Biology 2900 Principles of Evolution and Systematics

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Biology 2900Principles of Evolutionand
Systematics

• Dr. David Innes
• Jennifer Gosse
• Valerie Power

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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

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Evolution in the News
http//www.cbc.ca/quirks/archives/07-08/jan19.html
Audio Clip
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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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• Evolution by Natural Selection
• 1. Within species variation
• 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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• Population genetics
• The organization of genetic variation within and
  between populations
• - gene pool
• - deme (population)
• - panmictic unit (random mating)
• - measures of genetic variation

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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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• 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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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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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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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

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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

• connects physically separated populations
• migration homogenizes allele frequencies
• - barriers to migration?limited gene flow
• - defines randomly mating population

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Loci
Mussel Planktonic larval stage High
potential gene flow
0 20 60 600 610
615 3000 KM
Km
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Silene acaulis
Limited seed dispersal
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Limited gene flow by pollen (Wind pollinated corn)
Fig. 9.29
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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

• 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

Aa x Aa
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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F calculated from pedigree
Inbred mating ( half-sibs)
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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Inbreeding
F 1/4
F 1/8
Half-sibs
Cousins
F 1/16
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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Mortality rate of children from cousin marriages
mortality
gt gt gt gt gt gt gt gt
http//www.cousincouples.com/?pagefacts
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Children from cousins (F 1/16)
Different Human Populations
Equal mortality
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Children of cousin marriages 1/16 inbred
consequences?

• Genetic counseling
• Genetic testing

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Inbreeding Depression
Corn Yield
F
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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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Geoff Winsor, BSc Honours
Daphnia pulex (water flea)
Clone 1
Clone 2
Clone 3
Most normally outbreeding species show
inbreeding depression
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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
N population size
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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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Golden lion Tamarin endangered Brazilian monkey
Outcrossing scheme to avoid inbreeding
Fig. 9.11
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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

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Finite Population Size

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

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Finite Population Size

• Example
• - Pop. Size 5 2N genes 10
• - 2 alleles H, T f(H) f(T) .5
• NEXT Generation
• H, T, T, H, H, T, H, H, T, H
• f(H) .6 f(T) .4

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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)

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Random Walk
Fig. 10.2
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N 200 individuals (6 populations)
q f(A2)
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N 10 individuals (6 populations)
q f(A2)
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Simulation Programs
AlleleA1 http//faculty.washington.edu/herronjc/S
oftwareFolder/AlleleA1.html
Variables Fitness Mutation Migration Pop.
Size Inbreeding
N 10
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Frequency of Heterozygotes
N 10
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N 100
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Frequency of Heterozygotes
Why doesnt the Freq. increase above 0.5 ?
N 100
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Online Simulations
Lab 2 exercise http//darwin.eeb.uconn.edu/simul
ations/simulations.html 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)
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Consequences of FinitePopulation Size

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

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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

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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
  

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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

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

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

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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
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Genetic Differentiation

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

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

• Examples pattern of genetic differentiation

D
Kerri Anstey, BSc Honours
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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

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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
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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)
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Number of Migrants

• -
• Nm Estimated number of migrants per
• 
  generation

1
1
Nm
4Fst
4
Fst observed genetic differentiation
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Nm Fst
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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
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Population Genetics

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

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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