Amniote Phylogenomics: Testing Evolutionary Hypotheses with BAC Library Scanning and Targeted Clone Analysis of Large-Scale DNA Sequences from Reptile

Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing “genome scans” of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species.