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The evolutionary origin of orphan genes

Nature Reviews Genetics volume 12, pages 692–702 (2011)Cite this article

Subjects

Key Points

  • Current models of gene evolution have concentrated on mechanisms that are mediated by duplication and by transposable elements, but these models have not yet fully evaluated the possibility of de novo evolution.

  • Orphan genes with no homology to genes in other evolutionary lineages occur in all genomes and are candidates for the de novo evolution of genes.

  • Several examples of de novo evolved genes have now been found, and the emergence process can involve a phase in which a gene functions as a non-coding RNA.

  • Orphan gene emergence rates are elevated during adaptive radiations.

  • Orphan gene emergence over time appears to be continuously high, but most of these newly emerged genes are likely to be subsequently lost.

  • It is still an open question whether newly evolved genes can form new stable protein domains or whether they act as intrinsically unstructured proteins.

  • The emergence of new genes may contribute to evolutionary novelties to the same degree as does the emergence of new regulatory interactions.

Abstract

Gene evolution has long been thought to be primarily driven by duplication and rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood. Orphan genes might arise from duplication and rearrangement processes followed by fast divergence; however, de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism. This process appears to provide raw material continuously for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.

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Figure 1: Identification of orphan genes in a phylogenetic context.
Figure 2: Duplication–divergence model for orphan gene evolution.
Figure 3: De novo evolution model for orphan genes.
Figure 4: Emergence rates of founder genes in three different phyla.

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Acknowledgements

We thank former and current colleagues and laboratory members, as well as three anonymous reviewers who have contributed to the ideas presented here. We thank R. Neme, M. Matejcˇic´ and M. S. Šestak for providing phylostratigraphic maps. The work of the authors is supported by institutional funds of the Max-Planck Society, the Ruđer Boškovic´ Institute, the Zoological Institute of the Christian-Albrechts-University Kiel and the Unity Through Knowledge Fund (grant number 49).

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Authors and Affiliations

  1. Max-Planck Institut für Evolutionsbiologie, August-Thienemannstrasse 2, Plön, 24306, Germany

    Diethard Tautz

  2. Zoological Institute, Christian Albrechts University Kiel, Kiel, 24105, Germany

    Tomislav Domazet-Lošo

  3. Division of Molecular Biology, Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, P.P. 180, Zagreb, 10002, Croatia

    Tomislav Domazet-Lošo

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  1. Diethard Tautz
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Correspondence to Diethard Tautz.

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Glossary

Orphan genes

Genes that lack homologues in other lineages — that is, they cannot be linked by overall similarity or shared domains to genes or gene families known from other organisms.

Purifying selection

The removal of deleterious mutations through natural selection.

Basic Local Alignment Search Tool

(BLAST). A program that compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

Protostomes

The animal superphylum that includes nematodes (for example, Caenorhabditis elegans) and arthropods (for example, Drosophila melanogaster).

Deuterostomes

The animal superphylum that includes vertebrates (for example, zebrafish) and mammals (for example, humans).

Founder genes

The phylogenetically oldest genes forming the basis of a new gene lineage, new protein domain or new gene family. The origin of founder genes is expected to correlate with evolution of functional novelty.

Phylostratigraphy

A systematic procedure to identify the origin of genes within a comparative framework of fully sequenced genomes at multiple levels of the phylogenetic hierarchy (the phylostrata).

Horizontal gene transfer

(HGT). The exchange of genes between different evolutionary lineages.

Retrotransposons

Transposons that require an RNA intermediate for their transposition.

Sexual selection

A form of selection that arises from the interaction between the sexes and their gametes rather than from interactions with the environment.

Positive selection

The increase in frequency and fixation of alleles that contributes to the fitness of an organism.

Selective sweeps

The reduction or elimination of nucleotide variation in the genomic region that surrounds a positively selected new mutation.

Phylostratum

A node in the phylogenetic hierarchy that is represented by one or more fully sequenced genomes and where a set of genes from an organism coalesce to founder genes.

Synteny

Conserved genomic arrangements of genes in a linear order.

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Tautz, D., Domazet-Lošo, T. The evolutionary origin of orphan genes. Nat Rev Genet 12, 692–702 (2011). https://doi.org/10.1038/nrg3053

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