lecture 11: genetic drift and effective population size october 1, 2012
TRANSCRIPT
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 Hardy-Weinberg expectations (if the existence of subpopulations is ignored) (to be covered in more detail later)
Effects of DriftSimulation 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 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?
Conner and Hartl 2004
N=10
N=20
N=50
N=100
Effects of Selection on Allele Frequency Distributions
No Selection
N=20
s=0.1, h=0.5
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?
Drift can counter selection in very small populations
Problem 4 in Wednesday’s lab exercise contrasts two cases that fall on the middle curve
N=10, s=0.25
N=100, s=0.25
Fixation as a Function of Ns and Starting Allele Frequency
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 120 MbpPoplar 460 MbpRice 450 Mbp Maize 2,500
Mbp Barley 5,000
MbpHexaploid wheat 16,000
MbpFritillaria (lilly family) >87,000
Mbp
opossum ~ 52% rice ~ 35%
Arabidopsis ~ 14% Drosophila ~ 15%
pufferfish ~ 2%
barley ~ 55%
wheat ~ 80% corn ~ 70%
Human ~ 45%
mouse ~ 40%
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
Transposable elements and introns eliminated from finely-tuned populations, persist where drift can overwhelm selection
Lynch and Conery 2004 Science 302:1401
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
Table courtesy of K. Ritland
Effective Population Size: Effects of Different Numbers of Males and Females
See Hedrick (2011) page 213 for
derivation
Small population size in one generation can cause drastic reduction in diversity for many future generations
Effect is approximated by harmonic mean
Variation of population size in different generations
i
e
N
tN
1
te NNNNtN
1...
11111
321
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