Chapter 9- The history in our genes


9.1  Coalescing Genes  
  1. Genetic loci have their own genealogy  (Fig. 9.2)
  2. Alleles in populations coalesce to a common ancestor   (Fig. 9.3a)
  3. Coalescence time varies for different genes   (Fig. 9.3b)
  4. Key Concepts
    1. It is possible to trace gene genealogies and reconstruct the rise and spread of alleles
9.2 Gene Trees and Species Trees   
  1. Gene trees do not always match species trees  (Fig. 9.5)
    1. Data from several genes used to construct phylogenies
  2. Key Concepts
    1. Gene trees and species trees do not always match
    2. Data from multiple genes used in phylogeny construction
9.3 Methods of Molecular Phylogenetics   
  1. Building a phylogeny with genetic data
    1. Each nucleotide a potentially informative character
    2. But, homoplasy common-Only four possible character states
    3. Genes differ in rate of evolution-Slowly evolving genes useful for distantly related species-Rapidly evolving genes useful for closely related lineages
  2. Common methods
    1. Maximum parsimony-Simplest explanation favored
    2. Distance matrix (e.g. neighbor joining)-Clusters taxa based on genetic distance
    3. Maximum likelihood-Finds most likely tree given specific model of molecular evolution
    4. Bayesian methods-Looks at probability that a tree is correct given a specific model of molecular evolution
    5. Neighbor-joining example (Fig. 9.6)
  3. Key Concepts
    1. Phylogenetic trees are hypotheses that are constantly reevaluated when new data become available


9.4 Experimental Phylogeny   
  1. Experimental phylogenetics validates methods (Fig. 9.7)
    1. A large number of tree topologies are possible
  2. All methods performed well (Fig. 9.8)
  3. Key Concepts
    1. Scientists can test the effectiveness of phylogenetic methodologies
9.5 Four Case Studies in Molecular Phylogeny  
  1. Case study 1: origin of tetrapods (Fig. 9.9)
  1. Case study 2: human evolution (Fig. 9.10)
    1. Multiregional model of human origins
      1. Hominins across Old World were a single species connected by gene flow
      2. Multiregional differences the result of local adaptation
    2. Out-of-Africa model of human origins
      1. All human populations are derived from recent African ancestry
    3. Phylogenetic data supports Out-of-Africa model


  1. Case study: origin of Darwin's finches (Fig. 9.11)
    1. Multiple colonizations by different finch species
      1. Different species of Darwin's species should have closest relatives elsewhere
    2. Single colonization then diversification-Darwin's finches should form monophyletic group
    3. Colonization from Isla de Coco
      1. Cocos finch should be closest relative of all Darwin's finches
    4. Phylogenetic evidence supports single colonization
  2. Case study: human immunodeficiency virus (HIV) (Fig. 9.12)
9.6 Natural Selection versus Neutral Evolution 
  1. Neutral theory of molecular evolution
    1. Motoo Kimura (1968): most evolution at the molecular level is neutral (due to drift)
      1. Neutral substitutions should accrue in a clock-like fashion
      2. Different types of DNA should evolve at different rates
  2. Support for clock-like substitution (Fig. 9.13)
  3. Rate of evolution in different types of DNA does differ (Fig. 9.14)
  4. The molecular clock can be used to estimate date of common ancestor (Fig. 9.15)
  5. Molecular clock can be used to estimate diversification events (Fig. 9.16A)
  6. Two peaks in mammalian diversification rates (Fig. 9.16B)
  7. Detecting selection on DNA sequences
    1. Synonymous substitutions: do not change protein
      1. Should evolve at a neutral rate
    2. Nonsynonymous substitutions: change protein
      1. Faster evolution than synonymous sites indicates positive selection
      2. Slower evolution than synonymous sites indicates purifying selection
  8. Signature of positive selection (Fig. 9.17)
  9. Positive selection on FOXP2 (Fig. 9.18)
  10. Table 9.2 General Approaches and Timing of Detecting Selection in Genome-Wide Selection Studies
  11. Key Concepts
    1. The neutral theory of molecular evolution describes patterns of nucleotide substitution predicted under drift alone
    2. Neutral variation should accumulate in a clock-like fashion
    3. Both positive and purifying selection leave distinctive genetic signatures that can be detected
7.3 Genetic Drift and Molecular Evolution
  1. The Neutral Theory of Molecular Evolution

    1. It is important to distinguish between evolution of proteins and evolution of nucleotide sequences

    2. Much nucleotide sequence evolution is selectively neutral

    3. Are amino acid substitutions under selection or neutral?

  2. Neutral theory

    1. Advantageous mutations rare

    2. Most alleles are neutral

    3. Rate of evolution is equal to the mutation rate

    4. Genetic drift dominates evolution

  3. Evidence Supporting the Neutral Model

    1. Silent sites evolve should faster than replacement sites

    2. DNA sequences change steadily over time.

    3. Fig. 7.21  Molecular evolution in Flu Viruses is Consistent with the Neutral Model

    4. Molecular clock

    5. Pseudogenes

  4. Testing the neutral theory

    1. Neutral theory states that if we compare protein coding sequences  between species, there will be more nucleotide substitutions at synonymous than non-synonymous sites

    2. If evolution involves positive selection on alleles that increase fitness, then evolution at non-synonymous sites may be faster than at synonymous sites

  5. Positive Selection

    1. replacement substitutions outnumber synonymous substitutions

      1. genes that code for proteins involved in fertilization and disease resistance.

    2. Positive selection on exon 11 of the BRCA1 gene in humans and chimpanzees. (Fig. 7.23)

9.7 Deciphering the Genome 
  1. Genome alignments reveal conserved elements with important functions  (Fig. 9.19)
  2. Key Concepts
    1. Genome alignments provide valuable information about functionally important coding and non coding sequences



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