Solution to a gene divergence problem under arbitrary stable nucleotide transition probabilities |
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Authors: | Richard Holmquist |
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Affiliation: | (1) Space Sciences Laboratory, University of California, 94720 Berkeley, Ca., USA |
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Abstract: | Summary A nucleic acid chain L nucleotides in length, with the specific base sequence B1B2.BL, each Bi being A, G, C, or T, is defined by the L-dimensional vector B = (B1, B2, , BL), the kth position in the chain being occupied by the base Bk. Let PBB' be the twelve given constant non-negative transition probabilities that in a specified position the base B is replaced by the base B in a single step, and let PBB'(XX) be the probability that the position goes from base B to B in X steps. An exact analytical expression for PBB'(XX) is derived. Assuming that each base mutates independently of the others, an exact expression is derived for the probability PBB'(XX) that the initial gene sequence B goes to a sequence B = (B1, B2, , BL) after X = (X1, X2, , XL) base replacements, where Xk is the number of single-step base replacements in the kth position. The resulting equations allow a more precise accounting for the effects of Darwinian natural selection in molecular evolution than does the idealized but biologically less accurate assumption that each of the four nucleotides is equally likely to mutate to and be fixed as one of the other three. Illustrative applications of the theory to some problems in biological evolution are given. |
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Keywords: | Molecular Evolution Homologous Proteins and Nucleic Acids Stochastic Evolutionary Models Amino Acid and Nucleotide Substitutions Computer Simulations of Molecular Divergence Nucleotide Transition Probabilities Gene Divergence |
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