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Molecular Clocks Hypothesis and Discussion Molecular Clocks Hypothesis and Discussion Source :http://www.as.wvu.edu/~kgarbutt/QuantGen/Gen535Papers2/Molecular_Clocks.htm Does a molecular evolutionary clock exist? Since the proposal of the molecular clock hypothesis in the 1960πs, scientists have been pondering that particular question. This topic still remains one of the most controversial and debated subjects in evolutionary biology. The molecular clock hypothesis proposes that for any given protein, the rate of molecular evolution is approximately constant over time for all lineages. Therefore, molecular data can be used for the prediction of time. Some scientists argue that natural selection produces mutations in genes at such a variable rate that no gene or protein could effectively be used as a molecular clock. On the other hand, many studies have shown that point mutations can and do occur at relatively regular rates, offering noteworthy evidence for the molecular clock hypothesis. Problems with the Fossil Record Oftentimes, paleontologists and molecular biologists particularly disagree on this topic. The two fields take different approaches to answering evolutionary questions, and therefore, they often come to different conclusions (Hedges 1998). While the fossil record has provided us with valuable information on phylogeny and divergence times, some say that it is highly biased (Smith 1994). Some of this bias can be due to the abundance, habitat, or range of a species and sparse sampling (Martin 1993). Secondly, the fossil record is far from complete. Large gaps exist in paleontological data; therefore, it is frequently impossible to determine dates of divergence between species. In addition, oftentimes only a limited number of ≥characters≤ are available for the identification of a species in the fossil record. This means that some species are named from only a few bones or teeth, and this can lead to erroneous identification. Lastly, erroneous identification can also result from the fact that species are identified based upon morphology. This is problematic because species are grouped together by phenotypic traits, or more simply, because they look alike. However, this does not always indicate that they belong to the same group. Neutral Theory Because of these problems, in the 1950πs, some scientists began looking at molecules in hopes that they could provide us with additional information on phylogeny and divergence times that is absent from or misrepresented in the fossil record. The Neutral Theory, proposed by Kimura, argues that many amino acid and nucleotide substitutions have little or no functional consequence. He states that the majority of mutations are inconsequential and therefore, they are not strongly constrained by Natural Selection. Hence, evolution at the molecular level consists mostly of gradual random replacement of one allele by another that is its functional equivalent. The neutral mutation rate is therefore constant over evolutionary time because protein function should not alter over time. Or, in other words, most variation at the molecular level within and among species is effectively neutral and not subject to selection. Kimura argues that for each protein, evolutionary rate (in terms of amino acid substitutions) is approximately constant per amino acid site per year for various lineages (Nei and Koehn 1983). Kimura does not, however, claim that all mutations are selectively neutral and he does not claim that selection does not play an important role in shaping the characteristics of organisms. He proposes only that these cases represent the minority of changes at the molecular level. The Neutral Theory maintains that for a diploid species with 2N alleles, if the neutral mutation rate per generation is u, then 2Nu represents the number of new mutants arising in the population each generation. The probability that the allele will become fixed is 1/2N, so the rate of substitution of neutral alleles, k, is equal to the total number of mutations times the probability of their fixation, or k = (2Nu)(1/2N) Therefore, k = u (the rate of substitution is equal to the rate of mutation). Hence, the rate of change should be constant over time and independent of both selection and population size! The Molecular Clock Hypothesis The Molecular Clock Hypothesis is based upon the Neutral Theory. After the proposal of this theory, scientists began looking at molecules, particularly proteins, to see if Kimuraπs hypothesis would hold true. From their comparative studies of hemoglobin and cytochrome c protein sequences, Zuckerkandl and Pauling (1962 and 1965) and Margoliash (1963) noticed that rates of amino acid substitution in these proteins were approximately the same among various mammalian lineages (in Li and Graur 1991). They also noticed that these substitutions were roughly proportional to time as judged against the fossil record. This led to the proposal of the molecular clock hypothesis by Zuckerkandl and Pauling in 1965. They hypothesized that for any given protein, the rate of molecular evolution was approximately constant over time in all lineages, or there exists a molecular clock. According to this hypothesis, molecular data could be used for the prediction of time! Particularly, molecular data could be used to determine species divergence times and to construct phylogenetic relationships among species, allowing us to fill in the gaps where the fossil record is missing or inadequate. Their hypothesis proposes that changes in DNA and proteins accumulate at approximately constant rates over geological time. In this manner, the number of mutations or ≥ticks≤ in DNA and, therefore, the number of substitutions in proteins, is approximately the same per generation for any given organism. Or, in other words, these molecules change or mutate with clock-like regularity. This theory is also known as the rate-constancy hypothesis. Evidence for the Molecular Clock Hypothesis In 1967, Sarich and Wilson presented evidence that serum albumin proteins also change at a regular rate. From this, they proposed that observed differences in albumins between species could be used as an evolutionary clock to estimate times of divergence and help reconstruct phylogenies (Radinsky 1978). Futuyama (1986) says that the ≥albumin immunological distance≤ is moderately well correlated with divergence times estimated from paleontological data. However, there are discrepancies, but this is to be expected when only a single protein is used. In 1970, cytochrome c was the first protein actually used to estimate divergence time, as this protein was used to create the first phylogenetic tree based on molecular data. Cytochrome c, which is involved in cellular respiration, is an essential enzyme for all species. Because of this, gene homology has been maintained throughout phylogeny. The tree was created based on the number of nucleotide base substitutions in the cytochrome c gene for 29 eukaryotic species (Fitch and Margoliash 1970). Remarkably, the tree matched trees created from paleontological (therefore morphological) data in all but a few points. This is amazing since it was constructed using only one protein! Different Proteins Have the Ability to Time Different Evolutionary Events Based upon molecular clock theory, each particular gene or protein of an organism could possibly serve as a separate molecular clock. This is based upon the fact that each protein has a distinct rate of evolution depending upon how important its function is. The less functional constraint on a molecule, the faster it evolves in terms of mutant substitution than those molecules subject to stronger constraint (Nei and Koehn 1983). For example, histones bind DNA in chromosomes and regulate DNA activity. Thus, a histoneπs structure is strictly defined because its ability to bind DNA depends upon its particular structure and shape. The 103 amino acids in this protein are identical for nearly all plants and animals. It has been one billion years since plants and animals separated, yet of the 103 amino acids in this protein, there is only one difference between a pea and a cow (Zihlman 2001)! This is due to the enormous amount of functional constraint on this molecule as a result of its essential function. Conversely, fibrinopeptides can perform their role in blood clotting with almost any amino acid change. The 20 amino acids in this protein differ by 86% between a horse and a human (Zihlman 2001). Fibrinopeptides exhibit a very fast rate of change because theyπre subject to less functional constraint. Because of differing constraints, and, in turn, differing rates of mutation, different molecules can time events in different evolutionary time frames. For example, histones time once-in-a-billion year events, while fibrinopeptides can clock changes within the past five million years (Zihlman 2001). Therefore, when doing a study, it is essential to select a molecule that is appropriate to the time span of interest. Molecular Clocks are Stochastic Clocks There are two basic types of clocks, metronomic and stochastic. With the metronomic clock, the distance between ticks is uniform. In the stochastic clock, the distances fluctuate. Because of the randomness of nucleotide substitution, it is very unlikely that any molecular clock functions as a metronomic clock. Until recent years, few, if any, researchers proposed that molecular evolution could be stochastic. However, it now appears as if some molecular clocks may indeed behave in a stochastic pattern. Radioactive decay is an example of a stochastic
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