title: The gain and loss of genes during 600 million years of vertebrate evolution.
abstract: BACKGROUND
  Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years.
  
  
  RESULTS
  We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication (whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost.
  
  
  CONCLUSIONS
  Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication (probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.
authors.affiliation: Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark, B-9052 Ghent, Belgium.
authors.forename: Tine
authors.initials: T
authors.lastname: Blomme
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
authors.forename: Stefanie
authors.initials: S
authors.lastname: De Bodt
authors.forename: Cedric
authors.initials: C
authors.lastname: Simillion
authors.forename: Steven
authors.initials: S
authors.lastname: Maere
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D006801:Humans; D051379:Mice; D010802:Phylogeny; D051381:Rats; D014714:Vertebrates / Q000145:classification / Q000235:genetics*