542-488 million years ago


Not only can individual genes be duplicated, an organism can duplicate its entire genome. Although polyploid animal embryos do not survive as often as polyploid plant embryos, this type of genetic accident has been involved in the evolution of new species of animals and seems to have occurred early in the history of important groups of animals (such as teleost fish). Genetic analysis suggests that a genome duplication event occurred in primitive chordates prior to the evolution of the first fish. It is quite likely that the novel functions acquired by the duplicated genes were important in the evolution of fish.

One of the most significant conclusions from the analysis of genomes is the great role played by gene duplications to create gene families (Danielson, 1999). A large percentage of modern genomes appear to be homologous derivatives of ancestral genes which have resulted from multiple duplications and subsequent modification. This process continues today and individuals can vary in their possession of duplicates of individual genes (such as the globins and opsins). These duplications offer an evolutionary opportunity for genes to aquire new functions. For example, duplications of ancestral invertebrate immune cascades resulted in the vertebrate lectin and coagulation cascades and duplications of Hox clusters preceded greater specialization of the vertebrate head and limbs. Natural selection may be accelerated in these duplicates. The evolution of coding sequences in duplicated teleost Hox genes occurred at an increased rate compared to unduplicated sequences, seemingly through directional selection (Prohaska, 2004).
Duplications of the same ancestral genes can occur separately in different lineages. Although both tunicates and vertebrates both have duplicate gonadotropin releasing hormone receptors, they have arisen from independent duplications (Kusakabe, 2002). A number of genes have been duplicated in Amphioxus since its separation from other chordate lineages. These genes include a 14th gene in the Hox cluster, a duplicate Evx (whose function has diverged from the standard function of Evx), and a duplicate Emx gene (Minguillon, 2002).
Not only do many genes seem to be present in multiple copies resulting from duplications, entire chromosome segments seem to be duplicated. For example, human chromosomes 7p15-12, 17.q11-22, 12q12-13, and 2q31-34 not only contain homologous Hox clusters, but also EGFR homologs. Human chromosomes 6p21, 9q33-34, 1q22-31, and 19p13 possess homologs of nuclear receptors, vav-like oncogenes, notch-like receptors, pbx genes, tenascin homologs, complement proteins, abl-like kinases, TNF homologs, and MHC I related clusters (Spring, 1997).
Although it is possible that entire regions of chromosomes be duplicated, this can also result from polyploid events which duplicate the entire genome. A great deal of evidence suggests that two such genome duplications occurred before the evolution of the jawed vertebrates from primitive chordate ancestors. Tunicates have 6% DNA content as mammals (Lundin, 1993). The genome of tunicates, about 160 million base pairs, is about 20 times smaller than that of humans. The predicted 15,000-16,000 genes is a number similar to that found in other nonvertebrates (such as fruit flies, 14,000, and nematodes, 19,000). The tunicate genome is intermediate in many ways between invertebrates and vertebrates (Dehal, 2002). . A few hundred tunicate genes are more similar to those of protostomes than to those of vertebrates. Tunicates have 6 FGF genes (compared to 1-2 in protostomes and 22 in mammals), 5 Smad genes (which include TGF-ß and bone morphogenetic proteins; 8 genes of this family are known in mammals), and 10 T-box genes (mammals have 18) (Dehal, 2002).
From the analysis of Hox sequences in hagfish, it appears that at least one of the genome duplications early in vertebrate evolution occurred before craniates evolved and it seems that additional duplications occurred in hagfish after this. (Stadler, 2004; Hahn, 1998; Escriva, 2002; Hoyle, 1998).