title: Fourfold paralogy regions on human HOX-bearing chromosomes: role of ancient segmental duplications in the evolution of vertebrate genome.
abstract: BACKGROUND
  Susumu Ohno's idea that modern vertebrates are degenerate polyploids (concept referred as 2R hypothesis) has been the subject of intense debate for past four decades. It was proposed that intra-genomic synteny regions (paralogons) in human genome are remains of ancient polyploidization events that occurred early in the vertebrate history. The quadruplicated paralogon centered on human HOX clusters is taken as evidence that human HOX-bearing chromosomes were structured by two rounds of whole genome duplication (WGD) events.
  
  
  RESULTS
  Evolutionary history of human HOX-bearing chromosomes (chromosomes 2/7/12/17) was evaluated by the phylogenetic analysis of multigene families with triplicated or quadruplicated distribution on these chromosomes. Topology comparison approach categorized the members of 44 families into four distinct co-duplicated groups. Distinct gene families belonging to a particular co-duplicated group, exhibit similar evolutionary history and hence have duplicated simultaneously, whereas genes of two distinct co-duplicated groups do not share their evolutionary history and have not duplicated in concert with each other.
  
  
  CONCLUSIONS
  The recovery of co-duplicated groups suggests that "ancient segmental duplications and rearrangements" is the most rational model of evolutionary events that have generated the triplicated and quadruplicated paralogy regions seen on the human HOX-bearing chromosomes.
authors.affiliation: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
authors.forename: Zainab
authors.initials: Z
authors.lastname: Asrar
authors.forename: Farhan
authors.initials: F
authors.lastname: Haq
authors.forename: Amir Ali
authors.initials: AA
authors.lastname: Abbasi
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D005801:Genes, Homeobox / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D011123:Polyploidy; D016415:Sequence Alignment; D013045:Species Specificity; D014714:Vertebrates / Q000235:genetics*