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Genes from scratch--the evolutionary fate of de novo genes.

Schlötterer C - Trends Genet. (2015)

Bottom Line: Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes.Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks.Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes.

View Article: PubMed Central - PubMed

Affiliation: Institut für Populationsgenetik, Vetmeduni, Veterinärplatz 1, 1210 Wien, Austria. Electronic address: Christian.schloetterer@vetmeduni.ac.at.

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Phylogenetic analysis of de novo genes: de novo genes are identified in one focal species and their age is determined by the presence of an ortholog in sister taxa (red line). Using the parsimony criterion, the origin of the de novo gene is set to the most recent common ancestor of the focal species and the most diverged sister species. The evolutionary stability of de novo genes can be studied in those lineages that diverged after the origin of the de novo gene (green lines).
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fig0010: Phylogenetic analysis of de novo genes: de novo genes are identified in one focal species and their age is determined by the presence of an ortholog in sister taxa (red line). Using the parsimony criterion, the origin of the de novo gene is set to the most recent common ancestor of the focal species and the most diverged sister species. The evolutionary stability of de novo genes can be studied in those lineages that diverged after the origin of the de novo gene (green lines).

Mentions: The high rate of de novo gene birth [4,6,12] in combination with a rather constant number of genes over time [4] predicts that many of the de novo genes have only a short lifetime. Testing this prediction, however, requires a phylogenetic framework, which includes a range of species with different evolutionary distances [12,14,22]. Starting from one focal species, the origin of de novo genes can be dated by applying the parsimony principle to the presence of the de novo genes in the species studied (Figure 2). Once the birth of the de novo gene has been dated, its evolutionary dynamics can be studied in species that diverged subsequently (Figure 2). Although lineage-specific mutation patterns and rates are certainly interesting, the ability to study loss-of-function mutations (premature termination codons) and thus the death of de novo genes is the greatest benefit of this analysis [12]. Using this approach it has been shown that the probability of loss-of-function mutations is higher for de novo genes than for old genes [12,34]. This high death rate of young de novo genes explains why the total number of genes remains relatively constant despite the well-documented high rate of de novo gene birth [12]. By contrasting conserved de novo genes to those that acquired disabling mutations it was found that GC content, gene length, and expression level were positively correlated, and microsatellite number negatively correlated, with sequence conservation [12]. Particularly striking was the observation that de novo genes with male-biased gene expression were less likely to acquire premature termination codons. This differential conservation may explain why previous studies identified a high number of de novo genes based on gene expression in testis [35,36] or showed an excess of de novo genes with male-biased gene expression [37].


Genes from scratch--the evolutionary fate of de novo genes.

Schlötterer C - Trends Genet. (2015)

Phylogenetic analysis of de novo genes: de novo genes are identified in one focal species and their age is determined by the presence of an ortholog in sister taxa (red line). Using the parsimony criterion, the origin of the de novo gene is set to the most recent common ancestor of the focal species and the most diverged sister species. The evolutionary stability of de novo genes can be studied in those lineages that diverged after the origin of the de novo gene (green lines).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383367&req=5

fig0010: Phylogenetic analysis of de novo genes: de novo genes are identified in one focal species and their age is determined by the presence of an ortholog in sister taxa (red line). Using the parsimony criterion, the origin of the de novo gene is set to the most recent common ancestor of the focal species and the most diverged sister species. The evolutionary stability of de novo genes can be studied in those lineages that diverged after the origin of the de novo gene (green lines).
Mentions: The high rate of de novo gene birth [4,6,12] in combination with a rather constant number of genes over time [4] predicts that many of the de novo genes have only a short lifetime. Testing this prediction, however, requires a phylogenetic framework, which includes a range of species with different evolutionary distances [12,14,22]. Starting from one focal species, the origin of de novo genes can be dated by applying the parsimony principle to the presence of the de novo genes in the species studied (Figure 2). Once the birth of the de novo gene has been dated, its evolutionary dynamics can be studied in species that diverged subsequently (Figure 2). Although lineage-specific mutation patterns and rates are certainly interesting, the ability to study loss-of-function mutations (premature termination codons) and thus the death of de novo genes is the greatest benefit of this analysis [12]. Using this approach it has been shown that the probability of loss-of-function mutations is higher for de novo genes than for old genes [12,34]. This high death rate of young de novo genes explains why the total number of genes remains relatively constant despite the well-documented high rate of de novo gene birth [12]. By contrasting conserved de novo genes to those that acquired disabling mutations it was found that GC content, gene length, and expression level were positively correlated, and microsatellite number negatively correlated, with sequence conservation [12]. Particularly striking was the observation that de novo genes with male-biased gene expression were less likely to acquire premature termination codons. This differential conservation may explain why previous studies identified a high number of de novo genes based on gene expression in testis [35,36] or showed an excess of de novo genes with male-biased gene expression [37].

Bottom Line: Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes.Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks.Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes.

View Article: PubMed Central - PubMed

Affiliation: Institut für Populationsgenetik, Vetmeduni, Veterinärplatz 1, 1210 Wien, Austria. Electronic address: Christian.schloetterer@vetmeduni.ac.at.

Show MeSH