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BIOL2007 - EVOLUTION AT MORE THAN ONE GENE SO FAR  Evolution at a single locus

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BIOL2007 - EVOLUTION AT MORE THAN ONE GENE SO FAR  Evolution at a single locus  No interactions between genes  One gene - one trait REAL evolution: 10,000 - 100,000 genes producing mRNA linkage, a physical interaction mechanistic interactions in gene action. GENE INTERACTIONS

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slide1
BIOL2007 - EVOLUTION AT MORE THAN ONE GENE
  • SO FAR
  •  Evolution at a single locus
  •  No interactions between genes
  •  One gene - one trait
  • REAL evolution:
  • 10,000 - 100,000 genes producing mRNA
  • linkage, a physical interaction
  • mechanistic interactions in gene action
slide2
GENE INTERACTIONS
  • Pleiotropy
  • single gene affects multiple traits
  • Epistasis
  • multiple genes interact to affect a trait
  • multiple traits interact to produce fitness
  • therefore, natural selection for gene combinations
slide3
PLEIOTROPY AND EPISTASIS

e.g. polymorphic Batesian mimicry (palatable mimics)

papilio memnon a batesian mimic
Papilio memnon, a Batesian mimic

model

species

mimics

  • polymorphic Batesian mimicry
  • (palatable mimics):
  • frequency-dependent selection
  • for rare female-limited mimic
  • selection for coordinated
  • phenotype: gene combinations
  • In general, selection
  • is epistatic
  • acts on combinations of genes,
  • rather than single loci

male is

non-

mimetic

slide5
How do EPISTASIS AND PLEIOTROPY affect our view of evolution?

Gene interactions affect genotypic frequencies at many loci.

A/a (say) controls: forewing colour pattern

B/b controls: hindwing pattern

AB, ab combinations favoured at expense of Ab, aB

Inbreeding, selection, migration etc. cause a deviation from Hardy-Weinberg equilibrium at a single locus.

Similarly, selection (also migration, drift) can cause deviation from multilocus equilibria, and lead to prevalence of particular 2-locus combinations.

slide6
HOW DO WE MEASURE DISEQUILIBRIUM?

Expected gametic frequencies, if two genes are independently inherited and randomly combined, can be obtained from allelic frequencies in population:

Alleles A             a

allele pA 1-pA

freq.

B pB pApB (1-pA)pB

b 1-pB pA(1-pB) (1-pA)(1-pB)          Sum = 1

Non-randomness of the gametic frequencies means a deviation from two locus equilibrium

slide7
D is the gametic disequilibrium coefficient, or measure of deviation from 2 locus equilibrium:

Gametic  random

frequencies=    expectation   +  deviation

pAB=          pApB+ D

pAb=         pA(1-pB)- D

paB=(1-pA)pB - D

pab=(1-pA)(1-pB) + D

(Obviously, the sum pAB +pAb + paB + pab = 1 )

gametic disequilibrium,D

… also known as … linkage disequilibrium.

Also: D = pABpab - pAbpaB

slide8
STANDARDIZATION

Frequency of gamete AB, pAB= pApB+ D

D can vary between a maximum of +0.25 and a minimum of –0.25, but the range is often smaller if the frequency of alleles is not exactly 0.5.

To get an idea of the fraction of maximal possible disequilibrium, D is standardized in various ways. A common way is to use the correlation coefficient:

Can also useRAB2, which measures fraction of variance explained by relation between the two genes.

slide9
MORE THAN TWO LOCI

Even two loci: difficult maths

But real evolution: 10s or hundreds of loci affect traits.

Think of three loci, A,B,C,

3 possible 2-way gametic disequilibria: DAB,DAC,DBC… and one 3-way disequilibrium, DABC

(the effect of the DAB on C, of DAC on B etc.)

More loci, more multi-order disequilibria! Maths complex!

But, if D small, can assume few interactions between loci, and loci evolve independently; can use quantitative genetics approximations(see Kevin Fowler’s lectures next week)

Rest of this lecture: pairs of loci.

slide10
FACTORS THAT CAN DECREASE D

Recombination reduces disequilibrium

All deviation from Hardy-Weinberg is completely lost in 1 generation of random mating  

Deviation from 2 locus equilibrium more persistent. Recombination at a maximum of 50% of gametes.

D can therefore decline by at most 50% in each generation.

slide11
Disequilibrium actually declines by a fraction given bythe recombination rate) every generation

If c= % recombination, then:

Dt= Dt-1 (1 -c)

after many generations (t): Dt = D0(1 -c)t

slide12
Linkage

disequilibrium

RAB

slide13
FACTORS THAT CAN INCREASE D

A: Drift - random sampling of gametic frequencies, ~

e.g. Tightly linked markers: humans and Drosophila

At tightly linked sites, loss of D slow; drift, even in very large populations can therefore have an effect.

B:Selection - epistatic selection (for gene combinations)

For example: mimetic butterflies, Primula flower morphs…

C: Migration - mixing of populations with different frequencies

primula veris cowslip1
Primula veris – Cowslip

"Thrum" morph

"Pin" morph

primula veris cowslip2
Primula veris – Cowslip

"Thrum"

morph

"Pin" morph

primula veris cowslip3
Primula veris – Cowslip

"Thrum"

morph

"Pin" morph

slide19
"Thrum" morph

"Pin" morph

primula veris cowslip4
Primula veris – Cowslip

Supergene controls 3 major components:

Dominants are all 'thrum' form.

Style length: G – short style & short papillae on stigma surface

Pollen size: P – 'thrum' pollen ~ 1.5x dia 'pin' pollen

Anther position: A – 'thrum' anther position at mouth of corolla-tube

(Matings between pin & pin and thrum & thrum are also largely incompatible).

... occasional recombinants ('homostyles') occur naturally

Why are all thrum phenotypes dominant?

Why does each morph only have one allele at each gene (i.e. linkage disequilibrium complete, D≈1), and not recombinant phenotypes?

slide21
Human Leucocyte Antigens (HLA):
  • Part of Major Histocompatibility Complex (MHC), a large complex of loci involved in the immune system.
  • Involved in antibody/antigen reactions, involved in recognition, presents antigen to T-cell – for lysis
  • Highly polymorphic, involved in immunity to disease
  • Probable frequency-dependent selection for rare forms
  • Disequilibria over 10s-100s of millions of b.p., suggesting selection for combinations of loci.
slide22
USES for gametic disequilibria

1) Studying migration or dispersal

·between populations with different gene frequencies

·between species

Mixing will produce disequilibrium which will persist for some generations

slide23
2)Linkage mapping of loci when c = 0.01 or less difficult

For example, genetic disease locus D and marker loci m

In humans 1 million b.p. givesc≈ 1% = 1 map unit (centimorgan)

Can use “association studies” or “disequilibrium mapping”, to find disease genes and markers in populations. Humans: disequilibria significant between marker loci (e.g. microsatellites, SNPs) and between markers and genetic disease loci ~ 1Mb apart, due to drift

Linkage disequilibria useful for fine-scale gene mapping. D can quickly narrow search for the "candidate loci". Successfully used in recent studies. "Hapmap" project.

papilio memnon a batesian mimic1
Papilio memnon, a Batesian mimic

model

species

mimics

male is

non-mimetic

slide27
3) Human

mitochondrial DNA

recombination?

(now generally dis-

believed for humans, but is probable

in other species)

Awadalla et al.

Science 286: 2524-5

slide28
SUMMARY

Gene interactions: pleiotropy, epistasis

Evolution may affect frequencies of two- and more locus associations, as well as just gene frequencies.

Deviation from 2-locus equilibrium is known as gametic disequilibrium or linkage disequilibrium, measured by D

D is destroyed by recombination, c, so Dt= D0(1 -c)t

D can increased by selection, migration, drift

D is involved in maintaining 'supergenes'.

D can be used in linkage mapping, studies of migration in natural populations

READINGS:

Futuyma: Chapter 9: 205-207, Chapter 13: 303-304

Freeman & Herron: Chapter 7

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