MUTATION and GENETIC VARIATION

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• Mutations [Table 4.1]
  1. Point mutations: new alleles
  2. Gene duplications: new genes
  3. Chromosome inversion: tighter linkage
  4. Polyploidization: new species   

4.1  WHERE NEW ALLELES COME FROM

• the structure of the genetic material [Fig. 4.1]

• DNA forms a template for its synthesis [Fig. 4.2]
• information flows from DNA to RNA to proteins {Fig. 4.3]

Point Mutations: base pair substitutions

•  causes
  1. errors during DNA synthesis (assembly and proofreading)
  2. errors during repair of DNA damage
•  classification [Fig. 4.4]
  1. transitions
     1. a purine (A or G) is substituted for another purine
     2. a pyrimidine (T or C) is substituted for another pyrimidine
  2. transversions
     1. a purine (A or G) is substituted for a pyrimidine (T or C) (or vice versa)
     2. transitions are >2X more common
  3. replacement: changes the amino acid specified by the mRNA
  4. silent: no change (but still an allele)

• Sickle cell anemia [Fig. 4.5]
•  replacement substitutions: highly deleterious to beneficial

•  Rates of mutation [Table 4.2]
•   loss-of-function (gene inactivation) mutations [Fig. 4.6]
•  vary among genes within a species
  • (500 fold in corn [Table 4.2a])
•  vary among species 
  • (10⁶ fold [Table 4.2b])
•  human genome
  • 3 billion nucleotides (base pairs)
  • average gene size 20,000 bp
  • total number of genes: 35,000 (according to the Human Genome Project)
•  perhaps 10% of all human gametes carry a phenotypically detectable mutation

•  variation in base sequences of DNA polymerase and DNA repair loci alleles
•  tradeoff between speed and accuracy; natural selection optimizes tradeoff

•  rates are affected by the number of cell divisions that take place prior to gamete formation

• most transcriptionally active genes are repaired most efficiently

4.2  WHERE NEW GENES COME FROM

Gene Duplications

• unequal crossing over [Fig. 4.7]  produces gene families (actins, myosins, histones, immunoglobulins, globins...) [Table 4.3].
• Duplicated genes can
  1. retain original function and provide an additional locus
  2. mutate differently, adding new functions, via selection 
  3. become functionless pseudogenes

Gene Duplication Events in the Globin Gene Family

1. Time expression of different globin genes related to function [Fig. 4.8]
2. structural similarity of transcription units [Fig. 4.9] 

Other Mechanisms for Creating New Genes

1. overprinting
2. reverse transcription of mRNA

4.3  CHROMOSOME ALTERATIONS

• Categories of chromosome mutations
  1. Those that affect the structure of the chromosome
  2. Those that affect the number of chromosomes

1. Inversion [Fig. 4.10]
   1. changes gene order and lessens frequency of crossing over
   2. genes inside inversions tend to be inherited as a unit
   3. clines in frequency of an inversion [Fig. 4.11]
2. Translocation
3. Deletion 
4. Duplication

•  Polyploidy 
  1. examples
     • Triploids (3N) - 3 sets of chromosomes
     • Tetraploids (4N) - 4 sets of chromosomes, (etc.)
  2. Polyploid individuals are usually genetically isolated from parents
  3. Mechanisms: errors in meiosis form diploid gametes (mainly autopolyploidy)
     1. direct route": diploid gametes yield tetraploid offspring, which can self-fertilize [Fig. 4.12]
     2. "triploid block" [Fig. ]: triploid chromosomes do not synapse well 6 gametes with wrong numbers of chromosomes  6 decreased fertility; self fertilization  6 viable tetraploids

4.4  Measuring Genetic Variation in Natural Populations

• The traditional view (pre 1960's) was that allelic variation in populations would be limited
• most populations have extensive allelic variation

• gel electrophoresis (Box 4.1)
• determining CCR5 genotypes [Fig. 4.13]

• genetic variation is computed from the frequency of each allele present
• documenting allele frequencies can reveal interesting patterns [Table 4.4]

• polymorphic loci
  • gel electrophoresis of enzymes reveals almost all 
    • fly populations are polymorphic for two alleles of Adh [Fig. 4.14a]
    • Fundulus populations  are polymorphic for temperature dependent Ldh-B [Fig. 4.14b]
• in typical populations, protein variations indicate between a third and a half of all coding loci are polymorphic [Fig. 4.16]
• DNA sequence variation suggests even greater variation [Fig. 4.17]

• balance theory: genetic diversity is maintained by natural selection
• neutral theory: mutations are equivalent and not eliminated by selection

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