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Biology 2900 Principles of Evolution and Systematics

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in gamete pool. f(A1 ) = p f(A2 ) = q for both sexes. Proof of Hardy-Weinberg ... of 2 gametes with identical alleles equals: Inbreeding Depression ... – PowerPoint PPT presentation

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Title: Biology 2900 Principles of Evolution and Systematics


1
Biology 2900Principles of Evolutionand
Systematics
  • Dr. David Innes
  • Dr. Ted Miller
  • Jennifer Gosse
  • Valerie Power

2
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

3
Topics
  • The origin of genetic variation (Ch. 8)
  • Population genetics gene frequencies
  • within populations (Ch. 9)

4
  • Evolution a change over time of the proportions
    of individual organisms differing genetically in
    one or more traits

5
  • Evolution by Natural Selection
  • 1. Within species variation (Lab 1)
  • 2. Some variations inherited by offspring
  • 3. Some individuals more successful at surviving
    and reproducing than others
  • 4. Survival and reproduction not random

No Genetic Variation, No Evolution
6
Mutation and Genetic Variation Chapters 8 and 9
  • Mutations are the raw material of evolution
  • Mutation?genetic variation?natural selection

  • Evolution

7
  • Population genetics
  • - gene pool
  • - deme (population)
  • - panmictic unit (random mating)
  • - measures of genetic variation

8
Simple Population model
  • - single locus
  • - autosomal
  • - diploid
  • - 2 alleles (A , a)
  • - co-dominance (phenotype genotype)
  • AA Aa
    aa

9
  • Quantifying Genetic Variation
  • Sample size N n1 n2 n3
  • number of AA n1
  • Aa n2
  • aa n3

10
Genotype Frequencies
  • f(AA) n1 /N
  • f(Aa) n2 /N
  • f(aa) n3 /N

11
  • Allele frequencies AA n1

  • Aa n2

  • aa n3
  • f(A) (2n1 n2 ) (n1 ½ n2 ) p
  • 2N N
  • f(a) (2n3 n2 ) (n3 ½ n2 ) q
  • 2N N

12
  • Allele or gene frequency
  • f(A) p f(a) q

13
Genetic Variability
  • p 1.0 , q 0.0 no genetic variation (1
    allele)
  • p 0.0 , q 1.0 (monomorphic)
  • 0.0 lt p lt 1.0 genetic variation (gt 1 allele)
  • 0.0 lt q lt 1.0 (polymorphic)

14
Genetic Variability
  • Measures of genetic variability
  • 1. polymorphism ( of loci with gt 1
    allele)
  • 2. Number of alleles
  • 3. Heterozygosity Frequency of
    heterozygotes
  • H
    2pq

15
H 2pq
16
Example
  • Genotypes
    allele freq.
  • AA 42 f(A) p (4223)/100 .65
  • Aa 46
  • aa 12 f(a) q (1223)/100 .35
  • 100

H 2pq 0.46 (heterozygosity)
17
Genetic Variation in Natural Populations
  • How much genetic variation is there in natural
    populations?
  • What determines the level and pattern of genetic
    variation ?
  • 3. What role does natural selection play?

18
  • Protein
  • Electrophoresis (Fig. 9.13) DNA
    variation

Measuring genetic variation in natural populations
homozygote
AB AA BB BB
heterozygote
Co-dominant alleles
19
Alcohol dehydrogenase
Fig. 9.25
Drosophila
Genetic variation 2 alleles AdhS AdhF slow
fast
ADH breaks down ethanol
20
Lactate dehydrogenase
Fundulus heteroclitus
21
Genetic Variation
Vertebrates 648 spp.
Frequency
Invertebrates 370 spp.
Plants 785 spp.
Heterozygosity
22
Summary
  • High genetic diversity observed in natural
  • populations
  • What processes maintain genetic diversity ?
  • What role does Natural Selection play?

23
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

24
Fig. 9.3 Population gene pool
25
  • Genotype frequencies
  • A1A1 D
  • A1A2 H
  • A2A2 R
  • Allele frequencies
  • freq. (A1 ) p D
    ½ H
  • freq. (A2 ) q R
    ½ H

26
One Generation of Random Mating
  • - Random union of gametes
  • - allele freq. freq. in gamete pool
  • f(A1 ) p f(A2 ) q for both sexes

27
Proof of Hardy-Weinberg
  • Generation 1 A1A1 A1A2 A2A2 Total
  • 0.36 0.48 0.16
    1.00
  • f(A1) p 0.6
  • f(A2) q 0.4
  • Gamete pool sperm 0.6 A1 0.4 A2
  • eggs 0.6 A1 0.4
    A2

28
Proof of Hardy-Weinberg
  • Gamete pool combine at random
  • sperm
  • p q
  • p p2 pq
  • eggs
  • q pq q2

29
Proof of Hardy-Weinberg
  • Gamete pool combine at random
  • sperm
  • 0.6 A1 0.4 A2
  • 0.6 A1 0.36 A1A1 0.24 A1A2
  • eggs
  • 0.4 A2 0.24 A1A2 0.16 A2A2

30
Proof of Hardy-Weinberg
  • Generation 2 A1A1 A1A2 A2A2 total
  • 0.36 0.48 0.16
    1.00
  • f(A1 ) p 0.6
  • f(A2 ) q 0.4
  • A1A1 A1A2 A2A2
  • p2 2pq q2
    1

Allele frequencies
Genotype frequencies
31
  • Hardy-Weinberg Theorem
  • Relationship between allele
    frequencies and genotype frequencies
  • f(A1) p, f(A2) q
  • Freq. (A1A1) p2
  • Freq. (A1A2) 2pq HW proportions
  • Freq. (A2A2) q2

32
H-W. Theorem
  • - no change in allele freq. between generations
  • (equilibrium)
  • - genotype proportions reached in one generation
    of random mating ( p2 2pq q2)


33
Fig. 9.4
(Not in HW proportions)
p D H/2
q R H/2
34
Example
  • Gen A1A1 A1A2 A2A2 p q
  • 1 .4 .4 .2 .6 .4
  • 2 .36 .48 .16 .6 .4
  • p2 2pq q2
  • HW genotype proportions restored after one
    generation of random mating

sperm
0.6 A1 0.4 A2
0.6 A1 0.36 A1A1 0.24 A1A2
eggs 0.4 A2 0.24 A1A2 0.16 A2A2
35
Fig. 9.4
(D) Offspring genotype frequencies
(E) Offspring allele frequencies
36
Calculate allele frequencies
Silene acaulis
SS SF FF
  • Pgi
  • Genotypes freq (S) 104 ½(44)
  • SS 104 151
  • SF 44 0.834
  • FF 3 freq (F) 1
    0.834
  • Total 151 0.166

37
Testing for HWE
  • S F
  • p 0.834 q 0.166
  • Expected
    Observed
  • SS p2 151 105.03 104
  • SF 2pq 151 41.81 44
  • FF q2 151 4.16
    3

  • X2 0.44 ns
  • Conclusion No deviation from HWE

38
Fig. 9.5
Hardy-Weinberg genotype frequencies as a function
of allele frequencies
p2
H Heterozygosity
39
Hardy-Weinberg
  • Equilibrium Allele and genotype
  • frequencies do not change across generations
  • Assuming - random mating
  • - large population size
  • - no selection
  • - no migration
  • - no mutation

40
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
  • ( Lab. 2)

41
Mutation
  • How effective is mutation at changing allele and
    genotype frequencies over time ?

42
Mutation
  • Gen. 1
  • AA Aa aa p
    q
  • 0.81 0.18 0.01 0.9
    0.1
  • Mutation u 0.0001 A?a
  • A 0.90 (0.0001)(0.9) 0.89991
  • a 0.10 (0.0001)(0.9) 0.10009


43
Mutation
  • Gen. 2
  • AA Aa aa
  • 0.80984 0.18014 0.01002
  • Very little change in allele and genotype
  • frequencies


44
Mutation
  • one-way (irreversible)
  • A a Rate u per
    generation
  • u 2 x 10-6
    0.000002
  • f(A) p
  • p p - up p p - p
  • p - up

p 0 ?
0 - up
45
u 2 x 10-6
46
Mutation
  • - Ultimate source of genetic variation
  • - Not a potent factor in evolution by itself
  • But,
  • Mutation Selection a very potent factor in
    evolution (more later)


47
Migration
  • How effective is migration for changing allele
    frequencies in a population?

48
Lizard Island
Islands isolation,
colonization, migration
49
  • Islands
  • different sizes
  • diff. distances from mainland
  • natural laboratories
  • Examples
  • Hawaii
  • Galapagos

Lake Erie
50
Migration
ISLAND
Mainland (Continent)
  • Migration gene flow (migration

  • survival mating)

51
Migration (one way)
  • A1 , A2 alleles Island
    Continent
  • p q 1.0 pI
    pC
  • Next generation pI pI (1 - m) m pC
  • Island pop. receives a proportion (m) of its
    genes from continent each generation
  • m proportion of genes from continent
    population
  • 1-m proportion of genes from island
    population

52
Migration
  • Next generation pI pI (1 - m) m pC
  • pI pI - pI
  • pI
    m(pC - pI)
  • Equilibrium pI 0 pI
    pC
  • Migration homogenizes allele frequencies

53
Mussel life history
Example
Spat
Settlement
Planktonic larvae
54
(No Transcript)
55
0 20 60 600 610
615 3000 KM
Km
56
Migration

- connects physically separated populations
- determines degree of
panmixia - isolation by distance (dispersal
ability)
57
Hardy-Weinberg
  • Relax Assumptions
  • ? - Mutation
  • ? - Migration
  • - Non-random mating
  • - Finite population size
  • - Selection - differential survival,
  • fecundity etc. among genotypes

58
Non-Random Mating
  • Inbreeding (mating among relatives)
  • - increased freq. of homozygotes
  • - decreased freq. of heterozygotes
  • Self-fertilization - most extreme form
  • of inbreeding (many plants can self)

59
Selfing
Aa x Aa
  • Gen. AA Aa aa N

  • AA Aa aa
  • 0 20 40 20
    80 10 20 10
  • 1 2010 20 2010 80
  • Each individual leaves one offspring

¼
¼
½
3/8
3/8
2/8
60
Selfing
  • Gen. AA Aa aa q
    H F
  • 0 1/4 1/2 1/4
    1/2 1/2 0
  • 1 3/8 1/4 3/8
    1/2 1/4 1/2
  • 1/2 0 1/2
    1/2 0 1

8
61
Inbreeding Coefficient F
  • The amount of heterozygosity lost due to

  • inbreeding
  • F He - Ho
    Ho obs
  • He
    He exp 2pq
  • example
  • AA Aa aa p q
  • obs .20 .40 .40 .4 .6
  • exp .16 .48 .36 .4 .6
    F .167

62
Inbred Population
  • AA Aa
    aa
  • p2 Fpq 2pq - 2Fpq q2
    Fpq
  • F 0 no inbreeding F 1 completely
    inbred

63
Inbreeding Coefficient F
  • F probability 2 alleles in a homozygote are
  • identical by descent
  • - Calculate F from pedigree
  • - Inbreeding increases frequency of

  • homozygotes

64
F calculated from pedigree
8 alleles
Non-inbred mating
No chance of inheriting the same allele by descent
65
Inbred mating ( half-sibs)
F calculated from pedigree
Half Sibs
66
F calculated from pedigree
A
½
½
alleles
Half Sibs
½
½
Prob. ½ ½ ½ ½ 1/16
67
F calculated from pedigree
A
B
½
½
alleles
Half Sibs
½
½
Prob. ½ ½ ½ ½ 1/16
Prob. ½ ½ ½ ½ 1/16
F Prob. of A or B 1/16 1/16 1/8
(progeny from a half sib mating)
68
F 1/4
F 1/8
Half-sibs
F 1/16
Cousins
F 1/32
F 1/64
69
Increase in F with inbreeding
70
Inbreeding Depression
  • Loss of fitness on inbreeding
  • Inbreeding depression
  • recessive deleterious alleles exposed

71
Inbreeding Depression
  • d d
  • d d
  • d
  • d

X
Same chromosomes by descent
d deleterious recessive allele
Inbred progeny
72
Wild Drosophila pseudoobscura Chromosome 2
Fig. 9.9
(For whole chromosome)
Lower viability indicates the presence of
recessive deleterious alleles
Natural populations carry a genetic load of
deleterious alleles
73
Children of cousin marriages 1/16 inbred
consequences?
  • Genetic counseling
  • Genetic testing

74
Mortality rate of children from cousin marriages
mortality
http//www.cousincouples.com/?pagefacts
75
Different Human Populations
Children from cousins (F 1/16)
76
Inbreeding Depression
Corn Yield
F
77
Inbreeding in Small Pops.
  • F increases faster in
    small pops.
  • despite
    random mating

Prob. of 2 gametes with identical alleles equals
1
2N
78
Inbreeding Depression
  • - Genetic diseases (genetic load)
  • - Conservation genetics (Minimum
  • viable populations)
  • - rare species
  • - zoos
  • - Avoidance of inbreeding
  • - mating system, dispersal

79
Lion populations Genetic variation and
reproduction
Characteristics Tanzania 1
Tanzania 2 India Genetic Properties
Heterozygosity () 3.1
1.5 0.0 Reproductive Measures
Sperm Count 34
25 3 abnormal sperm
25 51
66 of Motile sperm 228
236 45
80
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
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