How evolution builds genes from scratch

  title={How evolution builds genes from scratch},
  author={Adam Levy},
  • Adam Levy
  • Published 16 October 2019
  • Education, Biology
  • Nature
Scientists long assumed that new genes appear when evolution tinkers with old ones. It turns out that natural selection is much more creative. Scientists long assumed that new genes appear when evolution tinkers with old ones. It turns out that natural selection is much more creative. 

Evolutionary New Genes in a Growing Paradigm

How new genes evolve has become an interesting problem in biology, particularly in evolutionary biology, and the search for new approaches to tackle this problem is under way.

Evolution of Complexity. Molecular Aspects of Preassembly

This work states that genetic material required for many complex traits, such as echolocation, was present long before emergence of the traits, and that Epigenetic factors ultimately promoted transfers from noncoding to coding genes, leading to abrupt formation of the trait via de novo genes.

Structural and functional characterization of a putative de novo gene in Drosophila

It is shown that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization, and Goddard’s structure appears to have been maintained with only minor changes over millions of years.

Modularity in Protein Evolution: Modular Organization and De Novo Domain Evolution in Mollusk Metallothioneins

A modular organization of mollusk MT is revealed, whose evolution has been impacted by duplication, loss, and de novo emergence of domains.

A computational exploration of resilience and evolvability of protein–protein interaction networks

It is demonstrated that adding nodes with gene-expression-based preferential attachment preserves and can increase the original resilience of PPI network in all three species, regardless of gene expression distribution or network structure.

A computational exploration of resilience and evolvability of protein-protein interaction networks

It is demonstrated that adding nodes with gene-expression-based preferential attachment preserves and can increase the original resilience of PPI network, and introduces a general notion of prospective resilience, which highlights the key role of network structures in understanding the evolvability of phenotypic traits.

The Evolution of Exaptation, and How Exaptation Survived Dennett’s Criticism

The concept of exaptation is one of the most original contributions given by the late palaeontologist Stephen J. Gould to evolutionary thinking. Exaptation was the focus of many of his theoretical

Standardized annotation of translated open reading frames.

A community-led effort involving Ensembl/ GENCODE, the HUGO Gene Nomenclature Committee (HGNC), UniProtKB, HUPO/ HPP and PeptideAtlas to produce a standardized catalog of 7,264 human Ribo-seq ORFs is outlined, outlining a path to bring protein-level evidence for Ribo’s ORFs into reference annotation databases; and a roadmap to facilitate research in the global community.

The Evolutionary Origin of Elastin: Is Fibrillin the Lost Ancestor?

Considering the remarkable similarities between the hydrophobic domains of the first recognizable elastin gene from the elasmobranch Callorhinchus milii with certain fibrillin regions from related fish species, the possibility that fibrillins might have provided protein domains to an ancestralElastin that thereafter underwent significant evolutionary changes to give the elastIn forms found today.

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, it is shown that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated.



Inverse relationship between evolutionary rate and age of mammalian genes.

It is shown that older genes tend to evolve more slowly than newer ones; that is, proteins that arose earlier in evolution currently have a larger proportion of sites subjected to negative selection.

Proto-genes and de novo gene birth

This work formalizes an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences and demonstrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation.

Evidence for de Novo Evolution of Testis-Expressed Genes in the Drosophila yakuba/Drosophila erecta Clade

Testis-derived expressed sequence tags from Drosophila yakuba are used to identify genes that have likely arisen either in D. yakuba or in the D. erecta ancestor, and several genes are found, which show testis-biased expression and are often X-linked.

Origin of primate orphan genes: a comparative genomics approach.

It is determined that codon usage values for most orphan genes fall within the bulk of the codon used distribution of bona fide human proteins, supporting their current protein-coding annotation and obtaining evidence that a small fraction of primate orphan genes might have originated de novo from mammalian noncoding genomic regions.

De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data

It is demonstrated that afgps in codfishes have evolved de novo from non‐coding DNA 13–18 Ma, coinciding with the cooling of the Northern Hemisphere, and evolution of afgp‐assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage‐specific losses of af gp.

From De Novo to “De Nono”: The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates

  • C. Casola
  • Biology
    Genome biology and evolution
  • 2018
Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes.

Recently Evolved Genes Identified From Drosophila yakuba and D. erecta Accessory Gland Expressed Sequence Tags

A genomic analysis of previously unknown genes isolated from cDNA libraries of these species revealed several cases of genes present in one or both species, yet absent from ingroup and outgroup species, which suggests the possibility that Acp's or other genes coding for small proteins may originate from ancestrally noncoding DNA.

Random sequences are an abundant source of bioactive RNAs or peptides

Contrary to expectations, it is found that random sequences with bioactivity are not rare and may become an effective new source of molecules for studying cellular functions, as well as for pharmacological activity screening.

Creating sense from non-sense DNA: de novo genesis and evolutionary history of antifreeze glycoprotein gene in northern cod fishes (gadidae)

This work constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries of two gadids, the high Arctic polar cod Boreogadus saida and the coldtemperate Atlantic tomcod Microgadus tomcod, to isolate their AFGP genomic loci for analyses and identified three distinct AFGP gene clusters.

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

FLJ33706 provided the strongest evidence so far that human-specific de novo genes can have protein-coding potential and differential protein expression, and be involved in human brain functions.