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 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)
• Selection Ch 12 (pp.
  273 282)
• Genetic Drift Ch 10 (pp.
  226 231)
• 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

• 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
• 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

• Population genetics
• The organization of genetic variation within and
  between populations
• - gene pool
• - deme (population)
• - panmictic unit (random mating)
• - measures of genetic variation

7

• Genotype frequencies
• A1A1 D n1/N n1
• A1A2 H n2/N n2
• A2A2 R n3/N n3
• 
  N
• Allele frequencies
• freq. (A1 ) p D
  ½ H
• freq. (A2 ) q R
  ½ H

8
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

9
H 2pq
10

• Protein
• Electrophoresis (Fig. 9.13) DNA
  variation

Measuring genetic variation in natural populations
homozygote
AB AA BB BB
heterozygote
Co-dominant alleles
11
Summary

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

12

• 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

13
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

14
H-W. Theorem

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

15
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

16
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)

17
Migration

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

18
Loci
Mussel Planktonic larval stage High
potential gene flow
0 20 60 600 610
615 3000 KM
Km
19
Silene acaulis
Limited seed dispersal
20
Limited gene flow by pollen (Wind pollinated corn)
Fig. 9.29
21
Hardy-Weinberg

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

22
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)

23
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
24
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
25
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

26
Inbred Population

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

27
Inbreeding Coefficient F

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

28
F calculated from pedigree
8 alleles
Non-inbred mating
No chance of inheriting the same allele by descent
29
Inbred mating ( half-sibs)
F calculated from pedigree
Half Sibs
30
F calculated from pedigree
A
½
½
alleles
Half Sibs
½
½
Prob. ½ ½ ½ ½ 1/16
31
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)
32
F 1/4
F 1/8
Half-sibs
F 1/16
Cousins
F 1/32
F 1/64
33
Increase in F with inbreeding
34
Inbreeding Depression

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

35
Inbreeding Depression

• d d
• d d
• d
• d

X
Same chromosomes by descent
d deleterious recessive allele
Inbred progeny
36
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
37
Children of cousin marriages 1/16 inbred
consequences?

• Genetic counseling
• Genetic testing

38
Mortality rate of children from cousin marriages
mortality
http//www.cousincouples.com/?pagefacts
39
Children from cousins (F 1/16)
Different Human Populations
Equal mortality
40
Inbreeding Depression
Corn Yield
F
41
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
42
Inbreeding Depression

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

43
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
44
Golden lion Tamarin endangered Brazilian monkey
Outcrossing scheme to avoid inbreeding
Fig. 9.11
45
Geoff Winsor, BSc Honours
Daphnia pulex (water flea)
Clone 1
Clone 2
Clone 3
Most normally outbreeding species show
inbreeding depression
46
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

47
Finite Population Size

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

48
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

49
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)

50
N 200 individuals (6 populations)
q f(A2)
51
N 10 individuals (6 populations)
q f(A2)
52
Simulation Programs
AlleleA1 http//faculty.washington.edu/herronjc/S
oftwareFolder/AlleleA1.html
Variables Fitness Mutation Migration Pop.
Size Inbreeding
N 10
53
Frequency of Heterozygotes
N 10
54
N 100
55
Frequency of Heterozygotes
Why doesnt the Freq. increase above 0.5 ?
N 100
56
Online Simulations
Lab 2 exercise http//darwin.eeb.uconn.edu/simul
ations/simulations.html
57
Consequences of FinitePopulation Size

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

58
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)

59
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
  

60
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

61
Newfoundland
Quebec
Iceland
Taking advantage of founder effect for Gene
discovery high freq. of
disease alleles pedigree
information
62
Population Differentiation

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

63
Population Structure

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

64
Genetic Differentiation

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

65
Increased genetic distance with increased
geographic distance between populations
Genetic Distance
Geographic Distance
66
Correlation between genetic and geographic
distance among populations of Gyliotrachela
hungerfordiana from West-Malaysian limestone
hills.
67
Genetic Differentiation

• Examples pattern of genetic differentiation

D
Kerri Anstey, BSc Honours
68
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

69
Genetic Differentiationdue to genetic drift

• Fst 0
  1.0
• N population size
• m proportion of the pop. that are
• 
  migrants

1
4Nm 1
70
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)
71
Number of Migrants

• -
• Nm Estimated number of migrants per
• 
  generation

1
1
Nm
4Fst
4
Fst observed genetic differentiation
72
Nm Fst
73
Population Genetics

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

74
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