Molecular clocks: When timesare a-changin'

Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
Trends in Genetics (Impact Factor: 9.92). 03/2006; 22(2):79-83. DOI: 10.1016/j.tig.2005.11.006
Source: PubMed


The molecular clock has proved to be extremely valuable in placing timescales on evolutionary events that would otherwise be difficult to date. However, debate has arisen about the considerable disparities between molecular and palaeontological or archaeological dates, and about the remarkably high mutation rates inferred in pedigree studies. We argue that these debates can be largely resolved by reference to the "time dependency of molecular rates", a recent hypothesis positing that short-term mutation rates and long-term substitution rates are related by a monotonic decline from the former to the latter. Accordingly, the extrapolation of rates across different timescales will result in invalid date estimates. We examine the impact of this hypothesis with respect to various fields, including human evolution, animal domestication and conservation genetics. We conclude that many studies involving recent divergence events will need to be reconsidered.

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Available from: Greger Larson, Oct 03, 2015
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    • "Systemic bias in molecular age estimates has been demonstrated in numerous studies (Ho and Jermiin 2004, Jansa et al. 2006, Norris et al. 2015). Deep branches may be underestimated relative to more recent branches (Ho and Larson 2006), especially in situations where fast-evolving genes have become saturated (Hugall et al. 2007, Dornburg et al. 2014). If such systemic bias is present, it may affect both chipmunks and Holarctic ground squirrels equally, but the bias would be corrected only for the Holarctic ground squirrels, thanks to the presence of a calibrating fossil. "
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    ABSTRACT: The chipmunks are a Holarctic group of ground squirrels currently allocated to the genus Tamias within the tribe Marmotini (Rodentia: Sciuridae). Cranial, post-cranial, and genital morphology, cytogenetics, and genetics each separate them into three distinctive and monophyletic lineages now treated as subgenera. These groups are found in eastern North America, western North America, and Asia, respectively. However, available genetic data (mainly from mitochondrial cytochrome b) demonstrate that the chipmunk lineages diverged early in the evolution of the Marmotini, well before various widely accepted genera of marmotine ground squirrels. Comparisons of genetic distances also indicate that the chipmunk lineages are as or more distinctive from one another as are most ground squirrel genera. Chipmunk fossils were present in the late Oligocene of North America and shortly afterwards in Asia, prior to the main radiation of Holarctic ground squirrels. Because they are coordinate in morphological, genetic, and chronologic terms with ground squirrel genera, the three chipmunk lineages should be recognized as three distinct genera, namely, Tamias Illiger, 1811, Eutamias Trouessart, 1880, and Neotamias A. H. Howell, 1929. Each is unambiguously diagnosable on the basis of cranial, post-cranial, and external morphology.
    Mammalia 05/2015; DOI:10.1515/mammalia-2015-0004 · 0.68 Impact Factor
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    • "Additionally, it is not clear to what extent they can be extrapolated to other taxa. Ultimately, it might be best to use only calibrations that are reasonably close in time to the evolutionary events of interest (Ho & Larson, 2006). "
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    ABSTRACT: Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to muta-tional saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.
    PeerJ 03/2015; 3(3). DOI:10.7717/peerj.821 · 2.11 Impact Factor
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    • "Humans represent one example where comparisons can be made, but in contrast to previous assertions derived from aDNA (e.g. Ho et al. 2005, 2007a,b, 2011a,b; Penny 2005; Ho & Larson 2006), data suggest no elevation of generational mutation rates above phylogenetic estimates (Altshuler et al. 2010; Awadalla et al. 2010; Lynch 2010; Roach et al. 2010; Nelson et al. 2012; O'Roak et al. 2012; Sanders et al. 2012), indicating that theoretical models cannot explain exponential rate decay curves from the behaviour of de novo mutations (Woodhams 2006; Peterson & Masel 2009), but such curves can be explained by the segregation patterns of ancestral polymorphisms (Peterson & Masel 2009). Rate estimates derived from temporally sampled DNA sequence data have increasingly been presented as evidence for rate decay relationships that may extend back several millions of years. "
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    ABSTRACT: There is increasing momentum surrounding the hypothesis that rates of molecular evolution between individuals within contemporary populations are high, and that these rates decrease as a function of time, perhaps over several millions of years, before reaching stationarity. The implications of this are powerful, potentially reshaping our view of how climate history impacts upon both species distribution patterns and the geographic structuring of genetic variation within species. However, our assessment of the hypothesis reveals a lack of theoretical support and empirical evidence for hypothesized magnitudes of time-dependent rates of molecular evolution, with much of the apparent rate changes coming from artefacts and biases inherent in the methods of rate estimation. Our assessment also reveals a problem with how serial sampling is implemented for mutation rate estimation using ancient DNA samples, rendering published estimates unreliable.This article is protected by copyright. All rights reserved.
    Molecular Ecology 01/2015; 24(4). DOI:10.1111/mec.13070 · 6.49 Impact Factor
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