Orphan genes are genes that occur in specific evolutionary lineages without similarity to genes outside of these lineages and have, therefore, alternatively been named taxonomically restricted genes. They were so far considered to emerge through duplication–divergence processes, but it is now becoming clear that they can also arise
de novo
out of noncoding deoxyribonucleic acid (DNA). This latter process may even occur much more frequently than previously assumed. It appears that genomes harbour many transcripts in a transition stage from nonfunctional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become fixed when they turn out to be useful. Orphan genes may have played key roles in generating lineage‐specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.
Key Concepts:
Orphan genes, or taxonomically restricted genes, have arisen at all levels of the phylogenetic hierarchy.
All genes that cannot be traced to the first cellular ancestor are orphan genes in some lineages.
New genes may not only arise through gene duplication, but also through
de novo
evolution.
Spurious transcripts can give rise to protogenes, from which new functional genes evolve.
Emergence of new genes from protogenes is an active process in all extant genomes.
New genes may first act as noncoding RNAs before obtaining a functional reading frame.
Overprinting of existing reading frames with new reading frames is another possibility of
de novo
evolution of gene functions.
Orphan genes may contribute to lineage‐specific adaptations.
Orphan genes may carry information on the evolutionary past that can be harnessed by the phylostratigraphic approach.
There is a continuous birth–death dynamics of gene evolution.