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Biology 2900 Principles of Evolution and Systematics

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Lab 2 (Group 1) handout print from course web page: ... Golden lion Tamarin endangered Brazilian monkey. Outcrossing scheme to avoid inbreeding ... – PowerPoint PPT presentation

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Title: Biology 2900 Principles of Evolution and Systematics


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

2
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

3
Evolution in the News
http//www.cbc.ca/quirks/archives/07-08/jan19.html
Audio Clip
4
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

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
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

8
  • 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

9
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

10
H-W. Theorem
  • - no change in allele freq. between generations
  • (equilibrium)
  • - genotype proportions reached in one generation
    of random mating ( p2 2pq q2)


11
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

12
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)


13
Migration
  • connects physically separated populations
  • migration homogenizes allele frequencies
  • - barriers to migration?limited gene flow
  • - defines randomly mating population

14
Loci
Mussel Planktonic larval stage High
potential gene flow
0 20 60 600 610
615 3000 KM
Km
15
Silene acaulis
Limited seed dispersal
16
Limited gene flow by pollen (Wind pollinated corn)
Fig. 9.29
17
Hardy-Weinberg
  • Relax Assumptions
  • ? - Mutation
  • ? - Migration
  • - Non-random mating
  • - Finite population size
  • - Selection - differential survival,
  • fecundity etc. among genotypes

18
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)

19
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
20
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
21
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

22
Inbred Population
  • AA Aa
    aa
  • p2 Fpq 2pq - 2Fpq q2
    Fpq
  • F 0 no inbreeding F 1 completely
    inbred

23
Inbreeding Coefficient F
  • F probability 2 alleles in a homozygote are
  • identical by descent
  • - Calculate F from pedigree
  • - Inbreeding increases frequency of

  • homozygotes

24
F calculated from pedigree
8 alleles
Non-inbred mating
No chance of inheriting the same allele by descent
25
F calculated from pedigree
Inbred mating ( half-sibs)
Half Sibs
26
F calculated from pedigree
A
½
½
alleles
Half Sibs
½
½
Prob. ½ ½ ½ ½ 1/16
27
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)
28
Inbreeding
F 1/4
F 1/8
Half-sibs
Cousins
F 1/16
F 1/32
F 1/64
29
Increase in F with inbreeding
30
Inbreeding Depression
  • Loss of fitness on inbreeding
  • Inbreeding depression
  • recessive deleterious alleles exposed

31
Inbreeding Depression
  • d d
  • d d
  • d
  • d

X
Same chromosomes by descent
d deleterious recessive allele
Inbred progeny
32
Mortality rate of children from cousin marriages
mortality
gt gt gt gt gt gt gt gt
http//www.cousincouples.com/?pagefacts
33
Children from cousins (F 1/16)
Different Human Populations
Equal mortality
34
Children of cousin marriages 1/16 inbred
consequences?
  • Genetic counseling
  • Genetic testing

35
Inbreeding Depression
Corn Yield
F
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
Geoff Winsor, BSc Honours
Daphnia pulex (water flea)
Clone 1
Clone 2
Clone 3
Most normally outbreeding species show
inbreeding depression
38
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
39
Inbreeding Depression
  • - Genetic diseases (genetic load)
  • - Conservation genetics (Minimum
  • viable populations)
  • - rare species
  • - zoos
  • - Avoidance of inbreeding
  • - mating system, dispersal

40
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
41
Golden lion Tamarin endangered Brazilian monkey
Outcrossing scheme to avoid inbreeding
Fig. 9.11
42
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

43
Finite Population Size
  • Introduces sampling error
  • allele proportions not transmitted
  • precisely between generations
  • sampling error increases with
  • decrease in population size

44
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

45
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)

46
Random Walk
Fig. 10.2
47
N 200 individuals (6 populations)
q f(A2)
48
N 10 individuals (6 populations)
q f(A2)
49
Simulation Programs
AlleleA1 http//faculty.washington.edu/herronjc/S
oftwareFolder/AlleleA1.html
Variables Fitness Mutation Migration Pop.
Size Inbreeding
N 10
50
Frequency of Heterozygotes
N 10
51
N 100
52
Frequency of Heterozygotes
Why doesnt the Freq. increase above 0.5 ?
N 100
53
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)
54
Consequences of FinitePopulation Size
  • Random drift of allele frequencies
  • Divergence of allele freq. among populations
  • Loss of genetic variation (heterozygosity)

55
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

56
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

57
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

58
Quebec
Newfoundland
Iceland
Taking advantage of founder effect for Gene
discovery high freq. of
disease alleles pedigree
information
59
Population Differentiation
  • Allele frequencies can diverge among
  • populations due to random processes
  • 1. Founder effect
  • 2. Random genetic
  • drift

60
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
61
Genetic Differentiation
  • D (genetic distance)
  • - allele frequency differences between
  • pairs of populations
  • Fst (fixation index)
  • - degree of genetic differentiation among a
    number of populations

62
Increased genetic distance with increased
geographic distance between populations
Genetic Distance
Geographic Distance
63
Genetic distance
Correlation between genetic and geographic
distance among populations of Gyliotrachela
hungerfordiana from West-Malaysian limestone
hills.
Land Snail
64
Genetic Differentiation
  • Examples pattern of genetic differentiation

D
Kerri Anstey, BSc Honours
65
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

66
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
67
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)
68
Number of Migrants
  • -
  • Nm Estimated number of migrants per

  • generation

1
1
Nm
4Fst
4
Fst observed genetic differentiation
69
Nm Fst
70
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)
71
Population StructureBreeding population
Gene Flow
A
B
C
72
Population Genetics
  • Genes in populations
  • - inbreeding
  • - genetic differentiation
  • - gene flow
  • Genetic structure Neighbourhood size
  • Size of breeding population

73
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
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