Gene flow

1
Chapter 5/6
2
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

4
(No Transcript)
5
(No Transcript)
6
(No Transcript)
7
(No Transcript)
8

• 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.
10
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

11
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

13
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

14
1. Directional Selection

• Favors variants of one extreme.

15
(No Transcript)
16
2. Balancing Selection

• Acts upon extremes and favors the intermediate.

17
(No Transcript)
18
3. Diversifying Selection

• Favors variants of opposite extremes.

19
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!)

22
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

23
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

24
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

26
III. Pedigree analysis.
Expression
27
Chapter 6

• Measuring genetic diversity

28
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

29
Measuring genetic diversity

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

30
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

31
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

32
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

33
frequency differences
34
mismatch distributions
35
What md tell us about pops
36
(No Transcript)