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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    • "Gaut et al. 2011), but estimates of rates also appear to scale negatively with the age of the calibration on which they are based (Ho et al. 2005, 2011a). The most striking examples of this pattern have been the disparities between mitochondrial estimates of rates of spontaneous mutation and of the rates at which these mutations are fixed as substitutions over time (Ho & Larson 2006). Here, we respond to a recent critique by Emerson & Hickerson (2015), who claim that there is a lack of support for such a time-dependent pattern in rate estimates. "
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    ABSTRACT: We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates.
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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.
    Full-text · Article · May 2015 · Mammalia
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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.
    Full-text · Article · Mar 2015 · PeerJ
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