BOLIVARIAN REPUBLIC OF VENEZUELA UNIVERSIDAD DEL ZULIA NEUROSCIENCES INSTITUTE GENETICS OF COMMON HERITABLE DISORDERS IN VENEZUELA RESEARCH TRAINING PROGRAM PROFESSOR: GLADYS MAESTRE, M.D Development of the Neutral Theory: Some molecular evidences for the neutralism vs. selectionism debate Evelyn B. Córdova Villanueva Maracaibo, December 2005 1 Development of the Neutral Theory: Some molecular evidences for the neutralism vs. selectionism debate Evelyn B. Córdova Villanueva The hypothesis that most molecular polymorphism and substitutions are due to neutral mutations and genetic drift, the neutral theory, was first proposed in the 1960’s [1]. Based on amino acid sequences, Zuckerkandl and Pauling [2] proposed that there was a constant rate of amino acid substitution over time. Accordingly, Kimura [3] proposed that many of the substituted alleles must be neutral, and later ([4]) argued that the rate of amino acid substitutions of homologous proteins (the rate of molecular evolution) is almost constant. He further argued that protein evolution is uncorrelated with phenotypic evolution. The apparent constancy of the amino acid substitution rate, the molecular clock, was thought to support the neutral theory [1]. In 1969, King and Jukes [5] published a paper that independently proposed that most amino acid substitutions are neutral and stated the inverse relationship between the importance of a protein or site within a protein and its rate of evolution. This would later be developed into the Principle of Molecular Evolution that provided support for the neutral theory [6]1. Since the theory and application of molecular clocks (the neutral theory) was proposed in the 1960s, much controversy has arisen (cfr. [1], [7], [8]). Through the next four decades, the most debated topics on molecular clocks - and, hence, on Neutral Theory - concerns variations in the mutation rate and substitution rate among lineages in a phylogeny; the influence of life history (e.g. generation time, body size, metabolic rate) on the rate of substitution; lineage–specific rate variation in the mitochondrial genome of animals [9]; and the role of adaptive selection in protein evolution. In this short essay, how the generation time, very low mutation rate and adaptive selection related to changes in the environment can affect the molecular clock will be discussed. To illustrate this discussion, consider a pair of orthologs in mouse and rat. The discussion will start by explaining how the evolution of the mouse lineage at a significantly shorter generation time will affect the molecular clock as kept by orthologs; then, it will be explained the effect on the molecular clock when the rat lineage evolves at very low mutation rates; and, finally, changes in the environment that cause the mouse orthologs to be unnecessary and its effect on the molecular clock will be discussed. One of the curious facts that appeared to be contrary to predictions of the neutral theory is the generation-time effect [1]. Let consider the case of the evolution of the mouse lineage at a shorter generation time. The natural unit of time for the neutral theory is a single generation. Therefore, species with shorter generation times should evolve faster in real (clock) time than those with longer generation times [1] (cfr. [8]). This implies that the molecular clock for the mouse lineage will tick faster, since the rate of substitution will be higher than in those species with longer generation times. Martin and Palumbi [10] stated, as a hypothesis, that generation-time effect might rely on the concept of nucleotide generation time: the amount of time needed for a given nucleotide position to be copied. Nucleotide positions that have short generation times are those that are replicated most often. Thus, species with short organism generation times may also have high substitution rates because of short nucleotide generations, associated with fast rates of molecular evolution and faster molecular clocks if compared with other species (cfr. [11]). During the 1990s, several theories of molecular evolution where natural selection rather than genetic drift is the main force, causing fixations, have been pursued. One of these is called the mutational landscape model ([12], [13], [14]), which was proposed to explain the episodic nature of amino acid “Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones” [6: 2848] 1 2 substitutions. The model pictures molecular evolution as generally stagnated at a local optimum due to the very low mutation rates to sequences that are more than one mutational step away from the locally optimal sequence. An environmental shift is needed to move the population off of the local peak and into a burst of substitutions until it stagnates once again at another local maximum. Thus, environmental changes set the pace of evolution rather than the mutation rate [1]. This model seems to explain the case of the rat lineage that evolves at very low mutation rates – which would lead to stagnation due to the slow tick of the molecular clock. However, this mutational landscape model does not account for where new genes come from or why some others become unnecessary. Some findings on adaptive selection in protein evolution ([15], [16], [17], [18], [19]) have shed some light on when and how new functions in genes – and new genes – have appeared as a result from adaptive fixation of selectively advantageous mutations rather than a steady accumulation of neutral ones. Furthermore, the cited evidences, and many more that has been neglected in this essay due to the lack of space, have shown that positive selection in protein-coding genes are not as rare as the neutral theory proposed, contrary to what the previously stated Principle of Molecular Evolution argued2. Different genes evolve at different rates because of natural selection on gene function [9]. Molecular clocks therefore have wide applicability across the tree of life, from recent divergences among populations (using fast evolving genes) to the deepest splits among prokaryotes and eukaryotes (using the slowest evolving genes). Nevertheless, if the rate with which a particular gene or protein evolves is not the same in all lineages, then use of a single rate will result in biased time estimates. Some rate variation could go undetected, possibly resulting in biased time estimates. On the other hand, it has been proposed that some lineages might increase in substitution rate concordantly during an adaptive radiation, resulting in biased time estimates. Moreover, a correlated rate increase in many lineages would cause a distortion in the timescale, leading to inconsistencies between molecular times and the earlier or later fossil record [9]. References [1] Ohta T, Gillespie J (1996). Development of Neutral and Nearly Neutral Theories. Theoretical Population Biology 49: 128-142. [2] Zuckerkandl E, Pauling L (1965). Evolutionary divergence and convergence in proteins, in Evolving Genes and Proteins (V. Bryson and H. J. Vogel, Eds.), pp. 97-166, Academic Press, New York. [3] Kimura M (1968). Evolutionary rate at the molecular level. Nature 217: 624-626. [4] Kimura M (1969). The rate of molecular evolution considered from the standpoint of population genetics. Proc. Natl. Acad. Sci. USA 63: 1181-1188. [5] King J L, Jukes T H (1969). Non-Darwinian evolution. Science 164: 788-798. [6] Kimura M, Ohta T (1974). On some principles governing molecular evolution. Proc. Natl. Acad. Sci. USA 71: 2848-2852. [7] Beatty J (1984). Chance and Natural Selection. Philosophy of Science, 51: 183-211. 2 Special attention must be paid to [15] and [16] for this purpose. 3 [8] Kreitman M, Akashi H (1995). Molecular Evidence for Natural Selection. Annual Review of Ecology and Systematics, 26: 403-422. [9] Hedges SB, Kumar S (2003). Genomic clocks and evolutionary timescales. 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