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40 Introduction A major goal in biology is to understand the molecular basis of pheno­ typic evolution, in particular that of humans and other mammals. Shared mammalian traits include lactation, hair, and relatively large brains with unique structures (e.g., the neocortex). In addition, individual species or lineages evolved distinct anatomical, physiological and behavioral cha- racteristics, relating to differences in reproduction, life span, cognitive abilities and disease susceptibility. For example, humans have evolved particularly large and complex brains, even when compared to their closest evolutionary relatives, the chimpanzees, and also exhibit profound differ­ ences in disease susceptibility (e.g, chimpanzees do not develop AIDS upon HIV infection), life span (the maximum life span of a human is ap- proximately twice that of a chimpanzee), and various, more obvious, ana- tomical differences relative to chimpanzees and other primates1 . Examp- les of distinct (reproductive) features of the major mammalian lineages include the placenta of placental mammals, the elaborate lactation system of marsupials, and the intriguing combination of egg yolk nourishment and lactation of the young in monotreme mammals such as the platypus. What are the genomic changes and molecular mechanisms underlying all of these phenotypic innovations? When and how did they occur? What is the nature of the associated selective pressures?Answers to these ques- tions, which motivate our research, can be sought in the analysis of sev­ eral types of genomic alterations. In fact, mutations that may underlie phenotypic innovation can be grouped into only two major classes. The first class consists of mutations that change the sequence and, conse- quently, the function of the final gene product (i.e., the protein or RNA). The second class encompasses mutations in regulatory sequences (e.g. in promoter regions) that affect transcription, post-transcriptional proces- sing, translation, or transcript/protein degradation. But it should be noted that certain gene product sequence alterations that change the function of the protein (e.g., mutations in transcription factors2 ) may also affect gene regulation. How do these mutations drive phenotypic evolution? Generally, both clas- ses of mutations may contribute to the evolution of distinct tissue mor-