Population genetics

1
Population genetics

• Study of genes and genotypes in a population
• Want to know extent of genetic variation, why it
  exists and how it changes over time
• Helps us understand how genetic variation is
  related to phenotypic variation

2
Gene pool

• All of the genes in a population
• Study genetic variation within the gene pool and
  how variation changes from one generation to the
  next
• Emphasis is often on variation in alleles between
  members of a population

3
Population

• Group of individuals of the same species that can
  interbreed with one another
• Some species occupy a wide geographic range and
  are divided into discrete populations

4
Genes in Natural Populations Are Usually
Polymorphic

• Polymorphism many traits display variation
  within a population
• Due to 2 or more alleles that influence phenotype
• Polymorphic gene- 2 or more alleles
• Monomorphic predominantly single allele
• Single nucleotide polymorphism (SNPs)
• Smallest type of genetic change in a gene
• Most common 90 of variation in human gene
  sequences
• Large, healthy populations exhibit a high level
  of genetic diversity
• Raw material for evolution

5

• Hardy-Weinberg Principle
• Explains the movement of genes and alleles in
  populations
• Essential to understanding mechanisms of
  evolutionary change

Aa
Mm
ZZ
DdEE
Kkpp
6
Hardy-Weinberg Equation

• Relates allele and genotype frequencies under
  certain conditions
• p2 2pq q2 1
• p frequency of dominant allele
• q frequency of the recessive allele
• The genotype frequencies of a population arep2 is
  frequency of homozygous dominant genotype
• 2pq is frequency of heterozygous genotype
• q2 is frequency of homozygous recessive genotype

7
Sickle-Cell Anemia

• In sickle-cell anemia, hemoglobin (Hbs) has poor
  oxygen affinity
• Sequencing of the hemoglobin gene revealed one
  change from the normal a.a. sequence

8

• Evolution of populations is best understood in
  terms of frequencies
• Phenotype
• Genotype
• Allele

9
Ex Sickle Cell Anemia
Phenotypes
Sickle cell gene (h)
CAC
Alleles
Genotypes
CTC
Normal globin gene H
10
Phenotype Frequencies Sickle Cell Anemia in the
African American Population
11
Genotype Frequencies Sickle Cell Anemia in the
African American Population
12
Allele Frequencies

• A populations gene pool
• Includes all the alleles for all the loci present
  in the population
• Diploid organisms have a maximum of two different
  alleles at each genetic locus
• Typically, a single individual therefore has only
  a small fraction of the alleles present

13

• Genotype and allele frequencies

14
Allele Frequencies Sickle Cell Anemia Sickle
Cell Anemia in the African American Population
p q 1
15
Allele and genotype frequencies

• Related but distinct calculations

16
Example

• Allele frequency of r
• 1.0 - 0.3 0.7 frequency of R
• Genotype frequency of rr

• 49 red-flowered RR
• 42 pink-flowered Rr
• 9 white-flowered rr

17
Hardy-Weinberg equation

• Relates allele and genotype frequencies under
  certain conditions

18
(No Transcript)
19
Hardy-Weinberg describes a population at genetic
equilibrium. Genetic equilibrium requires

• No new mutations
• Large population size- The population is so large
  that allele frequencies do not change due to
  random sampling error
• No migration-No exchange of individuals between
  different populations
• Random mating- The members of the population mate
  with each other without regard to their
  phenotypes and genotypes
• No natural selection- No survival or reproductive
  advantage exists for any of the genotypes

20
The fundamental evolutionary event is
Microevolution

• a change in the frequency of genes and chromosome
  configurations in a population.

Hardy-Weinberg Equilibrium
21
Microevolution

• Changes in a populations gene pool from
  generation to generation
• Change because
• Introduce new genetic variation (mutations, gene
  duplication, exon shuffling, horizontal gene
  transfer)
• Population will not evolve with mutations as the
  only source
• Evolutionary mechanisms that alter the prevalence
  of an allele or genotype (natural selection,
  random genetic drift, migration, nonrandom
  mating)
• Potential for widespread genetic change

22
Evolutionary mechanisms and their effects on
populations

• Natural selection
• Genetic drift (the random loss of alleles in
  small, isolated populations)
• Migration (gene flow)
• Nonrandom mating (inbreeding)

23
Natural Selection

• Selective survival of genotypes that confer
  greater reproductive success
• Natural selection acts on
• Characteristics with a survival advantage
• Make organisms better adapted, more likely to
  survive, greater chance to reproduce
• Favors individuals that produce viable offspring

24
Modern description of natural selection

• Allelic variation arises from random mutations
  that may alter the function of the protein.
• Some alleles may encode proteins that enhance an
  individuals survival or reproductive success
  compared to that of other members of the
  population
• Individuals with beneficial alleles are more
  likely to survive and contribute their alleles to
  the gene pool of the next generation
• Over the course of many generations, allele
  frequencies of many different genes may change
  through natural selection, thereby significantly
  altering the characteristics of a population
• Net result of natural selection is a population
  that is better adapted to its environment and/or
  more successful at reproduction.

25
(No Transcript)
26
Darwinian fitness

• Relative likelihood that a genotype will
  contribute to the gene pool of the next
  generation as compared with other genotypes
• Measure of reproductive success
• Hypothetical gene with alleles A and a
• AA, Aa, aa

27

• Suppose average reproductive successes are
• AA produces 5 offspring
• Aa produces 4 offspring
• Aa produces 1 offspring
• Fitness is W and maximum is 1.0 for genotype with
  highest reproductive ability
• Fitness of AA WAA 5/5 1.0
• Fitness of Aa WAa 4/5 0.8
• Fitness of aa Waa 1/5 0.2

28
Mean fitness of population

• Average reproductive success of members of a
  population
• As individuals with higher fitness values become
  more prevalent, natural selection increases the
  mean fitness of the population

29
Modes of Selection

• Three kinds of natural selection changes the
  normal distribution of phenotypes in a population
• Stabilizing
• Favors the mean
• Selects against phenotypic extremes
• Directional
• Favors one phenotypic extreme
• Disruptive
• Favors two or more phenotypic extremes

30
Natural selection can follow different patterns

• Directional selection
• Favors one phenotypic extreme
• Stabilizing selection
• Favors the mean
• Selects against phenotypic extremes
• Disruptive selection
• Favors two or more phenotypic extremes
• Balancing selection
• Heterozygote Advantage

31
Directional selection

• Favors individuals at one extreme of a phenotypic
  distribution that have greater reproductive
  success in a particular environment
• Initiators
• New favored allele introduced
• Prolonged environmental change

32
(No Transcript)
33
Stabilizing selection

• Favors the survival of individuals with
  intermediate phenotypes
• Extreme values of a trait are selected against
• Clutch size
• Too many eggs and offspring die due to lack of
  care and food
• Too few eggs does not contribute enough to next
  generation

34
(No Transcript)
35
Disruptive selection

• Favors the survival of two or more different
  genotypes that produce different phenotypes
• Likely to occur in populations that occupy
  diverse environments
• Members of the populations can freely interbreed

36
Disruptive selection pattern
37
Balancing selection

• Maintains genetic diversity
• Balanced polymorphism
• Two or more alleles are kept in balance, and
  therefore are maintained in a population over the
  course of many generations
• 2 common ways
• For a single gene, heterozygote favored
• Heterozygote advantage HS allele
• Negative frequency-dependent selection
• Rare individuals have a higher fitness

38
Frequency of the sickle cell allele
39
Sexual selection

• Form of natural selection
• Directed at certain traits of sexually
  reproducing species that make it more likely for
  individuals to find or choose a mate and/or
  engage in successful mating
• In many species, affects male characteristics
  more intensely than it does female

40
Intrasexual selection

• Between members of the same sex
• Horns in male sheep, antlers in male moose, male
  fiddler crab enlarged claws
• Males directly compete for mating opportunities
  or territories

41
Intersexual selection

• Between members of the opposite sex
• Female choice
• Often results in showy characteristics for males
• Cryptic female choice
• Genital tract or egg selects against genetically
  related sperm
• Inhibits inbreeding

42

• Explains traits that decrease survival but
  increase reproductive success
• Male guppy (Poecilia reticulata) is brightly
  colored compared to the female
• Females prefer brightly colored males
• In places with few predators, the males tend to
  be brightly colored
• In places where predators are abundant, brightly
  colored males are less plentiful because they are
  subject to predation
• Relative abundance of brightly and dully colored
  males depends on the balance between sexual
  selection, which favors bright coloring, and
  escape from predation, which favors dull coloring

43
2. Random Genetic Drift

• Large populations are more stable than small
  populations
• Random loss of alleles due to the effects of
  environmental change, catastrophe and natural
  selection are greater in small populations

44
Random genetic drift

• Changes allelic frequency due to random sampling
  error
• Random events unrelated to fitness
• Favors either loss or fixation of an allele
• Frequency reaches 0 or 100
• Faster in smaller populations
• Bottleneck is a sudden decrease in population
  size caused by adverse environmental factors
• Founder effect is genetic drift when a small
  population colonizes a new area

Result in decreases in genetic variation
45
Genetic Drift
Changes in the gene pool of a small population
due to chance.
46
(No Transcript)
47
Bottleneck

• Population reduced dramatically and then rebuilds
• Randomly eliminated members without regard to
  genotype
• Surviving members may have allele frequencies
  different from original population
• Allele frequencies can drift substantially when
  population is small
• New population likely to have less genetic
  variation

48
Bottlenecks

• Many populations become fragmented and isolated
  as a result of development
• Here, a forest is broken into isolated
  populations as part of a neighborhood
• The effect of isolating populations is the same
  as a bottleneck
• These small parcels (populations) are now more
  vulnerable to loss through
• Disease
• Death
• Catastrophe

49
Bottlenecks and Founder Effects

• Genetic Bottlenecks
• Endangered species are often the result of a
  genetic bottleneck
• The Black plague eliminated up to 75 of some
  European populations during the 1340s
• Founder Effects
• Dispersal and migration often lead to the
  establishment of new populations that are not
  genetically diverse

Both decrease the genetic diversity of a
population
50
Founder effect

• Small group of individuals separates from a
  larger population and establishes a new colony
• Relatively small founding population expected to
  have less genetic variation than original
  population
• Allele frequencies in founding population may
  differ markedly from original population

51
3. Migration and Gene Flow

• Movement of alleles caused by migration of
  individuals between populations
• Immigration
• Emmigration
• Movement of individuals in the form of animals,
  plants, pollen, or seeds
• Migration tends to reduce differences in allele
  frequencies between the 2 populations
• Tends to enhance genetic diversity within a
  population

52
Migration

• Gene flow occurs when individuals migrate between
  populations having different allele frequencies

53
(No Transcript)
54
Nonrandom mating

• One of the conditions required to establish the
  Hardy-Weinberg equilibrium is random mating
• Individuals choose their mates irrespective of
  their genotypes and phenotypes
• Forms of nonrandom mating
• Assortative/disassortative
• Inbreeding

55

• Assortative mating
• Individuals with similar phenotypes are more
  likely to mate
• Increases the proportion of homozygotes
• Disassortative mating
• Dissimilar phenotypes mate preferentially
• Favors heterozygosity

56

• Inbreeding
• Choice of mate based on genetic history
• Does not favor any particular allele but it does
  increase the likelihood the individual will be
  homozygous
• May have negative consequences with regard to
  recessive alleles
• Lower mean fitness of a population if homozygous
  offspring have a lower fitness value
• Inbreeding depression

57
(No Transcript)
58
The Carnivore Comeback

• Bears, wolves, lynx, and wolverines exterminated
  in the 18th and 19th centuries
• Reintroduction of bears to France from Eastern
  Europe
• Scientists are studying
• Viable population size
• Mating behavior
• Migrations
• Genetic diversity

59
The Carnivore Comeback

• Studying genetic Diversity
• Genotyping of hair and scat
• Signs of inbreeding
• Migration Patterns
• Take into account genetic diversity of the
  populations and open possible corridors among
  them

60

• Where do you expect the greatest genetic
  diversity?
• The smaller populations of in Western Europe How
  could you tell if they were remnant populations
  from the 18th century or founders from Eastern
  Europe?