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Genetic Linkage
Two pops may have the sameallele frequencies but differentchromosome frequencies.
Conditions for Linkage Equilibrium(Two locus case)
1) Frequency of B is the same on chromosome A and a
2) Frequency of haplotypes AB, ab, Ab, aB can be calculated from allele frequencies A=p, a=q, B=t, and b=s.
f(AB) = pt f(ab) = qs f(Ab) = ps f(aB) = pt
3) Coefficient of linkage disequilibrium (D) = 0
f(AB) x f(ab) - f(Ab) x f(aB) = D
ps x qt - pt x qs = 0
(ranges from -0.25 to +0.25)
Hardy Weinberg Principle for Two Loci
Chromosome frequencies remain unchanged across generations if loci are in linkage equilibria.
If loci are in linkage disequilibria, the chromosome frequencies will move closer to linkage equilibrium each generation.
What Creates Linkage Disequilibrium in a Population?
selection, drift, and population admixture
Effects of Selection on Chromosome Frequencies
ab/ab = body size of value 10each additional A or B adds 1 valuepredators eat all individuals of size 12 or less
65.28%survive
65.28%survive
Freq a = (0.1536 + 0.1536) / .6528)/2
= 0.24
Freq b = (0.0576 + 0.0576) / .6528)/2
= 0.09
Freq ab = .24 x .09 = .02
however!
Locus A and B are in disequilibrium among the survivors
Genetic Drift, followed by selection can cause linkage disequilibrium
Admixture
Combination of Two Different Gene Pools
Recombination Breaks Down Linkage Disequilibria
The rate of decline in LD increases with r
LD declines over time (rate depending on r)
r = D sqrt(pqst)
Concept of Linkage
aA
B b
Meiosis
Law of Independent Assortment
AB
Ab
aB
ab
= 0.25
= 0.25
= 0.25
= 0.25
All allele combinations in gametes
equally probable
A a
B b
Meiosis
Probability of recombination = 0.5
AB
Ab
aB
ab
= 0.25
= 0.25
= 0.25
= 0.25
All allele combinations in gametes
equally probable
A a
B b Meiosis
Probability of recombination = 0.3
A aB b Meiosis
Probability of recombination = 0.1
AB
Ab
aB
ab
All allele combinations in gametes NOTequally probable
= 0.15
= 0.15
= 0.35
= 0.35
AB
Ab
aB
ab
= 0.05
= 0.05
= 0.45
= 0.45
Linked Loci
All allele combinations in gametes NOTequally probable
Concept: The closer two loci are on a chromosome, the lower the probability of recombination.
Why important?
(1) Affects rate that LD is broken down.
(2) Allows one to determine the linear order of genes on a chromosome (make a genome map).
(3) Maps allow for the localization of genes, mutant phenotypes, and QTL in the genome.
Selection hasan effect on
frequency of Balleles
Selection at a single locus affects other loci under LD
LD among 1504 markerLoci on HumanChromosome 22.(Dawson et al. 2002)
Time (generations)
Lin
kage
Dis
equi
libr
iaDecay of LD
Present level
For neutral alleles: Genetic drift is the primary evolutionarymechanism. So:
Indicates alleles at the locus may be under selection.
How does LD help identify genes that may be underpositive natural selection?
If LD is not detectable, indicates that an allele is old.Expect old and frequent alleles, or old and rare alleles,But do not expect young, high frequency alleles.
If LD is detectable, indicates that an allele is young.Expect magnitude of LD is proportional to the age of an allele.
G6PD polymorphismand deficiency
Countries with malariahave highest frequencyof a reduced-activity allele.
Characterized SNPs for G6PD locus of 230 men
Nine different G6PD alleles diagnosed by 11 SNPs
Sabeti et al., 2002
Typed each allele for 14 SNPs outside the G6PD locus
LD is higher for the G6PD-202A allele;suggests positive selection
Probabilitythat 2 randomlychosen “a” chromosomeshave the same snpsacross a physicaldistance
The Evolutionary Biology of Sex
Kiwi Milk weed aphid
There is Amazing Diversity in Reproductive Mode
BlueheadedWrasse
Sexual Reproduction Probably Evolved Early In Life
Dandelion
Taraxacum officinale
Bdelloid rotifer
Examples of parthenogenesis
What Mode of Reproduction is Better?
An asexual female will have 2x as many grandchildren!
Why Aren’t All Species Asexual?
Because asexual populations accumulate deleterious mutations
Termed: Muller’s Rachet
Possibly leads to extinction
None of the 444 cultures hadhigher fitness than the wild type
Evidence for Muller’s Ratchet: Andersson and Hughes (1996)
Barrett and Charlesworth, (1991)
Eichhornia paniculata
Flower number declined ina natural out crossingpopulation, and heterosiswas observed.
Flower number stayedrelatively constant ina naturally self-fertilizingpopulation
Recombination Breaks the Ratchet
Sex maybe advantageousbecause it can recreatefavorable multilocus genotypes
However, adaptation by this process is only faster in largepopulations
However, Suppression of Recombinationis Important in the Evolution
of Sex Chromosomes
Hypotheses for Short-Term Advantages of Sex
• Recombination allows repair of damaged DNA
• Genetically diverse progeny may outcompete asexual progeny
• Muller’s ratchet
• Deleterious mutations are more easily purged in sexual pops
• Rate of evolution is higher in large sexual populations
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