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Gene flow

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Chapter 5/6. Gene flow. Gene Flow- The gain or loss ... Neutral theory of molecular evolution ... Molecular clock hypothesis. Expression. Molecular clock woes ... – PowerPoint PPT presentation

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Title: Gene flow


1
Chapter 5/6
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Gene flow
  • Gene Flow- The gain or loss of alleles from a
    population by the movement of individuals or
    gametes. Immigration or emigration
  • The two effects of gene flow
  • A. New genes can be introduced into a population
  • B. Gene flow between two populations will over
    time make them more similar.

3
Migration
  • Migration- i.e.gene flow cannot affect allele
    frequencies for an entire population(species) but
    it can effect frequencies for subpopulations
  • Colonization the process of movement into
    previously unoccupied lands (founder effect)
  • Migration is movement from one occupied area to
    another

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  • Models of migration
  • Island model - metapopulation split into islands
    of equal size N- which exchange genes under the
    same rate m.
  • Stepping-stone model - Adds geographic structure
    to the island model
  • Isolation by distance - genetic similarity
    related to distance.

Expression
9
Interplay among evolutionary forces
Mutation drift equilibrium- stable level of
genetic diversity reached when the rate at which
new variants are introduced by mutation is
balanced with the loss of drift.
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Reproductive success vs Ne
  • Wright Fisher model assumes that all parents have
    an equal chance of contributing to the next
    generation. This results in a poisson
    distribution of the number of offspring.
  • In reality there is tremendous variation in the
    contribution of individuals to the next
    generation
  • High variance in the number of offspring higher
    than expected under a poisson distribution.
  • Higher the reproductive variance the lower the Ne
    parental contributions are more and more
    unequal
  • Can be due to social causes.
  • Reproductive Variance can vary between sexes

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Effective population sizes of Different
genomes. Population of 2 , Male and Female 4 A
autosomes 3 X chromosomes 1 Y chromosome 1 mtDNA
genome mtDNA, Y chrom - 1/4 A X chromosome - 3/4
A
Expression
12
Population Subdivision and Ne
  • Most populations are not homogenous
  • Human mating is not random-
  • Involves conscious choice
  • Think of populations as subpopulations or demes
  • Population isolation leads to genetic
    differentiation

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Selection
  • Selection can also change allele frequencies
  • Differential reproduction of genotypes in
    succeeding generation.
  • Fitness
  • Viability - ability to survive to reproduce
  • Sexual selection - success in attracting a mate
  • Gamete selection - Ability to fertilize
  • Fecundity - number of progeny

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1. Directional Selection
  • Favors variants of one extreme.

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2. Balancing Selection
  • Acts upon extremes and favors the intermediate.

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3. Diversifying Selection
  • Favors variants of opposite extremes.

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Selection
  • Purifying selection (negative selection)-
    mutations which reduce your fitness are
    eliminated from population
  • Positive selection- mutations which increase your
    fitness are fixed in population
  • Codominant selection- selection where both
    alleles contribute to overall fitness
  • Balancing selection- the heterozygote is favored.
  • Frequency dependent selection-frequency of a
    genotype determines its fitness.

20
Expression
Codominant- selection of heterozygote and
homozygote fixes faster!
21
What type of selection?
  • Parameters allow us to determine what form of
    selection is acting on an allele in a population
  • Most new alleles are eliminated rather than fixed
  • As long as not deleterious allele can remain for
    a long time
  • Time to fix an advantageous allele is shorter
    than a neutral one
  • If selection is operating on diploid than s gt
    1/2Ne
  • If selection is operating on haploid than s gt
    2/Ne (1/4 the effective pop size!)

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Selection or drift determine the future of an
allele?
  • Remember drift affects smaller populations more
    than large ones
  • Drift vs selection depends
  • Ne
  • Selection coefficient
  • Type of selection
  • Frequency of the allele at t0

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Neutral theory of molecular evolution
  • Most polymorphisms and changes in allele
    frequencies from generation to generation are
    neutral- in that they have no affect on the
    individual or the population.
  • The polymorphisms that are present are subject to
    elimination and fixation at equal probability as
    they are neutral.
  • The rate of this has been assumed to be constant
    and linked to the rate of mutation in lineages.
  • Means that the genetic diversity between
    genes/populations could in theory be used to date
    the divergence of those lineages.
  • Molecular clock hypothesis

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Expression
25
Molecular clock woes
  • Different species have different mutation rates-
    thus cross comparisons are tricky
  • Lineage effects
  • Generation time hypothesis - males have more
    replication than females- can lead to bias in
    estimating times of divergence of genes say Y vs
    X vs autosomes.
  • Metabolic rate hypothesis

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III. Pedigree analysis.
Expression
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Chapter 6
  • Measuring genetic diversity

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Measuring nucleotide diversity
  • Under neutral evolution the level of diversity in
    a population will reach an equilibrium
  • New mutation cancelled out by drift
  • Ø 4Neµ where Ø is the genetic diversity, Ne, µ
    mutation rate- so if we know µ and Ø we can
    calculate Ne

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Measuring genetic diversity
  • How do we measure genetic diversity?
  • What are measures of genetic diversity?

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Measuring genetic diversity
  • Several ways to measure Ø (theta)
  • of alleles
  • Number of segrating sites
  • Segragation sites
  • Number of singletons
  • Mean number of pairwise differences

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Set of sequences
  • I A G T C T T A C G T A T C
  • II A G T C T T G C G T A T C
  • III A G T T T T A C G T A T C
  • IV A G T C T T G C G T G T C
  • V A G T C T T A C G T A T C

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Pairwise differences
  • I A G T C T T A C G T A T C
  • II A G T C T T G C G T A T C
  • III A G T T T T A C G T A T C
  • IV A G T C T T G C G T G T C
  • V A G T C T T A C G T A T C

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frequency differences
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mismatch distributions
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What md tell us about pops
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