The Nearly Neutral Theory of Molecular Evolution

Ohta, Takao

doi:10.1146/annurev.es.23.110192.001403

Cited by 958 publications

(520 citation statements)

References 100 publications

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“…Because dS estimates the number of "silent" substitutions that do not change the amino acid sequence, it will be predominantly influenced by the mutation rate (28); dN estimates the number of substitutions that change the amino acid sequence, which is likely to include both neutral and nearly neutral changes. Because of this, dN is expected to be influenced both by the mutation rate and by population size (17). Therefore, ω is expected to be influenced by selection and effective population size, but not the mutation rate.…”

Section: Resultsmentioning

confidence: 99%

“…For example, if speciation occurs by the subdivision of populations, then lineages that speciate more frequently may have lower average population sizes. Because nonneutral substitution rates tend to be higher in smaller populations (17), lineages with high speciation rates might also have higher overall substitution rates. However, there are other possible causal links between rates of molecular evolution and net diversification.…”

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confidence: 99%

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Mutation rate is linked to diversification in birds

Lanfear

Love

et al. 2010

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

130

150

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How does genome evolution affect the rate of diversification of biological lineages? Recent studies have suggested that the overall rate of genome evolution is correlated with the rate of diversification. If true, this claim has important consequences for understanding the process of diversification, and implications for the use of DNA sequence data to reconstruct evolutionary history. However, the generality and cause of this relationship have not been established. Here, we test the relationship between the rate of molecular evolution and net diversification with a 19-gene, 17-kb DNA sequence dataset from 64 families of birds. We show that rates of molecular evolution are positively correlated to net diversification in birds. Using a 7.6-kb dataset of protein-coding DNA, we show that the synonymous substitution rate, and therefore the mutation rate, is correlated to net diversification. Further analysis shows that the link between mutation rates and net diversification is unlikely to be the indirect result of correlations with life-history variables that may influence both quantities, suggesting that there might be a causal link between mutation rates and net diversification.D iversification is the net result of the addition of species by speciation and the removal of species by extinction. Understanding the causes and consequences of diversification is central to evolutionary biology. Correlations between diversification, life history, and ecology are becoming increasingly well understood (e.g., refs. 1-4). However, the link between diversification and the rate of molecular evolution is still debated, with much of the attention focused on the role speciation plays in driving genetic change (5-13). Changes to specific genes have been linked to the development of reproductive isolation during species formation, and in some cases such genes have been shown to be under strong positive selection (reviewed in refs. 14 and 15). However, there is a growing body of evidence showing that diversification correlates positively with rates of DNA sequence evolution in "house-keeping" genes, which are associated with basic metabolic functions and, therefore, not expected to be directly involved in the process of diversification. These results raise the possibility that there is a general association between diversification and rates of genomic change.Previous studies have noted that clades of flowering plants containing more species tend to have longer molecular branch lengths (6, 11), and that path lengths on molecular phylogenies from a range of taxa tend to be positively correlated to the number of nodes through which they pass (16). These results suggest that net diversification-the balance between speciation and extinction rates that gave rise to the extant diversity-is somehow linked to rates of DNA change over time.One hypothesis put forward to explain the correlation between rates of molecular evolution and net diversification is that the process of speciation increases the rate of molecular evolution (10, 16). This ...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Mutation rate is linked to diversification in birds

Lanfear

Love

et al. 2010

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

130

150

View full text Add to dashboard Cite

show abstract

“…The mutation rate is the result of a trade-off between the need for new variants to adapt to environmental changes and selection for a reduced mutation rate because mutations are more often deleterious than advantageous [15]. The substitution rate depends chiefly on fixation of neutral and slightly deleterious mutations [16] and it is thus positively correlated with mutation rate and negatively correlated with population size because selection is more efficient in large populations [17]. An unexpectedly low substitution rate could thus be the result of a peculiarly low mutation rate and/or an especially strong selection against deleterious mutations [16,17].…”

Section: Low Molecular Diversity and Low Geographic Differentiation Imentioning

confidence: 99%

“…The substitution rate depends chiefly on fixation of neutral and slightly deleterious mutations [16] and it is thus positively correlated with mutation rate and negatively correlated with population size because selection is more efficient in large populations [17]. An unexpectedly low substitution rate could thus be the result of a peculiarly low mutation rate and/or an especially strong selection against deleterious mutations [16,17].…”

Section: Low Molecular Diversity and Low Geographic Differentiation Imentioning

confidence: 99%

Why coelacanths are not ‘living fossils’

Casañe

Laurenti

2013

BioEssays

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A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a 'living fossil' that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra-specific molecular diversity does not imply low mutation rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra-species levels of molecular diversity, inter-species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as 'living fossil', 'basal lineage', or 'primitive extant species' do not make sense from a tree-thinking perspective.

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“…According to the nearly neutral theory of evolution (Ohta, 1987(Ohta, , 1992, small populations will experience reduced efficacy of selection and thus elevated rates of deleterious changes due to genetic drift. The study of complete genomes is valuable to weigh the respective effects of mutational pressures and selective pressures, both possibly acting at different levels, e.g.…”

Section: Introductionmentioning

confidence: 99%

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria

Schaber

Rispe²,

Wernegreen

et al. 2005

Gene

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Most endosymbiotic bacteria have extremely reduced genomes, accelerated evolutionary rates, and strong AT base compositional bias thought to reflect reduced efficacy of selection and increased mutational pressure. Here, we present a comparative study of evolutionary forces shaping five fully sequenced bacterial endosymbionts of insects. The results of this study were three-fold: (i) Stronger conservation of high expression genes at not just nonsynonymous, but also synonymous, sites. (ii) Variation in amino acid usage strongly correlates with GC content and expression level of genes. This pattern is largely explained by greater conservation of high expression genes, leading to their higher GC content. However, we also found indication of selection favoring GC-rich amino acids that contrasts with former studies. (iii) Although the specific nutritional requirements of the insect host are known to affect gene content of endosymbionts, we found no detectable influence on substitution rates, amino acid usage, or codon usage of bacterial genes involved in host nutrition. D

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The Nearly Neutral Theory of Molecular Evolution

Cited by 958 publications

References 100 publications

Mutation rate is linked to diversification in birds

Mutation rate is linked to diversification in birds

Why coelacanths are not ‘living fossils’

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria

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