Phylogenomic analysis reveals ancient segmental duplications in the human genome

Molecular Phylogenetics and Evolution
Madiha HafeezAmir Ali Abbasi

Abstract

Evolution of organismal complexity and origin of novelties during vertebrate history has been widely explored in context of both regulation of gene expression and gene duplication events. Ohno (1970) for the first time put forward the idea of two rounds whole genome duplication events as the most plausible explanation for evolutionarizing the vertebrate lineage (2R hypothesis). To test the validity of 2R hypothesis, a robust phylogenomic analysis of multigene families with triplicated or quadruplicated representation on human FGFR bearing chromosomes (4/5/8/10) was performed. Topology comparison approach categorized members of 80 families into five distinct co-duplicated groups. Genes belonging to one co-duplicated group are duplicated concurrently, whereas genes of two different co-duplicated groups do not share their duplication history and have not duplicated in congruency. Our findings contradict the 2R model and are indicative of small-scale duplications and rearrangements that cover the entire span of animal's history.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 5, 2001·Molecular Biology and Evolution·A Martin
Dec 26, 2001·Nucleic Acids Research·T HubbardM Clamp
May 25, 2002·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Rebecca F Furlong, Peter W H Holland
May 29, 2002·Nature Genetics·Aoife McLysaghtKenneth H Wolfe
Jan 10, 2003·Nucleic Acids Research·M ClampE Birney
Jan 10, 2003·Nucleic Acids Research·Maximilian DiehnAsh A Alizadeh
Dec 7, 2007·BMC Evolutionary Biology·Amir Ali Abbasi, Karl-Heinz Grzeschik
Apr 18, 2008·Briefings in Bioinformatics·Sudhir KumarKoichiro Tamura
Apr 29, 2008·Nucleic Acids Research·Mark JohnsonThomas L Madden
Dec 17, 2008·Biology Direct·Amir Ali Abbasi
Aug 5, 2009·Nature Reviews. Genetics·Yves Van de PeerAxel Meyer
Nov 15, 2013·Nucleic Acids Research·Henrik NordbergInna Dubchak
Dec 10, 2013·Nucleic Acids Research·Paul FlicekStephen M J Searle
Mar 5, 2014·Nature Reviews. Genetics·Diego VillarDuncan T Odom
Apr 9, 2014·Nature Reviews. Genetics·Jeffrey Rogers, Richard A Gibbs
May 14, 2014·Molecular Phylogenetics and Evolution·Sadaf AmbreenAmir Ali Abbasi

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Citations

Jun 25, 2016·Database : the Journal of Biological Databases and Curation·Bronwen L AkenStephen M J Searle
Jun 9, 2020·Algorithms for Molecular Biology : AMB·Mattéo DelabreMiguel Sautie Castellanos

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