1. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Puffer fish phylogeny From Figure 1 Mulley, J and Holland, P. (2004) “Small genome, big insights” Nature 431: 916-917.  Two sequenced puffer fish  Tetraodon nigroviridis  Takifugu rubripes  Last common ancestor: 13-18 million years ago  Last common ancestor with H. sapiens: 450 million years ago

2. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Evidence of a whole-genome duplication  Look for paralogous genes on different chromosomes  Number of duplicated (i.e. paralogous) genes on two different chromosomes is high  Evidence for a whole- genome duplication From Figure 4 Jaillon, O. (2004) “Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype” Nature 431: 946-957.

3. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Comparing synteny maps  Synteny defined as two or more orthologous puffer fish genes located on same human chromosome  Two orthologous puffer fish regions for every one human  Suggests that whole- genome duplication occurred after divergence of lineages From Figure 5 Jaillon, O. (2004) “Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype” Nature 431: 946-957.

4. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Deducing an ancestral karyotype  Use distribution of orthologs in human and puffer fish to determine common ancestor’s karyotype  Whole-genome duplication and just 10 interchromosomal rearrangements account for present puffer fish karyotype From Figure 9 Jaillon, O. (2004) “Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype” Nature 431: 946-957.