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The advancing technology that made it possible to detect the sequence of amino acids in a protein also made it possible to discover how much the proteins and DNA of various species differ. In chapter 17, we discussed the use of mitochondrial DNA (mtDNA) to determine evolutionary relationships. Currently, protein, nuclear DNA, and mtDNA clocks are being studied.
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Frequency distribution of the Es-5 alleles of an esterase locus in house mice. Each circle represents allelic frequencies at that geographic location. Note the general tendency for the Es-5b allele to increase from west to east in the continental United States. (From L. Wheeler
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and R. Selander, Genetic Variation in Populations of the House Mouse, Mus musculus, in the Hawaiian Islands, Studies in Genetics, VII, 1972. University of Texas Publication 7213. Reprinted with permission of M. R. Wheeler.)
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Isolated instances of selection, however, do not adequately prove the case for maintaining variation by means of natural selection or disprove the case for maintaining variation of neutral alleles. Both theories recognize natural selection as the guiding force in producing adapted organisms.What is needed is proof that the majority of poly-
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Tamarin: Principles of Genetics, Seventh Edition
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IV. Quantitative and Evolutionary Genetics
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21. Evolution and Speciation
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Genetic Variation
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Knowledge of the changes in amino acid sequences can be used to estimate the rate of evolutionary change. That is, the data show how many amino acid substitutions have occurred between two known groups of organisms. The genetic code dictionary allows us to estimate the minimum number of nucleotide substitutions required for this change. For example, if one protein contains a phenylalanine in position 7 (codons UUU, UUC), and the same protein in a different species has an isoleucine in the same position (AUU, AUC, AUA), we can see that the minimum number of substitutions to convert a phenylalanine codon to an isoleucine codon is one (UUU AUU). When we know the minimum number of substitutions, we can calculate molecular evolutionary rates, nucleotide substitutions per million years. In a sense, these rates provide us with a molecular evolutionary clock that measures evolutionary time in nucleotide substitutions. Many studies of the rate of amino acid and nucleotide substitutions have been done on hemoglobin, on cytochrome c, on a class of proteins involved in blood clotting called brinopeptides, and on many others. Figure 21.10 shows the way in which an amino acid sequence differs among species. From comparisons of this type, we can calculate the actual number of amino acid differences, as well as percentage differences. Table 21.4 is a compilation of percentage differences between various species based on the cytochrome c protein. This type of information can be used two ways. First, we can construct a phylogenetic tree that tells us the evolutionary history of the species under consideration ( g. 21.11). This tree can be compared with phylogenetic trees constructed by more classical means using fossil evidence and evidence from morphology, physiology, and development. From the comparisons, we can look at areas of disagreement in an attempt to nd out the best way to create phylogenetic trees. In addition, molecular phylogenies can give us information unattainable in any other way, as, for example, when the fossil record is incomplete or ambiguous. A second use of DNA or amino acid difference data is to determine average rates of substitution. Once we
know the current amino acid differences in the proteins of two species, it is possible to estimate the actual number of nucleotide substitutions that have taken place over evolutionary time using the statistical Poisson distribution, which deals with rare events. The index, K, is the average number of amino acid substitutions, per site, between two proteins: K ln(1 p)
in which ln is the natural logarithm (to the base e), and p d/n in which d is the number of amino acid differences and n is the total number of amino acid sites being compared. For example, in gure 21.10, n 8 and d 3 between the dog and chicken. Thus K ln(1 0.375) 0.47
Therefore, the average number of amino acid substitutions, per site, between dog and chicken is 0.47. We can take this calculation one step further by determining the per-year rate: k K/2T
in which k is the amino acid substitution rate per site per year, and T is the number of years since the two species diverged from a common ancestor. We divide by 2T because each side of the tree has evolved independently for T years. When k s are calculated for many proteins over many species, they cluster around 10 9 (table 21.5). In fact, Kimura has suggested the unit of a pauling to be equal to 10 9 amino acid substitutions per year per site in
Composite evolution of hemoglobin, cytochrome c, and brinopeptide A. The total number of nucleotide substitutions appears on the horizontal axis. Note how the tree groups similar organisms and generally agrees with classical systematics. (From
The amino acids making up the terminal portion of cytochrome c in three species. Note the similarities and differences.
C. H. Langley and W. M. Fitch, An examination of the constancy of the rate of molecular evolution, Journal of Molecular Evolution, 3:168. Copyright 1974 Springer-Verlag, Heidelberg. Reprinted by permission.)
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