title: Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates.
abstract: BACKGROUND
  Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared with invertebrates, two entire genome duplications (2R) were proposed during the early evolution of vertebrates. Most glycolytic enzymes occur as several copies in vertebrate genomes, which are specifically expressed in certain tissues. Therefore, the glycolytic pathway is particularly suitable for testing theories of the involvement of gene/genome duplications in enzyme evolution.
  
  
  RESULTS
  We assembled datasets from genomic databases of at least nine vertebrate species and at least three outgroups (one deuterostome and two protostomes), and used maximum likelihood and Bayesian methods to construct phylogenies of the 10 enzymes of the glycolytic pathway. Through this approach, we intended to gain insights into the vertebrate specific evolution of enzymes of the glycolytic pathway. Many of the obtained gene trees generally reflect the history of two rounds of duplication during vertebrate evolution, and were in agreement with the hypothesis of an additional duplication event within the lineage of teleost fish. The retention of paralogs differed greatly between genes, and no direct link to the multimeric structure of the active enzyme was found.
  
  
  CONCLUSIONS
  The glycolytic pathway has subsequently evolved by gene duplication and divergence of each constituent enzyme with taxon-specific individual gene losses or lineage-specific duplications. The tissue-specific expression might have led to an increased retention for some genes since paralogs can subdivide the ancestral expression domain or find new functions, which are not necessarily related to the original function.
authors.affiliation: Lehrstuhl für Evolutionsbiologie und Zoologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany. dsteinke@uoguelph.ca
authors.forename: Dirk
authors.initials: D
authors.lastname: Steinke
authors.forename: Simone
authors.initials: S
authors.lastname: Hoegg
authors.forename: Henner
authors.initials: H
authors.lastname: Brinkmann
authors.forename: Axel
authors.initials: A
authors.lastname: Meyer
mesh_terms: D000818:Animals; D030562:Databases, Protein; D019143:Evolution, Molecular; D005634:Fructose-Bisphosphate Aldolase / Q000235:genetics; D020440:Gene Duplication; D016678:Genome; D005956:Glucose-6-Phosphate Isomerase / Q000235:genetics; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) / Q000235:genetics; D006019:Glycolysis / Q000235:genetics*; D006593:Hexokinase / Q000235:genetics; D006801:Humans; D010732:Phosphofructokinase-1 / Q000235:genetics; D010735:Phosphoglycerate Kinase / Q000235:genetics; D010736:Phosphoglycerate Mutase / Q000235:genetics; D010751:Phosphopyruvate Hydratase / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011770:Pyruvate Kinase / Q000235:genetics; D014305:Triose-Phosphate Isomerase / Q000235:genetics; D014714:Vertebrates / Q000235:genetics*
chemical_list: D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating); D006593:Hexokinase; D010732:Phosphofructokinase-1; D011770:Pyruvate Kinase; D010735:Phosphoglycerate Kinase; D005634:Fructose-Bisphosphate Aldolase; D010751:Phosphopyruvate Hydratase; D014305:Triose-Phosphate Isomerase; D005956:Glucose-6-Phosphate Isomerase; D010736:Phosphoglycerate Mutase