (see Chapter 3). Also, a number of mechanisms other than DNA sequence—collectively designated epigenetic mechanisms—are being shown to represent additional means to pass information from cell to daughter cell, from parent to offspring. Looking beyond the inheritance mechanisms that act within species, increased exploration of the microbial world has profound implications for our understanding of how adaptive mechanisms can be inherited and shared. As introduced in Box 3-2, microbes live in complex multispecies communities where genes can be shared between distantly related organisms. Thus, genetic adaptations can spread across evolutionary lineages. Furthermore, many if not all eukaryotic organisms live in intimate association with microbial communities that provide a number of functions from nutrition to host defense, functions that are apparently coordinated over evolutionary time scales with the functions encoded by the host organism’s genome. Finally, behavioral, social, and symbolic structures (such as human language) have the potential to be carried from one generation to the next. These characteristics do not exist independently