Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520-8105, USA.
Science (Impact Factor: 33.61). 11/2008; 322(5898):86-9. DOI: 10.1126/science.1163197
Source: PubMed


Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain. In plants, it has been suggested that life history traits are correlated with the rate of molecular evolution, but previous studies have yielded conflicting results. Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times. Herbs show much higher rates of molecular change but also much higher variance in rates. Correlates of life history attributes have long been of interest to biologists, and our results demonstrate how changes in the rate of molecular evolution that are linked to life history traits can affect measurements of the tempo of evolution as well as our ability to identify and conserve biodiversity.

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    • "These results are unlikely to be due to the statistical errors of our method, because the estimated type I error is around 0.05 and the power is up to 80% for the mitochondrial results and the regression coefficients are consistently negative. The copy-frequency effect is a good explanation for many observed patterns in rate of molecular evolution, such as the widespread observation of a generation time effect (e.g., Mooers and Harvey 1994; Bromham et al. 1996; Smith and Donoghue 2008; Thomas et al. 2010), higher rates of molecular evolution in highly eusocial hymenopterans (Bromham and Leys 2005), faster rates of molecular evolution in shorter plants (Lanfear, Ho, et al. 2013; Bromham et al. 2015), and faster mutations in sequences that are carried more often in male germline than in female germline (Ellegren and Fridolfsson 1997; Whittle and Johnston 2002). So why do we not find evidence that the copy-frequency effect is a primary driver of differences in mutation rates between rockfish species? "
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    ABSTRACT: The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: that the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: covariation of mutation rates between species due to ancestry, covariation between life history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish (Sebastes). This method has better performance than traditional sister-species comparisons when sister species are too recently diverged to give reliable estimates of mutation rate. Rockfish are an ideal model system: they have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail:
    Molecular Biology and Evolution 06/2015; DOI:10.1093/molbev/msv137 · 9.11 Impact Factor
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    • "The low levels in Rhododendron were mainly due to shared sequence identity across the species. This may result from a slow evolutionary rate of woody taxa that have long generation times typical in the genus Rhododendron (Smith & Donoghue 2008). Another reason for the lack of sequence divergence in Rhododendron may be due to a short evolutionary history of speciation and diversification within the study region. "
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    ABSTRACT: The Himalaya-Hengduan Mountains encompass two global biodiversity hotspots with high levels of biodiversity and endemism. This area is one of the diversification centres of the genus Rhododendron, which is recognized as one of the most taxonomically challenging plant taxa due to recent adaptive radiations and rampant hybridization. In this study, four DNA barcodes were evaluated on 531 samples representing 173 species of seven sections of four subgenera in Rhododendron, with a high sampling density from Himalaya-Hengduan Mountains employing three analytical methods. The varied approaches (NJ, PWG and BLAST) had different species identification powers with BLAST performing best. With the PWG analysis, the discrimination rates for single barcodes varied from 12.21% to 25.19% with ITS < rbcL < matK < psbA-trnH. Combinations of ITS + psbA-trnH + matK and the four barcodes showed the highest discrimination ability (both 41.98%) among all possible combinations. As a single barcode, psbA-trnH performed best with a relatively high performance (25.19%). Overall, the three-marker combination of ITS + psbA-trnH + matK was found to be the best DNA barcode for identifying Rhododendron species. The relatively low discriminative efficiency of DNA barcoding in this genus (~42%) may possibly be attributable to too low sequence divergences as a result of a long generation time of Rhododendron and complex speciation patterns involving recent radiations and hybridizations. Taking the morphology, distribution range and habitat of the species into account, DNA barcoding provided additional information for species identification and delivered a preliminary assessment of biodiversity for the large genus Rhododendron in the biodiversity hotspots of the Himalaya-Hengduan Mountains. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 05/2015; 15:932-944. DOI:10.1111/1755-0998.12353 · 3.71 Impact Factor
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    • "As more and more molecular data (largely DNA sequences) became available across different taxonomic groups, the presence of rate heterogeneity among lineages seems to be the norm, rather than the exception. For example, in angiosperms, it has been shown that variation in rates across groups is tied to their life histories (Smith and Donoghue 2008), with herbaceous plants having faster rates of molecular substitutions than their woody relatives. Although Zuckerkandl and Pauling provided evidence for a linear relationship between the accumulation of amino acid differences and evolutionary time, they did not provide an explanation for why they observed this pattern. "
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    ABSTRACT: Abstract— Divergence time analyses have become increasingly popular over the past several decades, partly due to the proliferation of molecular data, but also because of the development of methods that do not assume a strict molecular clock. In this review, I provide a brief background to the topic, then highlight several methods for “relaxing” the assumptions of a strict molecular clock. I discuss the pros and cons of many of these methods. Finally, I discuss the various techniques for incorporating fossils in molecular studies to estimate absolute ages of clades.
    Systematic Botany 02/2015; 40(1):6-13. DOI:10.1600/036364415X686297 · 1.23 Impact Factor
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