Vertebrates As Paleopolyploid
The hypothesis of vertebrate paleopolyploidy originated as early as the 1970s, proposed by the biologist Susumu Ohno. He reasoned that the vertebrate genome could not achieve its complexity without large scale whole-genome duplications. The "two rounds of genome duplication" hypothesis (2R hypothesis) came about, and gained in popularity, especially among developmental biologists.
However, the 2R hypothesis has been questioned by many researchers. Based on the theory, vertebrate genomes should have a 4:1 gene ratio compared with invertebrate genomes. This is not supported by findings from the 48 vertebrate genome projects available in mid-2011, for example the human genome consists of ~21,000 protein coding genes according to June, 2011 counts at UCSC and Ensembl genome analysis centers while an average invertebrate genome size is about 15,000 genes. Further, the recent completion of the amphioxus genome sequence does not support any such whole genome duplication with largescale retention, as predicted by the hypothesis. Additional arguments against 2R were based on the lack of the (AB)(CD) tree topology amongst four members of a gene family in vertebrates. However, if the two genome duplications occurred close together, we would not expect to find this topology.
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