The evolutionary fate and consequences of duplicate genes.

  title={The evolutionary fate and consequences of duplicate genes.},
  author={Michael Lynch and John S. Conery},
  volume={290 5494},
Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate… 

The evolutionary demography of duplicate genes

The origin of a new function appears to be a very rare fate for a duplicate gene through the generation of microchromosomal rearrangements through reciprocal silencing of alternative copies, which can lead to the passive origin of post-zygotic reproductive barriers in descendant lineages of incipient species.

The evolution of gene duplicates.

Two Major Paths of Gene-Duplicates Evolution

"Two-stream" evolutionary pattern is revealed by the analysis of mutations in 2nd versus 3rd codon positions but not by the routinely used ratio of amino acid replacements (R) versus silent substitutions (S), i.e. the '2nd vs. 3rd' metric proved to be more resolving than the traditional 'R vs. S' metric.

The early stages of duplicate gene evolution

Analysis of recently duplicated genes in the Arabidopsis thaliana genome reveals significantly reduced species-wide levels of nucleotide polymorphisms in the progenitor and/or duplicate gene copies, suggesting that selective sweeps accompany the initial stages of the evolution of these duplicated gene pairs.

The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes

An increase in evolutionary rate in about half of the duplicated genes seems to suggest that either positive Darwinian selection has occurred or that functional constraints have been relaxed at one point in time during functional divergence.

Genome evolution: The infancy of duplicate genes

Using population genomics of the mustard Arabidopsis thaliana and its close relative A. lyrata, Moore and Purugganan (2003) investigated recent gene duplicates and discovered a prominent nurturing role for Darwinian selection.

Gene duplication as a mechanism of genomic adaptation to a changing environment

  • F. Kondrashov
  • Biology
    Proceedings of the Royal Society B: Biological Sciences
  • 2012
The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve the understanding of gene duplication as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.

Neofunctionalization of young duplicate genes in Drosophila

An approach for comparing genome-wide expression profiles of closely related species to disentangle the evolutionary forces operating on duplicate genes reveals that nearly all duplicates are retained by the evolution of a novel function in one copy, and illustrates how duplicates become incorporated into novel functional networks over evolutionary time.

Adaptive evolution of young gene duplicates in mammals.

It is found that a high proportion of young gene duplicates in the human, macaque, mouse, and rat genomes have experienced adaptive natural selection, larger than any reported amount of selection among single-copy genes in these lineages using similar methods.



Preservation of duplicate genes by complementary, degenerative mutations.

Focusing on the regulatory complexity of eukaryotic genes, it is shown how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions.

Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution.

Gene families resulting from genome duplications in humans and mice and the frequency distribution of gene family size showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function.

The probability of duplicate gene preservation by subfunctionalization.

The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.

Increasing Genomic Complexity by Gene Duplication and the Origin of Vertebrates

The results suggest that the genome complexity of contemporary vertebrates mostly reflect small‐scale DNA duplications instead of large‐scale (genomic) duplications, which does not refute the hypothesis that gene family evolution is governed by independent gene duplications occurring with identical probability across gene lineages.

Evolution of duplicate genes in a tetraploid animal, Xenopus laevis.

The results indicate that both copies of a duplicate gene can be subject to purifying selection and thus support the hypothesis of selection against all genotypes containing a null allele at either of two duplicate loci.

Gene Duplication and Gene Conversion in the Caenorhabditis elegans Genome

In general the closer the members of duplicated gene pairs are, the more likely it is that gene orientation is conserved, and this may contribute to the compactness of the C. elegans genome.

Phylogenies of Developmentally Important Proteins Do Not Support the Hypothesis of Two Rounds of Genome Duplication Early in Vertebrate History

  • A. Hughes
  • Biology
    Journal of Molecular Evolution
  • 1999
To test the 2R hypothesis, phylogenies for nine protein families important in development were constructed and in two cases there was significant support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes.

Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes.

  • M. Lynch
  • Biology
    Molecular biology and evolution
  • 1997
Molecular support is provided for the idea that asexually propagating genomes are subject to long-term, gradual fitness loss and questions about the role of organelle mutations in the long- term survival of major phylogenetic lineages are raised.

Gen(om)e duplications in the evolution of early vertebrates.

  • A. Sidow
  • Biology
    Current opinion in genetics & development
  • 1996

On the time for gene silencing at duplicate Loci.

The two-dimensional diffusion that models the evolution of the mutant allele frequencies at the two loci is studied by means of a transformation to two univariate diffusions having different time scales.