Biology 265 EVOLUTION

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Biology 265EVOLUTION

• Lecture 5

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Overview

• Molecular biology, polymorphism, and neutral
  evolution
• Non-Darwinian evolution?
• Chance processes in population genetics
• Drift
• Founder effects
• Gene flow
• Mutation

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1960s Protein electrophoresis revealed high
levels of variation

• Drosophila pseudoobscura
• 12 loci heterozygous per individual
• 30 loci polymorphic per population

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Explanations

• Lewontin and Hubby (1966)
• Neutral?
• Mutation-selection balance?
• Heterozygous advantage (selection)?

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Non-Darwinian evolution
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Rubbish!

• It puts too much emphasis on natural selection as
  the only mechanism of Darwinian evolution

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Charles Darwin(1859)

• Variations neither useful nor injurious would
  not be affected by natural selection
• They would be left a fluctuating element

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Selectionists vs. neutralists

• Fairer description of debate within evolutionary
  biology

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Neutral evolution is important

• True, Darwin probably did not consider neutral
  fluctuations to be that significant
• Indeed they do not lead to adaptation
• However, the neutral theory of molecular
  evolution (Kimura, 1983) is important
• Describes how evolution occurs through random
  processes associated with selectively neutral
  molecules

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Evolutionary forces

• Natural selection - adapts population to
  environment
• Mutation - random low frequency neutral,
  harmful or beneficial source of new genes
• Gene flow - migration and interbreeding
• Genetic drift - Bottlenecks and founder effect
• Nonrandom mating - assortative mating,
  inbreeding, sexual selection

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Null hypothesisHardy-Weinberg ratio

• Ratio of genotype frequencies that evolve when
• no selection
• random mating
• infinitely large populations
• no migration (gene flow)

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Relax H-W AssumptionsImportance of Sampling

• Assume no selection, no gene flow, and random
  mating
• But allow population size to be limited (not
  infinite)
• Each generation is a random sample of the
  previous generation

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Sampling gametes

• Sperm A or sperm a?
• From a heterozygous Aa male there is an equal
  probability that A or a sperm will fertilize the
  egg
• Assuming no fitness differences

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Reproductive success can be random

• Genes for malaria resistance wont protect you
  from lightning strikes
• Death is not always a function of being well
  adapted, chance also is important
• Similarly, mating success is not always due to
  ones inherent attractiveness or charm
• Right place at the right time...

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Soft selection

• Not all survival and reproduction is due to
  selection

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Sampling leads to drift

• Frequency of alleles with same fitness will
  change at random over time - genetic drift
• Alleles can go extinct or become fixed (100) in
  a population through genetic drift
• Alleles can be substituted without selection

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Consequences of genetic drift

• With genetic drift as the only force in operation
• the probability of a given allele eventually
  reaching a frequency of 1 (i.e. becoming fixed)
  is its frequency in the population.
• For example, allele A with a frequency of 0.8 has
  an 80 chance of becoming the only allele present
  in the population

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Population size and drift

• Small populations vary more in allele frequencies
  due to sampling effects from one generation to
  the next
• variance in frequency of an allele with frequency
  depends on population size, N
• Smaller N more variance, more drift

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Flip a coin

• Observe 10 sets of 20 coin tosses
• and 10 sets of 4000 coin tosses
• On average all sets would have 50 heads and
  tails
• But it is more likely to flip 12 heads 8 tails
  in the small population
• than 2400 heads 1600 tails in the large
  population

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Effective population size

• Count adults in field N
• For population genetics, N has been correctly
  measured when the chance of drawing 2 copies of
  the same gene is (1/2N)2
• In natural populations it is more likely than
  this that one will get the same gene
• Population geneticists use Ne to indicate the
  (usually smaller) effective population size

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Some factors causing Ne

Sex ratio (Wright, 1932). If one sex is less
common, the rarer sex dominates the change in
gene frequencies - fewer individuals contribute
to next generation

Inbreeding. Geographic subdivision, assortative,
non-random mating.

Population fluctuations. Bottlenecks reduce Ne
(average population size over many generations is
the harmonic mean)

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Inbreeding

• More likely to inherit the same gene (homozygous)
  if parents are close relatives
• Mutations are usually recessive and harmful
• Homozygous recessives most likely to occur as a
  result of inbreeding
• Inherited diseases are more common in the
  offspring of cousins than they are in the human
  population as a whole

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Bottlenecks

• Populations may go through a bottleneck in size
• Out of many individuals, only a few contribute to
  the next generation
• A special type of bottleneck is the reduction in
  population size associated with colonization -
  founder effect

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Founder effect

• The establishment of a new population by a few
  original founders (in an extreme case, by a
  single fertilized female) that carry only a small
  fraction of the total genetic variation of the
  parental population. (Mayr, 1963)

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Founder effect Example 1. Afrikaners

• Mainly descended from one shipload of Dutch
  immigrants to South Africa in 1652
• Carried some rare genes by chance
• these are now more common among Afrikaners than
  Dutch
• e.g. dominant gene causing porphyria variegata (a
  severe reaction to barbiturate anesthetics)

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Example 2. Amish

• Small group of Germans began the Amish community
  in Pennsylvania
• 1 possessed an allele for polydactylism (more
  than five fingers or toes on a limb).
• After 200 years of reproductive isolation
• the number of cases among the Amish population
• exceeds the number of cases occurring in the
  entire worlds population

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Gene flow

• When an individual or group of individuals
  migrate to (or from) one population to (or from)
  another and interbreed with its members
• Depends not only on the number of migrants but on
  their reproductive success in the new population

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Migration is not gene flow

• The arctic tern, Sterna paradiseae, migrates
  annually from one polar region to the other and
  back again
• but it breeds only in a restricted locality
  within the Arctic Circle

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Gene flow affects allele frequencies

• Assume that the frequency of allele A is 0.4 on
  the mainland but only 0.2 in Hawaii.
• The effect of immigration to Hawaii will depend
  on the genetic contribution of immigrants
• measured by m, the coefficient of replacement or
  rate of gene flow
• Change in the frequency of A in the island
  population is given by the equation

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• Change in frequency of A -m(p - pm)
• p frequency of allele A on the islandpm
  frequency of allele A among the immigrantsm
  coefficient of replacement
• Thus, if m is equal to ten percent, then
• Change in frequency -0.1(0.2 - 0.4) 0.02
• So the new frequency among the island population
  equals
• 0.2 0.02 0.22

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Gene flow homogenizes

• When p pm, an equilibrium will be established
• the change in frequency 0
• The mainland and island populations will have
  become genetically identical
• Assuming no drift

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Drift - gene flow equilibrium

• Gene flow homogenizes populations
• But drift causes them to diverge
• Initially, founder effects can lead to
  unpredictable levels of genetic similarity among
  ancestral and derived populations
• With time, an equilibrium is reached and the
  genetic distance among populations remains
  constant

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Wrights rule of thumb

• Only 1 individual need be exchanged each
  generation to prevent the fixation of different
  alleles in two populations

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Eve and Extinction is for good

• With time, all the genes in a population will be
  descended from a single gene like all humans are
  descended from Eve
• Rate of fixation is independent of population
  size
• 2N genes at each locus (2 per individual)
• some genes fail to reproduce by chance and
  extinction is final
• each gene has 1 in 2N chance of being the sole
  survivor (1/2N)

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US Open for coin flipping

• Knock-out tournament not tennis, coin flipping.
• First to throw heads wins.
• Eventually, only a single champion left!
• All down to chance (drift) not skill (selection)

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Rate of neutral evolution neutral mutation rate

• Any gene, even a new one, has 1/2N ( its
  frequency in the population) chance of being
  fixed
• Rate at which new neutral mutations arise u
• At each locus 2N genes, so number of neutral
  genes arising per generation 2N u
• Rate of neutral evolution is therefore
• 1/2N x 2Nu u

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Mutation rates

• Mutations are not all neutral
• Observed rates of molecular evolution vary
• They differ among genes and even within regions
  of the same gene
• Some parts of protein more conserved because they
  have structure-dependent function

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Mutation rates in hemoglobin
Number of amino acid changes per 109 years
(Kimura 1983)
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Synonymous mutations

• Mutations in non protein coding regions
• or mutations in a codon that do not change the
  amino acid
• genetic code is degenerate (more codons possible
  than needed for amino acids)
• synonymous sites evolve more rapidly

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What maintains genetic variation in nature?

• Most populations are mosaics, not one large,
  freely interbreeding unit (panmictic). Hence
  drift and gene flow operate.
• Selection pressures can vary from place to place
  and year to year due to different environmental
  conditions.
• Heterozygous advantage