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Lecture 11: Genetic Drift and
Effective Population Size
October 1, 2012
Last Time
Introduction to genetic drift
Fisher-Wright model of
genetic drift
Diffusion model of drift
Effects within and among
subpopulations
Simple Model of Genetic Drift
 Many independent subpopulations
 Subpopulations are of constant size
 Random mating within subpopulations
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Effects of Drift
 Within subpopulations
 Changes allele frequencies
 Degrades diversity
 Reduces variance
 Does not cause deviations from HWE
 Among subpopulations (if there are many)
 Does NOT change allele frequencies
 Does NOT degrade diversity
 Increases variance in allele frequencies
 Causes a deficiency of heterozygotes compared to HardyWeinberg expectations (if the existence of subpopulations is
ignored) (to be covered in more detail later)
Today
Interactions of drift and selection
Effective population size
Exams!
Effects of Drift
Simulation of 4 subpopulations with 20 individuals, 2 alleles
 Random
changes
through time
 Fixation or loss
of alleles
 Little change in
mean frequency
 Increased
variance among
subpopulations
Example: Drift and Flour Beetle Color
N=10
N=20
N=50
N=100
Conner and Hartl 2004
 Tribolium castaneum
experiment with lab
populations of different
sizes
 Frequency of body color
polymorphisms: single
locus, black, red, brown
 Why does frequency of
wild-type allele increase
over time?
 Why does this depend on
population size?
Effects of Selection on Allele Frequency
Distributions
s=0.1, h=0.5
No Selection
N=20
 Selection pushes A1 toward fixation
 A2 still becomes fixed by chance 3.1% of the time
Genetic drift versus directional selection
s=0.1,h=0.5, p0=0.5
 Drift eventually leads to
fixation and loss of alleles
 Drift and selection
combined push fit alleles to
fixation more quickly than
drift or selection alone
 Some “unfit” alleles do
become fixed
 What happens
without drift?
 No populations are
fixed for A1 after
20 generations
 How long until these
become fixed?
Fixation as a Function of Ns and Starting Allele Frequency
N=100, s=0.25
N=10,
s=0.25
 Drift can
counter
selection in
very small
populations
 Problem 4 in
Wednesday’s
lab exercise
contrasts two
cases that fall
on the middle
curve
Combined Effects of Drift and Selection
 Probability of fixation of a favorable allele will be a
function of initial allele frequency, selection coefficient,
heterozygous effect, and population size
 Favorable alleles won’t necessarily go to fixation when
drift is involved
 Drift reduces efficiency of selection in the sense that
unfavorable alleles may not be purged from population
 Favorable alleles do increase in frequency more quickly
when drift is involved over ALL subpopulations
 Can be simulated by allowing selection to alter allele
frequencies prior to effects of drift
Nuclear Genome Size
 Size of nuclear
genomes varies
tremendously among
organisms: C-value
paradox
 No association with
organismal complexity,
number of
chromosomes, or
number of genes
Arabidopsis thaliana
Poplar
Rice
Maize
Barley
Hexaploid wheat
Fritillaria (lilly family)
120 Mbp
460 Mbp
450 Mbp
2,500 Mbp
5,000 Mbp
16,000 Mbp
>87,000 Mbp
Noncoding DNA is part of Answer
Human: 3500 Mbp
Fugu: 365 Mbp
wheat ~ 80%
corn ~ 70%
barley ~
55%
opossum ~ 52%
Arabidopsis ~ 14%
pufferfish ~
mouse ~
40%
rice ~ 35%
Drosophila ~
Human ~
Why is there so much variation in genome size?
Why do microbes have so much simpler genomes
than eukaryotes?
Why do trees have such huge genomes?
The importance of Genetic Drift and Selection in
Determining Genome Size
 Large effective
population sizes
mean selection more
effective at wiping
out variations with
even minor effects
on fitness
Lynch and Conery 2004 Science 302:1401
 Transposable
elements and
introns eliminated
from finely-tuned
populations, persist
where drift can
overwhelm selection
Historical View on Drift
 Fisher
 Importance of selection in determining variation
 Selection should quickly homogenize populations (Classical view)
 Genetic drift is noise that obscures effects of selection
 Wright
 Focused more on processes of genetic drift and gene flow
 Argued that diversity was likely to be quite high (Balance view)
 Controversy raged until advent of molecular markers
showed diversity was quite high
 Neutral theory revived controversy almost immediately
Effective Population Size
 Census population size often inappropriate for population
genetics calculations
 Breeding population size often smaller
 For genetic drift, historical events or nonrandom mating
patterns might reduce EFFECTIVE size of the population
 Effective Population Size is an ideal population of size N
in which all parents have an equal probability of being
the parents of any individual progeny.
also
 The size of a theoretically ideal population that would
have the same observed level of genetic drift
Factors Reducing Effective
Population Size
Unequal number of breeding males and
females
Unequal reproductive success
Changes in population size through time
Bottlenecks
Founder Effects
Effective Population Size: Effects of
Different Numbers of Males and Females
See Hedrick (2011)
page 213 for derivation
Table courtesy of K. Ritland
Effect of Proportion of Males in the
Population on Effective Population Size
Variation of population size in different
generations
 Small population size in one generation can cause drastic
reduction in diversity for many future generations
 Effect is approximated by harmonic mean
1 1 1
1
1
1
  

 ... 
N e t  N1 N 2 N3
Nt
Ne 
t
1
N
i



See Hedrick (2011)
page 219 for derivation
Effective Population Size: The bottleneck effect
“Alleles” in original population
“Alleles” remaining after bottleneck
The Founder effect
 Outlying populations
founded by a small
number of individuals
from source population
 Analogous to bottleneck
 Expect higher drift,
lower diversity in
outlying populations
Exam Issues
Genotype frequency versus allele frequency
(problem 2A, 7)
Meaning of the chi-square: larger than critical
value, reject null hypothesis
Recessive alleles and fitness (Multiple choice
problem 3; problem 5)