title: Integrating large-scale phylogenetic datasets to dissect the ancient evolutionary history of vertebrate genome.
abstract: BACKGROUND
  The vertebrate genome often contains closely spaced set of paralogous genes from distinct gene families on typically two, three or four different chromosomes (paralogons). This type of genome architecture is widely considered to be remnants of whole genome duplication events (WGD/2R).
  
  
  RESULTS
  Taking advantage of the well-annotated and high-quality human genomic sequence map as well as the ever-increasing accessibility of large-scale genomic sequence data from a diverse range of animal species, we investigated the evolutionary history of potential quadruplicated regions residing on human HOX-cluster bearing chromosomes (chromosomes 2/7/12/17). For this purpose a detailed phylogenetic analysis was performed for those multigene families, including members of at least three of the four HOX-bearing chromosomes. Topology comparison approach categorized the members of 63 families into distinct co-duplicated groups. Distinct gene families belonging to a particular co-duplicated group, exhibit similar evolutionary history and hence have duplicated concurrently, whereas genes of two different co-duplicated groups do not share their history and have not duplicated in concert with each other.
  
  
  CONCLUSIONS
  These results based on large-scale phylogenetic dataset yielded no evidence in favor of polyploidization events; instead it appears that triplicated and quadruplicated genomic segments on the human HOX-bearing chromosomes arose by small-scale duplication events that occurred at widely different time points in animal evolution.
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: Sadaf
authors.initials: S
authors.lastname: Ambreen
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: Faiqa
authors.initials: F
authors.lastname: Khalil
authors.affiliation: National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. Electronic address: abbasiam@qau.edu.pk.
authors.forename: Amir Ali
authors.initials: AA
authors.lastname: Abbasi
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002877:Chromosomes, Human; D019143:Evolution, Molecular; D005801:Genes, Homeobox; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D005810:Multigene Family; D010802:Phylogeny; D056916:Segmental Duplications, Genomic; D014714:Vertebrates / Q000235:genetics
keywords: HOX-cluster; Human paralogons; Phylogenetic analysis; Segmental duplication; Vertebrates; WGD/2R