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17 Comparing the Human and Chimpanzee Genomes: Searching for Needles in a Haystack

Ajit Varki, Tasha K. Altheide


Humans (Homo sapiens) and chimpanzees (Pan troglodytes) last shared a common ancestor ~5–7 million years ago (Mya) (Chen and Li 2001; Brunet et al. 2002). What makes humans different from their closest evolutionary relatives, and how, why, and when did these changes occur? These are fascinating questions, and a major challenge is to explain how genomic differences contributed to this process (Goodman 1999; Gagneux and Varki 2001; Klein and Takahata 2002; Carroll 2003; Olson and Varki 2003; Enard and Pääbo 2004; Gagneux 2004; Ruvolo 2004; Goodman et al. 2005; Li and Saunders 2005; McConkey and Varki 2005). Most genome projects focus on elucidating the sequence and structure of a species’ genome and then identifying conserved functionally important genes and genomic elements. The finished human genome (International Human Genome Sequencing Consortium 2004) provides such a catalog of genomic features that ultimately interact with the environment to determine our biology, physiology, and disease susceptibility. Completion of the draft chimpanzee genome sequence (The Chimpanzee Sequencing and Analysis Consortium 2005) provides a genome-wide comparative catalog that can be used to identify genes or genomic regions underlying the many features that distinguish humans and chimpanzees.

As humans, we have an inherent interest in understanding and improving the human condition. We also believe that we have many characteristics that are uniquely human. Table 1 lists some of the definite and possible phenotypic traits that appear to differentiate us from chimpanzees and other “great apes.”1 For the most part, we do not know which genetic features...

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