Biology 2900 Principles of Evolution and Systematics

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Biology 2900Principles of Evolutionand
Systematics

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

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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

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Topics

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

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

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• 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
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Mutation and Genetic Variation Chapters 8 and 9

• Mutations are the raw material of evolution
• Mutation?genetic variation?natural selection
• 
  Evolution

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

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Simple Population model

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

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

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Genotype Frequencies

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

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• 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

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

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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)

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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

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H 2pq
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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)
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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?

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• Protein
• Electrophoresis (Fig. 9.13) DNA
  variation

Measuring genetic variation in natural populations
homozygote
AB AA BB BB
heterozygote
Co-dominant alleles
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Alcohol dehydrogenase
Fig. 9.25
Drosophila
Genetic variation 2 alleles AdhS AdhF slow
fast
ADH breaks down ethanol
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Lactate dehydrogenase
Fundulus heteroclitus
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Genetic Variation
Vertebrates 648 spp.
Frequency
Invertebrates 370 spp.
Plants 785 spp.
Heterozygosity
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Summary

• High genetic diversity observed in natural
• populations
• What processes maintain genetic diversity ?
• What role does Natural Selection play?

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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

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

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One Generation of Random Mating

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

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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

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Proof of Hardy-Weinberg

• Gamete pool combine at random
• sperm
• p q
• p p2 pq
• eggs
• q pq q2

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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

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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
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• 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

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H-W. Theorem

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

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Fig. 9.4
(Not in HW proportions)
p D H/2
q R H/2
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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
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Fig. 9.4
(D) Offspring genotype frequencies
(E) Offspring allele frequencies
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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

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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

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Fig. 9.5
Hardy-Weinberg genotype frequencies as a function
of allele frequencies
p2
H Heterozygosity
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Hardy-Weinberg

• Equilibrium Allele and genotype
• frequencies do not change across generations
• Assuming - random mating
• - large population size
• - no selection
• - no migration
• - no mutation

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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)

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Mutation

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

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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

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Mutation

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

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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
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u 2 x 10-6
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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)

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Migration

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

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

Lake Erie
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Migration
ISLAND
Mainland (Continent)

• Migration gene flow (migration
• 
  survival mating)

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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

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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

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

- connects physically separated populations
- determines degree of
panmixia - isolation by distance (dispersal
ability)
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Hardy-Weinberg

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

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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)

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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
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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
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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

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Inbred Population

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

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Inbreeding Coefficient F

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

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F calculated from pedigree
8 alleles
Non-inbred mating
No chance of inheriting the same allele by descent
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Inbred mating ( half-sibs)
F calculated from pedigree
Half Sibs
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F calculated from pedigree
A
½
½
alleles
Half Sibs
½
½
Prob. ½ ½ ½ ½ 1/16
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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)
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F 1/4
F 1/8
Half-sibs
F 1/16
Cousins
F 1/32
F 1/64
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Increase in F with inbreeding
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Inbreeding Depression

• Loss of fitness on inbreeding
• Inbreeding depression
• recessive deleterious alleles exposed

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Inbreeding Depression

• d d
• d d
• d
• d

X
Same chromosomes by descent
d deleterious recessive allele
Inbred progeny
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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
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Children of cousin marriages 1/16 inbred
consequences?

• Genetic counseling
• Genetic testing

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Mortality rate of children from cousin marriages
mortality
http//www.cousincouples.com/?pagefacts
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Different Human Populations
Children from cousins (F 1/16)
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Inbreeding Depression
Corn Yield
F
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Inbreeding in Small Pops.

• F increases faster in
  small pops.
• despite
  random mating

Prob. of 2 gametes with identical alleles equals
1
2N
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Inbreeding Depression

• - Genetic diseases (genetic load)
• - Conservation genetics (Minimum
• viable populations)
• - rare species
• - zoos
• - Avoidance of inbreeding
• - mating system, dispersal

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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
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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