Molecular Clock

8 Key excerpts on "Molecular Clock"

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  Molecular Panbiogeography of the Tropics

  • Michael Heads(Author)
  • 2012(Publication Date)
  • University of California Press

    (Publisher)

  These studies often assume that evolution is clock-like, with lineages showing a constant rate of sequence divergence of, say, 2% per million years. But whether evolutionary mode may in fact deviate from clock-like, and if so, by how much, is debated, and the different statistical tests for clock-like evolution make their own assumptions. The history of the evolutionary clock idea is implicated with the rise of the modern syn-thesis in 20th-century biology, and this history is worth outlining. The Biogeography of Hutton and Chapman Was Replaced with the Evolutionary Clock of Matthew, Mayr, and the Modern Synthesis Based on their broad knowledge of biogeography and geology, 19th-century evolutionists such as Hutton (1872) concluded that “dif-ferentiation of form, even in closely allied species, is evidently a very Evolution in Time | 61 fallacious guide in judging of lapse of time.” Nevertheless, the idea that morphological or molecular evolution is roughly clock-like was accepted by the initiators of the modern synthesis. Matthew (1915) and most subsequent authors overlooked the 19th century work and assumed that evolution (morphological or molecular) is indeed clock-like. It follows from this that the groups in a biogeographic pattern must have all evolved at different times, as reflected in their degree of divergence, and so community-wide vicariance can be rejected. This idea became the dominant paradigm and one of the foundations of the modern synthesis. For example, employing the evolutionary clock idea, Matthew (1915) concluded that “the Malagasy mammals point to a number of colonizations of the island by single species of animals at dif-ferent times,” and this remains the standard interpretation (Yoder and Nowak, 2006).

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  Biological Systematics

  Principles and Applications

  • Andrew V. Z. Brower, Randall T. Schuh(Authors)
  • 2021(Publication Date)
  • Comstock Publishing Associates

    (Publisher)

  While some genes appeared to have evolved in a clocklike manner among some taxa for some periods of evolutionary history, by the 1980s it became clear that the Molecular Clock was not a general phenomenon. Wu and Li (1985) and Britten (1986) offered some of the earliest critical reviews of the accumulating data, showing significant inferred rate variability among lineages. To save the clock hypothesis, several ad hoc sources of variation were proposed: an inverse correlation of molecular evolutionary rates with generation times of organisms or cell lineages, a positive correlation of rates with metabolic rate, and/or rate variability due to historical differences in population size (the last, being impossible to measure, is a favorite refuge of irrefutability for population geneticists when the data do not fit their preferred model). Ayala (1999) reviewed patterns that falsified these explanations, since even when examined in the same taxa (thereby controlling for generation time, metabolic rate, and historical population size) rates vary among genes in different directions in different groups, with one gene apparently speeding up in one lineage versus another, and another slowing down. His conclusion was that “only fluctuating and unpredictable natural selection can account for these erratic patterns of molecular evolution”—a clear refutation of the clock hypothesis.

  But a good story is hard to quell, and with the advent of the polymerase chain reaction and increasingly automated DNA amplification and sequencing in the late 1980s, the abundance of DNA sequences offered a great temptation to continue to seek clocklike patterns in molecular data. Particularly among closely related taxa, such as those examined in phylogeographic studies (see Chapter 7), most variability might be expected to occur in relatively unconstrained third-codon-position silent sites. At least in the initial stages of divergence, most observed sequence differences might represent unique, selectively neutral mutational events that could accumulate in a reasonably clocklike manner. Brower (1994b) used this as a rationale to propose an arthropod mitochondrial DNA clock, with the explicit caveat that it should not be extrapolated to infer ages of clades above some three million years, beyond which the linearity of nucleotide substitutions with time might be expected to be dampened by selective constraint (Brown 1983). Others felt no qualms in extending Molecular Clock estimates to infer ages of much older and more inclusive taxa, including vertebrates and metazoans inferred to have diverged tens or hundreds of millions of years ago (Hedges et al. 1996; Wray et al. 1996). Once this Pandora’s box was opened, the allure of Molecular Clock narratives became too strong for many researchers to resist. The past two decades have seen a vast proliferation of time-calibrated evolutionary scenarios. Let us now examine some of the assumptions that underlie modern Molecular Clock estimates.

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  The Cambridge Encyclopedia of Darwin and Evolutionary Thought

  • Michael Ruse(Author)
  • 2013(Publication Date)
  • Cambridge University Press

    (Publisher)

  The enormous potential of the molecular evolutionary clock lies in the fact that each gene or protein is a separate clock. Each clock ticks at a different rate – the rate of evolution characteristic of a particular gene or protein – but each of the thousands and thousands of genes or proteins provides an independent measure of the same evo- lutionary events. Evolutionists have found that the amount of variation observed in the evolution of DNA and proteins is greater than is expected from a stochastic clock – in other words, the clock is overdispersed, or somewhat erratic. The discrepancies in evolutionary rates along different lineages are not exces- sively large, however. So it is possible, in principle, to time phylogenetic events with considerable accuracy, but more genes or proteins must be examined than would be required if the clock were stochastically constant in order to achieve a desired degree of accuracy. The average rates obtained for several proteins, taken together, become a fairly precise clock, particularly when many species are studied. This conclusion is illustrated in Figure 49.4, which plots the cumulative number of nucleotide changes in seven proteins against the dates of divergence of seventeen species of mam- mals (sixteen pairings) as determined from the fossil record. The overall rate of nucleotide substitution is fairly uniform. Some primate species (represented by the points below the line at the lower left of the figure) appear to have evolved at a slower rate than the average for the rest of the species. This anomaly occurs because the more recent the divergence of any two species, the more likely it is that the changes observed will depart from the average evolutionary rate. As the length of time increases, periods of rapid and slow evolution in any lineage will tend to cancel one another out.

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  Molecular Ecology

  • Joanna R. Freeland(Author)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  These and many more examples mean that we no longer think of the Molecular Clock running at a universal rate that can be applied across taxa, across genes, and across time periods. As the complexity of Molecular Clocks became more apparent, there was a shift away from strict Molecular Clocks that apply a single rate of sequence evolution across all taxa being compared. These have been increasingly replaced with models that use relaxed Molecular Clocks, in other words models that allow the rates of sequence evolution to vary across the taxa being compared (Sanderson 1997; Thorne et al. 1998). The analyti- cal methods behind relaxed clocks are extensive and complex (reviewed in Ho 2014). Molecular Clocks are ideally calibrated from the timing of an independent event such as specimens collected from the fossil record, or from geological or climatic biogeo- graphical events (reviewed in Ho et al. 2015) (Table 4.2). Unfortunately, this can be more difficult than it sounds, because reliable calibration sources are not always avail- able. Furthermore, calibrations based on independent data may include uncertainties around processes such as radiometric dating, or issues such as the completeness of the fossil record. This is illustrated by turtles, which have a rich fossil record that identified the origin of living turtles in the Late Triassic or Early Jurassic, although fragmented or morphologically obscure fossils have led to conflicting interpretations of turtle evolu- tionary history. Shaffer et al. (2017) therefore disregarded the oldest turtle fossil records and instead used Caribemys oxfordiensis, a fossil turtle from the suborder plurodira dating to the Late Jurassic, as a minimum age constraint when estimating divergence times of multiple taxa. This calibration, in combination with sequence data from 539 nuclear loci obtained from 26 species representing the diversity of extant turtles, led to age estimates for most of the currently recognized turtle families.

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  An Introduction to Molecular Anthropology

  • Mark Stoneking(Author)
  • 2016(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  N, and neutral mutation rate μ (by neutral mutation rate, we mean the rate of new mutations that are neither advantageous nor disadvantageous to have). Then,

  Probability that a new mutation will reach fixation = 1/2N (recall that the probability of fixation of an allele via genetic drift is equal to the frequency of the allele, and by definition a new mutation is present in just one copy in the gene pool).

  Rate of molecular evolution = (rate at which new mutations arise) (probability of fixation) = (2Nμ)(1/2N) = μ.

  It, therefore, follows that if the neutral mutation rate is constant over time, then the rate of molecular evolution will also be constant over time. It may seem somewhat counterintuitive that the rate of (neutral) molecular evolution does not depend at all on the population size. The reason is that in a small population, there are fewer new mutations occurring each generation but fixation goes more quickly. Conversely, in a big population, there are more new mutations occurring each generation but fixation takes longer. Remarkably, these two processes balance each other exactly, so the overall rate of molecular evolution is the same regardless of the population size.

  The Molecular Clock has been an extremely powerful tool and has provided some important insights into our evolutionary history. For example, as we shall see in Chapter 13, Molecular Clock approaches provided the first evidence of a close evolutionary relationship between humans and chimpanzees, as well as strongly supporting a recent African origin of our species. Nevertheless, there are important issues–-and limitations—that arise with dating via Molecular Clocks, and the use—and misuse—of Molecular Clocks will be discussed in more detail later. For now, just be aware that Molecular Clocks provide a powerful and important alternative to fossil or archaeological evidence for dating species or population divergence times.

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  Population Genetics

  • Matthew Hamilton(Author)
  • 2011(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  T in practice and so the degree of over-estimation of the species divergence time is usually unknown.

  Relative rate tests of the Molecular Clock

  One method to circumvent some of the limitations inherent in comparing absolute rates of divergence is to compare relative rates instead. The relative rate test compares the number of nucleotide or amino acid changes since divergence from an ancestor represented by a DNA sequence from closely related species (Sarich & Wilson 1967; Fitch 1976). Rates of nucleotide substitution in two different species can be estimated by comparing the number of DNA or amino acid changes that have occurred independently in each of two species using a third outgroup species to assign sequence changes to each lineage.If rates of substitution are equal in the two species, then the number of sequence changes should be equal in the two species within a statistical confidence interval. Unequal numbers of sequence changes lead to rejection of the null hypothesis that the two species have an equal rate of substitution. Relative rate tests avoid the need for a date of divergence that is often imprecise and also do not rely on the dispersion index and its underlying assumption that the Molecular Clock is a simple Poisson process.

  Tajima’s (1993a) 1D test of the Molecular Clock is a relative rate test that uses the number of nucleotide substitutions that occurred along two lineages being compared as well as an outgroup lineage. The basis of the test is shown in Fig. 8.18 . In the figure, the letters i , j , and k are used to represent the identity of the nucleotide found at the same nucleotide site in each of the three sequences. The outgroup is used to identify the point in time that nucleotide changes took place since lineages 1 and 2 should share the same base pair as the outgroup due to identity by descent if no substitution has occurred. Only changes that can be assigned unambiguously to a lineage are useful when comparing rates between lineages 1 and 2. Nucleotide substitutions of the pattern iji indicate the change occurred on lineage 2 whereas pattern ijj indicates the change occurred on lineage 1. These two instances allow unambiguous assignment of a substitution to a lineage to estimate the numbers of substitutions. The other three possible nucleotide patterns cannot be used to estimate rates of substitution for one lineage. Nucleotide sites with the pattern iii are not useful because no substitution occurred and there is no information available to estimate the rate of change. For nucleotide sites with the pattern jji , the substitution to j could have occurred in the ancestor to lineages 1 and 2 or both lineages 1 and 2 could have experienced a substitution but it is not clear which event occurred. The pattern ijk

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  Population Genetics

  • Matthew B. Hamilton(Author)
  • 2021(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  The sec- ond time interval t is the period when substitutions accumulated after the current species split. Estimates of time since divergence estimate the total elapsed time since the divergence of the two lineages rather than just the time since divergence of the two spe- cies. Thus, the use of the Molecular Clock to date divergence time yields over-estimates of the species divergence time. As the divergence time t increases relative to the polymorphism time T, the degree of over-estimation shrinks. However, it is usually impossible to determine t relative to T in practice and so the degree of over-estimation of the species divergence time is usually unknown. Relative rate tests of the Molecular Clock One method to circumvent some of the limitations inherent in comparing absolute rates of divergence is to compare relative rates instead. The relative rate test compares the number of nucleotide or amino acid changes since divergence from an ances- tor represented by a DNA sequence from closely related species (Sarich and Wilson 1967; Fitch 1976). Rates of nucleotide substitution in two differ- ent species can be estimated by comparing the num- ber of DNA or amino acid changes that have occurred independently in each of two species using a third outgroup species to assign sequence changes to each lineage. If rates of substitution are equal in the two species, then the number of sequence changes should be equal in the two species within a statistical confidence interval. Unequal numbers of sequence changes lead to rejection of the null hypothesis that the two species have an equal rate of substitution. Relative rate tests avoid the need for a date of divergence that is often imprecise and also do not rely on the dispersion index and its under- lying assumption that the Molecular Clock is a simple Poisson process.

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  Time Blind

  Problems in Perceiving Other Temporalities

  • Kevin K. Birth(Author)
  • 2016(Publication Date)
  • Palgrave Macmillan

    (Publisher)

  Biological mechanisms did not evolve in response to the clock, or even to clock time, and a more accurate picture of these mechanisms will emerge when they are studied in relationship to the pres- sures that acted upon their selection rather than in relationship to homo- geneous, uniform clock time. CONCLUSION Barbara Adam writes, “Unlike the variable rhythms of nature, the invari- ant, precise measurement is a human invention and in our society it is this created time which has become dominant to the extent that it is related to as time per se, as if there were no other time” (1995, 25). Hassan argues that clock time has “displaced and dulled our sensitivity to other tempo- ralities that exist in the natural world and in our very bodies” (2003, 27). Is the clock a good representation for biological timing processes, then? The controlled light/dark cycles of the laboratory are unlike the condi- tions in which the SCN evolved. More important is how methodologi- cal decisions result in the unwarranted dominance of the clock metaphor. When single variables are studied in the laboratory using clock measure- ments, there is a strong tendency to treat biological systems as if they func- tioned like clocks; when multiple variables are studied or adaptive fitness is emphasized, the flexibility of the biological systems results in a minimizing of the clocklike metaphor, if not its absolute absence. The responsiveness of internal timing and the SCN to environmental influences is also not clocklike. Whereas the history of clocks has been a story of innovations to limit environmental influences on clock perfor- mance, biological systems should not be viewed in this way—it makes 44 K.K. BIRTH no evolutionary sense to suggest that timing mechanisms are not part of an organism’s ability to respond to variable environments. The evidence for environmental influences on internal timing and the SCN supports the evolutionary importance of internal timing.

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