The “Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes” Is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence

Elhaik, Eran; Sabath, Niv; Graur, Dan

doi:10.1093/molbev/msj006

Cited by 79 publications

(87 citation statements)

References 5 publications

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“…The observations on the age classes of genes and their distinct evolutionary rate distributions are, at least, qualitatively, compatible with the previous findings that genes in new age classes evolve, on average, faster than genes in old classes (45). It was argued that the age classes are sheer artifacts of sequence similarity detection so that the only conclusion possible from this type of analysis was that ''slowly evolving genes evolve slowly'' (46). Our findings are hardly compatible with this viewpoint.…”

Section: Discussionsupporting

confidence: 86%

“…As shown above, the age classes of eukaryotic genes have significantly different distributions of sequence evolution rates and protein lengths. A previous analysis of age classes of genes (45) has been countered with the hypothesis that the appearance of the age classes and all of the differences between them are explained solely by the homolog detection bias, i.e., that the ''new'' classes emerge solely because the respective genes encode short and/or fast-evolving proteins so that their homologs in distant taxa are hard to detect (46). This interpretation was supported by the results of a simulation of evolution of genes of the same age (46).…”

Section: Functional Distribution Of the Genes In Different Age Classementioning

confidence: 95%

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The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Wolf

Novichkov²,

Karev³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

210

214

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The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals. This universal distribution implies a steady-state process, with identical distributions of evolutionary rates among genes that are gained and genes that are lost. A mathematical model of such process is developed under the single assumption of the constancy of the distributions of the propensities for gene loss (PGL). This model predicts that genes of different ages, that is, genes with homologs detectable at different phylogenetic depths, substantially differ in those variables that correlate with PGL. We computationally partition protein-coding genes from humans, flies, and Aspergillus fungus into age classes, and show that genes of different ages retain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in ''younger'' classes but also with a substantial overlap. The only exception involves human primate-specific genes that show a heavy tail of rapidly evolving genes, probably owing to gene annotation artifacts. As predicted, the gene age classes differ in characteristics correlated with PGL. Compared with ''young'' genes (e.g., mammal-specific human ones), ''old'' genes (e.g., eukaryotespecific), on average, are longer, are expressed at a higher level, possess a higher intron density, evolve slower on the short time scale, and are subject to stronger purifying selection. Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation.gene age ͉ gene expression ͉ genome evolution ͉ intron density

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Section: Discussionsupporting

confidence: 86%

Section: Functional Distribution Of the Genes In Different Age Classementioning

confidence: 95%

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Wolf

Novichkov²,

Karev³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

210

214

View full text Add to dashboard Cite

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“…It takes ;40 million yr before new genes start to acquire alternative splice forms, while the process seems more rapid with duplicates. Of note, the potential bias induced by fast-evolving genes, whose age tends to be underestimated (Elhaik et al 2006;Alba and Castresana 2007), goes against the trend observed here, making our model a conservative estimate. Besides, binning genes evolving at different rates (d N /d S ) yields the same pattern (Supplemental Fig.…”

Section: à8mentioning

confidence: 57%

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

Roux

Robinson‐Rechavi

2010

Genome Res.

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We analyze here the relation between alternative splicing and gene duplication in light of recent genomic data, with a focus on the human genome. We show that the previously reported negative correlation between level of alternative splicing and family size no longer holds true. We clarify this pattern and show that it is sufficiently explained by two factors. First, genes progressively gain new splice variants with time. The gain is consistent with a selectively relaxed regime, until purifying selection slows it down as aging genes accumulate a large number of variants. Second, we show that duplication does not lead to a loss of splice forms, but rather that genes with low levels of alternative splicing tend to duplicate more frequently. This leads us to reconsider the role of alternative splicing in duplicate retention.

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“…A likely explanation for this is that dead-on-arrival pseudogenes [15] originating before the human-mouse species split have most often diverged beyond the limit of recognition. With approximately 0.5 substitutions per site, fewer than 10% of neutrally evolving genomic elements can be found using BLAST [16].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide survey for biologically functional pseudogenes

Svensson¹,

Arvestad²,

Lagergren³

2005

PLoS Comp Biol

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According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3), and one from the Spinocerebellar ataxia type 1 protein (ATX1). Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios.

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The “Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes” Is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence

Cited by 79 publications

References 5 publications

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

Genome-wide survey for biologically functional pseudogenes

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