New review of de novo gene birth

PLoS Genetics has a nice, new review of what is known about the evolution of de novo genes, which seems to be a topical of perennial interest here.

De novo gene birth

De novo gene birth is the process by which new genes evolve from DNA sequences that were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes [1]. The processes that govern de novo gene birth ( Fig 1A ) are not well understood, though several models exist that describe possible mechanisms by which de novo gene birth may occur. Although de novo gene birth may have occurred at any point in an organism’s evolutionary history, ancient de novo gene birth events are difficult to detect. Most studies of de novo genes to date have thus focused on young genes, typically taxonomically-restricted genes (TRGs) that are present in a single species or lineage, including so-called orphan genes, defined as genes that lack any identifiable homolog. It is important to note, however, that not all orphan genes arise de novo , and instead may emerge through fairly well-characterized mechanisms such as gene duplication (including retroposition) or horizontal gene transfer followed by sequence divergence, or by gene fission/fusion [2, 3] ( Fig 2 ) Though de novo gene birth was once viewed as a highly unlikely occurrence [4], there are now several unequivocal examples of the phenomenon that have been described. It furthermore has been advanced that de novo gene birth plays a major role in the generation of evolutionary innovation [5, 6].


Poe’s Law activate:

Thanks for sharing but I already don’t trust it when it says:

Competing interests: The authors have declared that no competing interests exist.

I can easily see the authors are evolutionists and thus everything in their paper must be subject to a reinterpretation through a Biblical worldview. Perhaps some here can help reinterpret this paper for us.


@pevaquark and @davecarlson

I guess I’ve been sleeping for a few decades. I had no idea that “de novo gene birth” was viewed as a highly unlikely occurrence! I can understand why it might not be a driver of evolution, but it never occurred to me that we would need a drawing to show that it is conceivable!

This is the footnote for FN 4, but it’s from 1977 and is more a philosophical article about science than a scientific one about cell genetics. Not a bad article… just not much meat.

Evolution and tinkering
By F Jacob
Science 10 Jun 1977:
Vol. 196, Issue 4295, pp. 1161-1166
DOI: 10.1126/science.860134


These two links are the footnotes 5 and 6:

More than just orphans: are taxonomically-restricted genes important in evolution?
by Konstantin Khalturin, Georg Hemmrich, et al.

ABSTRACT: Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs in other species. Do such ‘orphan’ or ‘taxonomically-restricted’ genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.


The evolutionary origin of orphan genes

Nature Reviews Genetics volume12 , pages692–702 (2011) | Download Citation


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.


That would seem to be a self-canceling activation, as no actual creationist would make such an announcement. Thus we can indeed tell that it was a parody.