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Sensory systems function as the interface between organisms and their environment, playing a pivotal role in animal biology. In vertebrates, habitat diversity and niche specialization contributed to the emergence of fascinating examples of sensory adaptation, allowing animals to better perceive, interact, and explore their surroundings. Recent advances have greatly expanded our understanding of vertebrate sensory biology, particularly regarding the molecular mechanisms of sensory transduction as well as the evolutionary processes underlying sensory adaptation. Here we review our current knowledge of the molecular evolution of vertebrate sensory systems.

Recreating ancestral proteins in the laboratory increasingly is being used to study the evolutionary history of protein function. More efficient gene synthesis techniques and the decreasing costs of commercial oligosynthesis are making this approach both simpler and less expensive to perform. Developments in ancestral reconstruction methods, particularly more realistic likelihood models of molecular evolution, allow for the accurate reconstruction of more ancient proteins than previously possible. This chapter reviews phylogenetic methods of ancestral inference, strategies for investigating alternative reconstructions, gene synthesis, and design, and an application of these methods to the reconstruction of an ancestor in the green fluorescent protein family.

Publisher Summary A novel and important application of synthetic gene technology in studies of G protein-coupled receptors (GPCRs) is the recreation of ancestral receptors. The superfamily of GPCRs consists of a large number of related seven transmembrane proteins of highly varied function. Recreating fossil receptors for functional studies in the laboratory can provide important insights into the constraints that shaped molecular structure and function in this diverse superfamily that are difficult to attain by using more traditional mutagenesis methods. In addition, in studying receptor function via heterologous expression of mutant receptors, it is often useful to create chimeric receptors in which putative functional domains are exchanged. This chapter presents a summary of methods and applications of synthetic gene technology, with an emphasis on synthesizing ancestral genes. Algorithms for inferring ancestral sequences and general considerations for designing synthetic genes are discussed in detail in the chapter. Detailed laboratory procedures for the various steps in gene synthesis, from oligonucleotide preparation to cassette mutagenesis, are also given.