Selection in the evolution of gene duplications

By Fyodor A. Kondrashov, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin. Genome Biology, 2002

781 citations recorded by the source corpus.

BackgroundGene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function.ResultsIn search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins.ConclusionsThe results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.

Subfields: Astronomy and Astrophysics, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8cba79e09e93e03c4bdff166564d484b7bff0360

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Astronomy and Astrophysics

Eugene V. Koonin

In Ecology

In Molecular Biology

Citations in the corpus

Turning a hobby into a job: How duplicated genes find new functions (2008, background): “Because dosage selection allows duplications to be selectively advantageous at birth, they can be fixed by positive selection and not by genetic drif”
Probability Models for DNA Sequence Evolution (2002, background): “Analyses of the human genome by Li et al. (2001) have revealed that at least 15% of human genes are indeed duplicates, with segmental duplications covering 5.”
Orthologs, Paralogs, and Evolutionary Genomics 1 (2005, background): “The subfunctionalization mode of evolution of paralogs that has been explored theoretically in great detail by Lynch and coworkers (27, 60, 61) seems best compatible with the demonstration that selective constraints affect paralogs even immediately after duplication (45).”
Duplication and divergence: the evolution of new genes and old ideas. (2004, result): “The first genome-scale analyses tend to support a “very little” hypothesis (69, 145), although more recent analyses yield larger rate differences.”
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae (2004, methodology): “However, this model has been contested by others, who argued that both copies would diverge more rapidly and acquire new functions 20–22 .”
The evolutionary consequences of polyploidy. (2007, background): “Other mechanisms that preserve newly duplicated genes include the requirement for gene balance, heterozygote advantage, and selection for higher levels of gene expression (see references in Otto and Yong, 2002 and Kondrashov et al., 2002).”
Human and chimpanzee Luteinizing hormone/ Chorionic Gonadotropin beta (LHB/CGB) gene clusters: diversity and divergence of young duplicated genes (2009, background): “…rates after duplication, the relaxation of purifying selection due to the duplication of functional genes, the action of positive diversifying selection on one or both copies, or a combination of these (Conant and Wagner 2003; Kondrashov et al. 2002; Lynch and Conery 2000; Zhang et al. 2003).”
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome (2010, background): “The generation of so many duplicated genes likely gave rise to a large number of new, novel and perhaps unique gene functions [4,5].”
Using PhyloSuite for molecular phylogeny and tree‐based analyses (2023, background): “In multilocus datasets, different loci (gene or codon sites) may evolve at different rates and patterns, as they often have different biological functions and evolve under different selection pressures [37, 38].”
The evolution of gene duplications: classifying and distinguishing between models (2010, background): “Hardly any aspect of genome evolution or function is not somehow linked to gene duplications, which occur in all kinds of life form”
DAGchainer: a tool for mining segmental genome duplications and synteny (2004, background): “The duplicated genome segments yield a source of functional redundancy and provide substrates for the evolution of new gene functions (Kondrashov et al., 2002).”