Abstract
Gene copy-number differences due to gene duplications and deletions are rampant in natural populations and play a crucial role in the evolution of genome complexity. Per-locus analyses of gene duplication rates in the pre-genomic era revealed that gene duplication rates are much higher than the per nucleotide substitution rate. Analyses of gene duplication and deletion rates in mutation accumulation lines of model organisms have revealed that these high rates of copy-number mutations occur at a genome-wide scale. Furthermore, comparisons of the spontaneous duplication and deletion rates to copy-number polymorphism data and bioinformatic-based estimates of duplication rates from sequenced genomes suggest that the vast majority of gene duplications are detrimental and removed by natural selection. The rate at which new gene copies appear in populations greatly influences their evolutionary dynamics and standing gene copy-number variation in populations. The opportunity for mutations that result in the maintenance of duplicate copies, either through neofunctionalization or subfunctionalization, also depends on the equilibrium frequency of additional gene copies in the population, and hence on the spontaneous gene duplication (and loss) rate. The duplication rate may therefore have profound effects on the role of adaptation in the evolution of duplicated genes as well as important consequences for the evolutionary potential of organisms. We further discuss the broad ramifications of this standing gene copy-number variation on fitness and adaptive potential from a population-genetic and genome-wide perspective.
Highlights
The publication of Ohno’s “Evolution by Gene Duplication” is fittingly viewed as a milestone in the study of gene duplications (Ohno, 1970)
ANALYTICAL METHODS USED TO ESTIMATE THE GENE DUPLICATION AND DELETION RATE Several approaches have been used to estimate the spontaneous gene duplication and deletion rates. These estimates have primarily come from four sources: (i) direct measurements on a single locus where gene copy-number differences resulted in a distinct phenotype or genotype, (ii) analyses of frequencies of duplication polymorphisms in populations, (iii) calculations based on the abundance of evolutionarily recent gene duplications in sequenced genomes, and (iv) direct genome-wide estimates of the duplication/deletion rate from molecular analyses of mutation accumulation (MA) lines evolved experimentally under a regime of minimal natural selection
Empirical estimates of the spontaneous duplication rate, be they locus-specific or genome-wide from MA studies, invariably exceed estimates from analyzing the age distribution of gene duplicates in sequenced genomes. What may explain this discrepancy, with empirical estimates exceeding bioinformatically based ones by two to four orders of magnitude? We have previously proposed that the degree of discrepancy in bioinformatic and empirical estimates of the gene duplication rate is influenced by differences in the efficacy of selection in species due to their varying Ne (Katju et al, 2009; Lipinski et al, 2011; Katju, 2012)
Summary
The publication of Ohno’s “Evolution by Gene Duplication” is fittingly viewed as a milestone in the study of gene duplications (Ohno, 1970). Ohno perceived that segmental duplications would be associated with problems with gene dosage balance and genetic instability, and he placed a great significance on whole-genome duplications He viewed the duplicate copy of a gene as an initially passive element in the evolution of new genes. Soon after the discovery of the bar mutation, Bridges (1935, 1936) suggested that the duplication of genes provided a mechanism for increasing chromosome length and providing material for subsequent functional changes. This potential borne by gene duplication for evolutionary change was further emphasized by early geneticists and evolutionary biologists like Haldane, Müller, and Huxley (Haldane, 1933; Müller, 1935, 1936; Huxley, 1942). Sturtevant and Morgan (1923) discovered that the segmental duplications that gave rise to the bar www.frontiersin.org
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