Understanding Gene Duplication Through Biochemistry and Population Genetics

Abstract

Gene duplication has emerged as an important process supporting the functional diversification of genes. Since publication of the seminal book Evolution by Gene Duplication by Ohno (1970), the hypothesis regarding the importance of gene duplication in the generation of evolutionary novelty has steadily gained support as we have entered the genome-sequencing era. It is through the link to functional biology that an ultimate understanding of the preservation and diversification of duplicate genes will be accomplished.Genes can diverge in function through accumulation (fixation) of coding sequence changes, which may influence binding interactions and/or catalysis, through the evolution of splice variants, and through spatial, temporal, and concentration-level changes in the expression of the protein product. Governing these processes is an interplay among mutational opportunity, population dynamics, protein biochemistry, and systems and organismal biology. This interplay is described systematically in this chapter. SYSTEMS BIOLOGY AND HIGHER-LEVEL ORGANIZATIONAt the level of biological systems, two early but still relevant views suggested a role for gene duplication in constructing pathways. These views are both dependent on a new function emerging in one of the duplicates, but differ in the manner in which it occurs. One view, patchwork evolution, involved a conservation of catalytic activity coupled with the evolution of a new substrate after duplication (Jensen, 1976). An alternative view, retrograde evolution, suggested that pathways are built up backward, with product becoming substrate based on recognition of the transition state in the Evolution After Gene Duplication, Edited by Katharina Dittmar and David Liberles

Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty

“…As seen in the above case studies, gene duplication is frequently associated with the evolution of novel functions ( Stephens 1951 ; Nei 1969 ; Ohno 1970 ; Kaessmann 2010 ; Liberles et al 2010 ). The most extensively documented proposal for the evolution of novel gene function is the classic gene duplication model proposed by Ohno (1970) and extended by Force, Lynch, and many others ( Force et al 1999 ; Lynch and Conery 2000 ; Tirosh and Barkai 2007 ; Liberles et al 2010 ). Following gene duplication, one copy may retain its original function, whereas the other copy diverges, and can have a variety of different fates, including pseudogenization ( Lynch and Conery 2000 ), hypofunctionalization ( Duarte et al 2006 ), subfunctionalization, or neofunctionalization.…”

“…Following gene duplication, one copy may retain its original function, whereas the other copy diverges, and can have a variety of different fates, including pseudogenization ( Lynch and Conery 2000 ), hypofunctionalization ( Duarte et al 2006 ), subfunctionalization, or neofunctionalization. Subfunctionalization is due to complementary loss of some of the functional attributes that are initially shared by the new paralogs following duplication, whereas neofunctionalization can occur when one of the paralogs evolves a new expression pattern or sequence attribute and acquires a new function ( Force et al 1999 ; Lynch and Conery 2000 ; Tirosh and Barkai 2007 ; Liberles et al 2010 ). Subneofunctionalization was proposed to describe processes that involved both ( He and Zhang 2005 ).…”

Genetic variability in the region encompassing reiteration VII of herpes simplex virus type 1, including deletions and multiplications related to recombination between direct repeats

“…Gene duplication is an important process supporting the functional diversification of genes in the evolutionary change of DNA (Liberles et al 2010 ; Nei 1987 ). Genes with improved function may arise by the elongation of genes, and gene elongation is usually caused by the duplication of a gene or part of a gene.…”

On the Need for Mechanistic Models in Computational Genomics and Metagenomics

“…Ideally, all of the processes discussed earlier should be simultaneously modeled to fully characterize the evolution of gene content and the consequent evolution of species (Roth et al 2007; Liberles et al 2010). Although much of the discussion will assume that the species tree is known topologically, a mechanistic framework has been proposed to infer species trees from multiple genes in the context of incomplete lineage sorting (Liu and Pearl 2007; Heled and Drummond 2010).…”