Biology 2900 Principles of Evolution and Systematics

1
Biology 2900Principles of Evolutionand
Systematics

• Dr. David Innes
• Jennifer Gosse
• Valerie Power

2
Announcements

• Lab 2 (Group 1) handout ?print from course web
  page
• Important Do the population genetics review
  before Lab.
• Readings for Lab. 2 (Futuyma)
• HWE Ch 9 (pp.
  190 - 197)
• Selection Ch 12 (pp.
  273 282)
• Genetic Drift Ch 10 (pp.
  226 231)
• http//www.mun.ca/biology/dinnes/B2900/B2900.html

Clip board found. See Jennifer
3
Biology 2900Principles of Evolution and
Systematics

• Topics
• - the fact of evolution
• - natural selection
• - population genetics
• - natural selection and adaptation
• - speciation, systematics and
• phylogeny
• - the history of life

4
Hardy-Weinberg Theorem (1908)
Chapter 9

• Null model
• Allele and genotype frequencies will not change
  across generations (equilibrium)
• Assuming - random mating
• - large population size
• - no selection
• - no migration
• - no mutation

5
Hardy-Weinberg

• p2 2pq q2
• AA Aa aa
• Relax Assumptions
• ? - Mutation
• ? - Migration
• ? - Non-random mating
• - Finite population size (small pop., founder
  effect)
• - Selection - differential survival,
• fecundity etc. among genotypes

6
Finite Population Size

• Introduces sampling error
• allele proportions not transmitted
• precisely between generations
• sampling error increases with
• decrease in population size

7
N 200 individuals (6 populations)
q f(A2)
8
N 10 individuals (6 populations)
q f(A2)
9
Consequences of FinitePopulation Size

• Random drift of allele frequencies
• Divergence of allele freq. among populations
• Loss of genetic variation (heterozygosity)

10
Founder Effect

• Sampling process during the founding of new
  populations
• - small number of individual founders
• - allele frequencies differ by chance
• reduced allelic diversity (esp. rare alleles)
• allele frequency differences among populations

11
Population Differentiation

• Allele frequencies can diverge among
• populations due to random processes
• 1. Founder effect
• 2. Random genetic
• drift

12
Population Structure

• Assuming no selection or mutation
• Pattern of allele freq. variation a
  function
• of
• - founder effect
• - random drift
• - migration (gene flow)

Increase genetic differentiation
decrease genetic differentiation
13
Genetic Differentiation

• D (genetic distance)
• - allele frequency differences between
• pairs of populations
• Fst (fixation index)
• - degree of genetic differentiation among a
  number of populations

14
Genetic distance
Correlation between genetic and geographic
distance among populations of Gyliotrachela
hungerfordiana from West-Malaysian limestone
hills.
Land Snail
15
Migration and Genetic Differentiation

• How much migration will prevent genetic
  differentiation by random drift ?
• (neutral genes, no selection)
• - Genetic drift
  increases differentiation
• - Migration (gene
  flow) decreases differentiation

16
Genetic Differentiationdue to genetic drift

• Fst ( 0
  1.0 )
• N population size
• m proportion of the pop. that are migrants
• Fst index of genetic differentiation

1
4Nm 1
17
Island Model For
any population of size N A small number of
migrants can offset differentiation by genetic
drift
Different

• N Drift m Nm Fst
• strong .1 1 0.20
• 1000 weak .001 1 0.20

Fst
Same
Number of migrants per generation (Nm)
18
Number of Migrants

• -
• Nm Estimated number of migrants per
• 
  generation

1
1
Nm
4Fst
4
Fst observed genetic differentiation
19
Nm Fst
20
Drift Migration Simulation
http//darwin.eeb.uconn.edu/simulations/simulation
s.html Cases 1. Small populations N 25
Low migration m 0.001 (Nm 0.025) 2.
Small populations N 25 High migration
m 0.1 (Nm 2.5) 3. Large populations
N 250 Low migration m 0.001 (Nm
0.25) 4. Large populations N 250 High
migration m 0.1 (Nm 25)
21
Population StructureBreeding population
Gene Flow
A
B
C
Gene flow increases breeding population size
22
Population Genetics

• Genes in populations
• - inbreeding
• - genetic differentiation
• - gene flow
• Genetic structure
• Neighbourhood size Size of breeding
  population

23
Hardy-Weinberg
p2 2pq q2 AA Aa aa

• Relax Assumptions
• ? - Mutation
• ? - Migration
• ? - Non-random mating
• ? - Finite population size
• - Selection - differential survival,
• fecundity etc. among genotypes

24
Selection

• Selection occurs when
• some phenotypes have higher survival and/or
  reproduction than other phenotypes
• Selection -----gt Evolution
• when phenotypes heritable
• (change in allele frequencies)

25
Selection

• - Random drift-------gt stochastic
• - Selection------------gt deterministic
• Fitness differences
• differences in the potential to donate genes to
  future generations among phenotypes
• 
  (genotypes)
• Fitness values relative

26
Selection

• Differential fitness ? change in allele freq.
• q gt 0 q ? 1 fixation q 1.0
• q lt 0 q ? 0 loss q 0.0
• q 0 q equilibrium 1
  gt q gt 0

Outcomes
v
27
Selection

• Differential fitness
• differences among phenotypes (genotypes) in
  survival, fertility, fecundity, mating success,
  etc.
• 
  
• Example differential survival
• survival rate ( U )
• relative fitness (w)

28
Selection

• Differential survival
• 1. average survival rate (U) for each
  genotype
• 2. relative fitness w wmax
  1.0

U
Umax
29
Selection

• Genotype A1A1 A1A2
  A2A2
• Survival (U) 0.8 0.6
  0.2
• Fitness(w) w11 w12
  w22
• 1.00 gt 0.75
  gt 0.25

Directional selection favouring the A1 allele
30
SimulationExample of Directional Selection

• Genotype A1A1 A1A2
  A2A2 Fitness(w) w11
  w12 w22
• 1.00 gt 0.75
  gt 0.25
• Box 12A Population Mean fitness
• w p2 w11 2pq w12 q2 w22

31
w111.0 w12 .75 w22 .25
Freq(A1) allele
A1 allele frequency
Directional Selection
32
Initial p 0.40
A1A1 A1A2
A2A2
33
? p rate of change of allele freq.
Maximum rate
34
w p2 w11 2pq w12 q2 w22
35
Strength of Selection
Directional selection
36
Directional Selection
Outcome fixation of one allele (loss of
other allele) Rate dependent on strength
of selection Pattern of change in allele
frequency a function of dominance relationship
37
Selection

• Selection (fitness of
  phenotype)
• Favoured allele
• 1) Dominant w11 w12
  gt w22
• 2) Recessive w11
  w12 lt w22

38
Fig. 12.6
Fitness of A1 allele Dominant
Intermediate Recessive
A1A1 1.0 1.0 1.0
A1A2 1.0 0.9
0.8 A2A2 0.8 0.8 0.8
Increase of an advantageous allele (directional
selection) Depends on - initial allele
frequency - selection coefficient -
degree of dominance
39
Examples of Selection

• Single gene polymorphisms
• Colour Polymorphisms
• British School of Ecological Genetics
• (Snails, Butterflies)

40
Examples of Selection

• Single gene polymorphisms
• Colour Polymorphisms
• British School of Ecological Genetics
• (Snails, Butterflies)

41
Cepaea nemoralis
Snail
Butterflies
Peppered moth Biston betularia
42
Peppered Moth
Cryptic coloration
43
Decline in melanic form as air pollution declines
Fig. 12.25
Natural light tree trunks
Soot covered tree trunks
44
http//www.biologycorner.com/worksheets/pepperedmo
th.html
45
Mytilus edulis
Cepaea nemoralis
46
Examples of Selection

• Single gene polymorphisms
• 1966 Lewontin and Hubby
• Protein electrophoresis
• Many polymorphic enzyme loci
• Variation neutral or maintained by selection ?

47
Protein Electrophoresis
Pgm
Origin
48
Examples of Selection

• 1. Laboratory natural selection experiments

49
Directional selection
AdhF allele
50
Examples of Selection

• 2. Geographic clines in allele frequency
• - gradient due to migration history
  (neutral) ?
• - selection due to environmental gradient ?

51
Geographic clines

• Migration history
• mixing of alleles
• (neutral)

52
Six enzyme loci
insecticide
none
53
Geographic clines

• Mosquito enzyme genes
• cline for AceR allele correlated with
• pesticide usage
• Selection ?
• Five control genes no cline
• What type of experiment would be useful ?

54
Selection for Pesticide Resistance

• Chemical Year Deployed Resistance observed
• DDT 1939 1948
• 2,4-D 1945 1954
• Dalapon 1953 1962
• Atrazine 1958 1968
• Picloram 1963
  1988
• Trifluralin 1963
  1988
• Triallate 1964
  1987
• Diclofop 1980
  1987

55
Number of insecticide resistance pest species
Fig. 12.9
Total
56
Fig. 12.8
Rat poison
57
Selection for Antibiotic Resistance

• Antibiotic Year Deployed
  Resistance observed
• Penicillin 1943
  1946
• Streptomycin 1943
  1959
• Tetracycline 1948
  1953
• 
  

methicillin-resistant Staphylococcus aureus, or
MRSA
58
Genetic Variation

• Loss of genetic variation
• - random genetic drift
• - inbreeding
• - migration
• - directional selection
• How can genetic variation be maintained ?

59
Maintenance of Genetic Variation

• Balance of gain and loss of alleles
• - balance of forward and reverse mutation
• - selection - mutation balance
• - selection - migration balance
• - heterozygote advantage
• - frequency-dependent selection

60
Mutation Balance

• two-way (reversible)
• v equilibrium
  q 0
• A a
• u q
• p

u u v
V
v u v
V

61
Mutation Balance
Equilibrium Freq. (A)
(fixed)
v u v
V
V
(equilibrium) p

0.00001
(variable)
u v
62
Selection - Mutation Balance

• Most mutations deleterious
• Selection acts to remove deleterious alleles
• New mutations created continuously
• Balance - rate mutations added
• - rate selection removes
• q equilibrium frequency of deleterious
• 
  allele

v
63
Selection - Mutation Balance

• A1 dominant, A2 recessive deleterious mutation
• w11 w12 1 w22 1 - s m
  mutation
• 
  rate
• q Ö

s selection coefficient (lethal s 1)
m
v
s
64
Selection - Mutation Balance
m

• q Ö
• s low and high then q high
• s high and low then q low
• if s 1 then q Ö m
• (lethal)

v
s
v
m
v
m
65
Selection Mutation Balance
? 1.0 x 10-6
v
m
v
q Ö
s
Strong (lethal)
(selection)
weak
66
Selection - Mutation Balance

• Human genetic diseases
• Cystic fibrosis (recessive allele c)
• f(cc) 1/2500 0.0004 q2 s
  1(lethal)
• q
  .02
• q Ö

m
m 0.0004
v
s
67
Selection - Mutation Balance

• Mutation - selection balance ?

m 0.0004 unusually high Assumptions
incorrect ??? - selection scheme (Fitness
of CC lt Cc?) - not in equilibrium ( f(c)
allele decreasing?) - genetic drift
increased f(c) allele?
68
Selection Migration Balance
Spatial varying fitness among genotypes -
different environments favour different alleles
in different populations - frequency of
the favoured allele will increase to fixation
(loss of unfavoured alleles) - gene flow
can introduce alleles removed by selection -
polymorphism (genetic variation) maintained by a
balance between selection (removing) and gene
flow (reintroducing)
69
Selection Migration Balance
Fig. 12.10
g gene flow
A2
width
Spatial varying fitness
Cline in allele frequency
70
Migration Selection Balance
Fig. 12.11
Low salinity
High salinity
Selection against ap94 allele. Polymorphism
maintained by gene flow
71
Maintenance of Genetic Variation

• Balance of gain and loss of alleles
• ? - balance of forward and reverse mutation
• ? - selection - mutation balance
• ? - selection - migration balance
• - heterozygote advantage
• - frequency-dependent selection

Selection
72
Heterozygote Advantage

• Directional selection - one allele or other fixed
• Selection favours heterozygotes (heterosis
• 
  overdominance)
• A1A2 maintains both alleles
• A1A2 X A1A2 1A1A1 2 A1A2
  1A2A2

73
Selection FavouringHeterozygotes

• Genotype A1A1 A1A2
  A2A2
• p2 2pq
  q2
• Fitness(w) w11 w12
  w22
• 1 - s 1
  1 - t
• w12 gt w11, w22 if s gt 0 and
  t gt 0

74
Selection FavouringHeterozygotes

• Equilibrium
• q
  p
• if t 0 q 1.0 (A2
  dominant)
• if s 0 q 0.0 (A1
  dominant)

t
s
v
v
s t
s t
v
v
75
Selection FavouringHeterozygotes

• Example
• t 0.80
• s 0.90
• Fitness

w11 w12 w22 1 - .90
1 1 - .80 0.10
1 0.20
76
v
w11 w12 w22 1 - .90
1 1 - .80
q 0.33
v
p .66
77
Box 5.8
stable equilibrium

-
p
78
PopulationMean Fitness ( w )

• w p2 w11 2pq w12 q2
  w22

A1A1 1.0
Directional Selection
79
Heterozygote advantage
p .66
80
, 0, -
gt 0
p
81
Selection FavouringHeterozygotes

• Sickle-cell anemia
• hemoglobin gene w
• AA normal 0.9
• AS some sickle 1.0
• SS sickle 0.2
• favoured in the
• presence of malaria

82
Selection FavouringHeterozygotes

• Further information
• http//en.wikipedia.org/wiki/OverdominanceHeteroz
  ygote_advantage_and_sickle-cell_anemia

83
Sickle-cell allele frequency
Malaria Zone
84
Maintenance of Genetic Variation

• Balance of gain and loss of alleles
• ? - balance of forward and reverse mutation
• ? - selection - mutation balance
• ? - selection - migration balance
• ? - heterozygote advantage
• - frequency-dependent selection

Selection