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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    • "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.
    PeerJ 03/2015; 3(3). DOI:10.7717/peerj.821 · 2.11 Impact Factor
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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.
    Molecular Ecology 01/2015; 24(4). DOI:10.1111/mec.13070 · 6.49 Impact Factor
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    • "Ancient and archived samples can also resolve inconsistencies when timing of older divergence events is underestimated (Wertheim and Pond, 2011). Although calibrating evolutionary clocks is notoriously difficult, current methods account for temporally sampled sequences and attempt to model the uncertainty in sample ages, which pose problems for phylogenetic and dating reconstructions (Ho et al., 2005, 2007, 2011; Ho and Larson, 2006; Debruyne and Poinar, 2009; Ho and Phillips, 2009). Sample-dating errors, however, appear to inflict only minor effects on substitution rate and dating estimates, a conclusion that Molak et al. (2013) extrapolate further to include errors inherent in calibrating radiocarbon dates to calendar ages. "
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    ABSTRACT: Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
    Journal of Human Evolution 12/2014; 79. DOI:10.1016/j.jhevol.2014.11.002 · 3.73 Impact Factor
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