Time Dependency of Molecular Rates in Ancient DNA Data Sets, A Sampling Artifact?

Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada.
Systematic Biology (Impact Factor: 14.39). 06/2009; 58(3):348-60. DOI: 10.1093/sysbio/syp028
Source: PubMed

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    • "In particular, ancient DNA sequences have the potential to provide clock calibrations for time depths that are intermediate between those of pedigree studies and fossilcalibrated analyses (Ho et al. 2011a). However, as pointed out by Emerson & Hickerson (2015) and others (Debruyne & Poinar 2009; Navascu es & Emerson 2009; Ho et al. 2011b), rate estimates from time-structured data are subject to various potential sources of error. There are several methods of addressing these potential problems. "
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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.
    Preview · Article · Dec 2015
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    • "Our results also support a gradual decay from high pedigree to low phylogenetic rate estimates through time. Intermediate rate estimates, such as those obtained from ancient DNA studies, have previously been attributed to various methodological biases (Debruyne & Poinar, 2009; Emerson & Hickerson, in press; Navascues & Emerson, 2009). However, our results do not indicate that rate estimates based on ancient DNA are anomalous. "
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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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    • "Against expectations from the TDMR hypothesis, all three estimates are higher than the pedigree rate for Ad elie penguins, and in the case of Ho et al. (2007a), significantly so. Concerns regarding the calculation and interpretation of rate estimates from aDNA have been raised because of the potentially confounding effects of demographic model misspecification , and information content limitation (Emerson 2007; Debruyne & Poinar 2009; Navascu es & Emerson 2009; Ramakrishnan & Hadly 2009). Other factors may also confound rate estimates, such as the sampling of shared variation across time points, where sample sizes for different time points are limited (Fig. 2). "
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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.
    Full-text · Article · Jan 2015 · Molecular Ecology
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