Gene X ppt(Gene10 基因十)--Chapter08

Genome Evolution

Chapter 8 Genome Evolution

Genome Evolution

8.2 DNA Sequences Evolve by Mutation and a Sorting Mechanism The probability of a mutation is influenced by the likelihood that the particular error will occur and the likelihood that it will be repaired. synonymous mutation – A change in DNA sequence in a coding region that does not alter the amino acid that is encoded. nonsynonymous mutation – A change in DNA sequence in a coding region that alters the amino acid that is encoded.

Genome Evolution

8.2 DNA Sequences Evolve by Mutation and a Sorting Mechanism In small populations, the frequency of a mutation will change randomly and new mutations are likely to be eliminated by chance. fixation – The process by which a new allele replaces the allele that was previously predominant in a population.

Genome Evolution

8.2 DNA Sequences Evolve by Mutation and a Sorting Mechanism The frequency of a neutral mutation largely depends on genetic drift, the strength of which depends on the size of the population. The frequency of a mutation that affects phenotype will be influenced by negative or positive selection.FIGURE 02: The fixation or loss of alleles by random genetic drift occurs more rapidly in (A) populations of 10 than in (B) populations of 100

Data courtesy of Kent E. Holsinger, University of Connecticut [http://darwin.eeb.uconn.edu]

Genome Evolution

8.3 Selection Can Be Detected by Measuring Sequence Variation The ratio of nonsynonymous to synonymous substitutions in the evolutionary history of a gene is a measure of positive or negative selection. Low heterozygosity of a gene may indicate recent selective events. genetic hitchhiking – The change in frequency of a genetic variant due to its linkage to a selected variant at another locus.

Genome Evolution

8.3 Selection Can Be Detected by Measuring Sequence Variation Comparing the rates of substitution among related species can indicate whether selection on the gene has occurred. linkage disequilibrium – A nonrandom association between alleles at two different loci, often as a result of linkage.FIGURE 04: A higher number of nonsynonymous substitutions in lysozyme sequences in the cow/deer lineage as compared to the pig lineageAdapted from N. H. Barton, et al. Evolution. Cold Spring Harbor Laboratory Press, 2007. Original figure appeared in J. H. Gillespie, The Causes of Molecular Evolution. Oxford University Press, 1991.

Genome Evolution

8.3 Selection Can Be Detected by Measuring Sequence Variation

FIGURE 05: Nucleotide diversity (pi) of the tb1 region in domesticated maize is much lower than in wild teosinte, indicating strong selection on this locus in maizeReproduced from R. M. Clark, et al., Proc. Natl. Acad. Sci. USA 101 (2004): 700-707. Copyright © 2004 National Academy of Sciences, U.S.A. Courtesy of John F. Doebley, University of Wisconsin, Madison

Genome Evolution

8.3 Selection Can Be Detected by Measuring Sequence Variation

FIGURE 06: The G6PD allele has rapidly increased in frequency by positive selectionAdapted from E. T. Wang, et

al., Proc. Natl. Acad. Sci. USA 103 (2006): 135-140.

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular Clock The sequences of orthologous genes in different species vary at nonsynonymous sites (where mutations have caused amino acid substitutions) and synonymous sites (where mutation has not affected the amino acid sequence). Synonymous substitutions accumulate ~10× faster than nonsynonymous substitutions.

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular ClockFIGURE 07: The rate of evolution of three types of proteins over time

Reproduced with kind permission from Springer Science+Business Media: J. Mol. Evol., The structure of cytochrome and the rates of molecular evolution, vol. 1, 1971, pp. 26-45, R. E. Dickerson, fig. 3. Courtesy of Richard Dickerson, University of Californi

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular Clock The evolutionary divergence between two DNA sequences is measured by the corrected percent of positions at which the corresponding nucleotides differ. Substitutions may accumulate at a more or less constant rate after genes separate, so that the divergence between any pair of globin sequences is proportional to the time since they shared common ancestry.

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular Clock

FIGURE 08: Divergence of DNA sequences depends on evolutionary separation

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular ClockFIGURE 09: All globin genes have evolved by a series of duplications, transpositions, and mutations from a single ancestral gene

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular Clock

FIGURE 10: Nonsynonymous site divergences between pairs of beta-globin genes allow the history of the human cluster to be reconstructed

Genome Evolution

8.4 A Constant Rate of Sequence Divergence Is a Molecular Clock codon bias – A higher usage of one codon in genes to encode amino acids for which there are several synonymous codons.

Genome Evolution

8.5 The Rate of Neutral Substitution Can Be Measured from Divergence of Repeated Sequences The rate of substitution per year at neutral sites is greater in the mouse genome than in the human genome, probably because of a higher mutation rate.FIGURE 11: An ancestral consensus sequence for a family is calculated by taking the most common base at each position