Biology 2900 Principles of Evolution and Systematics

1
Biology 2900Principles of Evolutionand
Systematics

• Dr. David Innes
• Dr. Ted Miller
• Jennifer Gosse
• Valerie Power

2
Announcements

• Lab 1 Group 2 Wed lab. Make up Thursday 2 pm or
  7 10 pm
• Lab 2 (Group 1) handout ? print from course web
  page
• Do the population genetics review
  before Lab.
• Readings for Lab. 2 (Futuyma)
• HWE Ch 9
  (pp. 190 - 197)
• Genetic Drift Ch 10 (pp.
  226 231)
• Selection Ch 12
  (pp. 273 282)
• Gene Flow Ch 12 (pp.
  278 280)
• http//www.mun.ca/biology/dinnes/B2900/B2900.html

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
Relax Assumptions

• Processes that can change allele and/or genotype
  frequencies
• - Mutation
• - Migration
• - Non-random mating
• - Finite population size
• - Selection ? differential survival,
• fecundity etc. among genotypes

6
Hardy-Weinberg

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

7
Finite Population Size

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

8
Consequences of FinitePopulation Size

• - q random (non-direction) , 0, -
• - random genetic drift
• - occurs in all pops., especially small pops.
• - ultimate result loss q 0
• fixation q
  1.0
• (loss of genetic variation eg. heterozygosity)

9
N 200 individuals (6 populations)
q f(A2)
10
N 10 individuals (6 populations)
q f(A2)
11
N 10
N 100
Frequency of Heterozygotes
Frequency of Heterozygotes
500 generations
12
Online Simulations
Lab 2 exercise http//darwin.eeb.uconn.edu/simul
ations/simulations.html
13
Consequences of FinitePopulation Size

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

14
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

15
Founder Effect

• Isolated human populations
• Amish population (Pennsylvania)
• N 200 (18th
  century)
• Ellis-van Creveld dwarfism q
  0.07
• Most populations
  q 0.001
• not due to selection or mutation
• http//www.ncbi.nlm.nih.gov/SCIENCE96/gene.cgi?EVC
  

16
Founder Effect in Newfoundland

• High incidence of several congenital illnesses
• - rare forms of cancer
• - heart disease
• - hearing loss
• - psoriasis
• - Bardet Biedl Syndrome (BBS)
• (leads to obesity and
  blindness)
• 1 in 17,000 Newfoundlanders
• 1 in 160,000 General Population

17
Newfoundland
Quebec
Iceland
Taking advantage of founder effect for Gene
discovery high freq. of
disease alleles pedigree
information
18
Population Differentiation

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

19
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
20
Genetic Differentiation

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

21
Increased genetic distance with increased
geographic distance between populations
Genetic Distance
Geographic Distance
22
Genetic distance
Correlation between genetic and geographic
distance among populations of Gyliotrachela
hungerfordiana from West-Malaysian limestone
hills.
Land Snail
23
Genetic Differentiation

• Examples pattern of genetic differentiation

D
Kerri Anstey, BSc Honours
24
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

25
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
26
Different
Island Model For
any population of size N A small number of
migrants can offset differentiation by genetic
drift

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

Fst
Same
Number of migrants per generation (Nm)
27
Number of Migrants

• -
• Nm Estimated number of migrants per
• 
  generation

1
1
Nm
4Fst
4
Fst observed genetic differentiation
28
Nm Fst
29
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)
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Population StructureBreeding population
Gene Flow
A
B
C
31
Population Genetics

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

32
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

33
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)

34
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

35
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
36
Selection

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

37
Selection

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

U
Umax
38
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
39
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

40
w111.0 w12 .75 w22 .25
Freq(A1) allele
Directional Selection
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Initial p 0.40
A1A1 A1A2
A2A2
42
? p rate of change of allele freq.
Maximum rate
43
w p2 w11 2pq w12 q2 w22
44
Strength of Selection
Directional selection
45
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
46
Selection

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

47
Fig. 12.6
Fitness 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
48
Examples of Selection

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

49
Cepaea nemoralis
Snail
Butterflies
Peppered moth Biston betularia
50
Peppered Moth
Cryptic coloration
51
Decline in melanic form as air pollution declines
Fig. 12.25
http//www.biologycorner.com/worksheets/pepperedmo
th.html
52
Mytilus edulis
Cepaea nemoralis
53
Examples of Selection

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

54
Protein Electrophoresis
Pgm
Origin
55
Examples of Selection

• 1. Laboratory natural selection experiments

56
Directional selection
AdhF allele
57
Examples of Selection

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

58
Geographic clines

• Migration history
• mixing of alleles
• (neutral)

59
Six enzyme loci
insecticide
none
60
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 ?

61
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

62
Number of insecticide resistance pest species
Fig. 12.9
Total
63
Fig. 12.8
Rat poison
64
Selection for Antibiotic Resistance

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

65
Genetic Variation

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

66
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

67
Mutation Balance

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

u u v
V
v u v
V

68
Mutation Balance
Equil. Freq. (A)
v u v
V
V
(equilibrium) p

0.00001
u v
69
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
70
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
71
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
72
Selection Mutation Balance
? 1.0 x 10-6
v
m
v
q Ö
s
Strong (lethal)
(selection)
weak
73
Selection - Mutation Balance

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

m
m 0.0004
v
s
74
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?
75
Migration - Selection Balance
Fig. 12.11
High salinity
Low salinity
Selection against ap94 allele maintained by gene
flow
76
Maintenance of Genetic Variation

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