Chapter 7: Migration, genetic drift and non-random mating

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Chapter 7 Migration, genetic drift and
non-random mating

• Migration movement of alleles between
  populations.
• Migration can cause allele and genotype
  frequencies to deviate from Hardy-Weinberg
  equilibrium.

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Migration

• Consider Continent-Island migration model.
• Migration from island to continent will have no
  effect of continental allele frequencies.
  Continental population much larger than island.
• However continent to island migration can greatly
  alter allele frequencies.

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Empirical example of migrations effects

• Lake Erie water snakes. Snakes range in
  appearance from unbanded to strongly banded.
• Banding caused by single locus banded allele
  dominant over unbanded.

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http//animaldiversity.ummz.umich.edu/site/account
s/pictures/Nerodia_sipedon.html
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Lake Erie water snakes

• Mainland almost all snakes banded.
• Islands many snakes unbanded.
• Unbanded snakes have selective advantage better
  camouflage on limestone rocks. Camouflage very
  valuable when snake is young.

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Fig 6.6
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Lake Erie water snakes

• If selection favors unbanded snakes on islands
  why arent all snakes unbanded?
• Migration introduces alleles for banding.

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Fig 6.7
A unbanded, BC some banding, D strongly banded
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Lake Erie water snakes

• Migration of snakes from mainland makes island
  populations more like mainland.
• This is general effect of migration Homogenizes
  populations (making them resemble each other).

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Genetic Drift

• Genetic drift results from the influence of
  chance. When population size is small, chance
  events more likely to have a strong effect.
• Sampling errors are very likely when small
  samples are taken from populations.

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Genetic Drift

• Assume gene pool where frequency A1 0.6, A2
  0.4.
• Produce 10 zygotes by drawing from pool of
  alleles.
• Repeat multiple times to generate distribution of
  expected allele frequencies in next generation.

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Fig 6.11
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Genetic Drift

• Allele frequencies much more likely to change
  than stay the same.
• If same experiment repeated but number of zygotes
  increased to 250 the frequency of A1 settles
  close to expected 0.6.

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6.12c
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Empirical examples of sampling error Founder
Effect

• Founder Effect when population founded by only a
  few individuals allele frequencies likely to
  differ from that of source population.
• Only a subset of alleles likely to be represented
  and rare alleles may be over-represented.

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Founder effect in Silvereye populations.

• Silvereyes colonized South Island of New Zealand
  from Tasmania in 1830.
• Later spread to other islands.

http//www.derwenttraders.com.au/contents /media/s
ilvereye-460.jpg
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6.13b
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Founder effect in Silvereyes

• Analysis of microsatellite DNA from populations
  shows Founder effect on populations.
• Progressive decline in allele diversity from one
  population to the next in sequence of
  colonizations.

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Fig 6.13 c
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Founder effect in Silvereyes

• Norfolk island Silvereye population has only 60
  of allelic diversity of Tasmanian population.

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Founder effect in human populations

• Founder effect common in isolated human
  populations.
• E.g. Pingelapese people of Eastern Caroline
  Islands are descendants of 20 survivors of a
  typhoon and famine that occurred around 1775.

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Pingelap Atoll
http//people.brandeis.edu/msitzman/docs/pingelap
_large.html
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Founder effect in human populations

• One survivor was heterozygous carrier of a
  recessive loss of function allele of CNGB3 gene.
• That gene codes for protein in cone cells of
  retina.
• 4 generations after typhoon homozygotes for
  allele began to be born.

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Founder effect in human populations

• People homozygous for the allele have
  achromotopsia (complete color blindness, extreme
  light sensitivity, and poor visual acuity).
• Achromotopsia is rare in most populations (lt1 in
  20,000 people). Among the 3,000 Pingelapese
  islanders the frequency is 1 in 20.

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Founder effect in human populations

• High frequency of allele for achromotopsia is not
  due to a selective advantage, just a result of
  chance.
• Founder effect followed by further genetic drift
  resulted in current high frequency.

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Effects of genetic drift over time

• Effects of genetic drift can be very strong when
  compounded over many generations.
• Simulations of drift. Change in allele
  frequencies over 100 generations. Initial
  frequencies A1 0.6, A2 0.4. Simulation run
  for different population sizes.

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6.15A
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6.15B
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6.15C
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Conclusions from simulations

• Populations follow unique paths
• Genetic drift has strongest effects on small
  populations.
• Given enough time, even in large populations
  genetic drift can have an effect.
• Genetic drift leads to fixation or loss of
  alleles, which increases homozygosity and reduces
  heterozygosity.

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6.15D
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6.15E
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6.15F
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Conclusions from simulations

• Genetic drift produces steady decline in
  heterozygosity.
• Frequency of heterozygotes is highest at
  intermediate allele frequencies. As one allele
  drifts to fixation the number of heterozygotes
  inevitably declines.

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Empirical studies on fixation

• Buri (1956) established 107 Drosophila
  populations.
• All founders were heterozygotes for an eye-color
  gene called brown. Neither allele gives selective
  advantage.
• Initial genotype bw75/bw
• Initial frequency of bw75 0.5

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Buri (1956) study

• Followed populations for 19 generations.
• Population size kept at 16 individuals.
• What do we predict will occur in terms of allele
  fixation and heterozygosity?

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Buri (1956) study

• In each population expect one of the two alleles
  to drift to fixation.
• Expect heterozygosity to decline in populations
  as allele fixation approaches.

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Buri (1956) study

• Distribution of frequencies of bw75 allele became
  increasingly U-shaped over time.
• By end of experiment, bw75 allele fixed in 28
  populations and lost from 30.

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Fig 6.16
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Buri (1956) study

• Frequency of heterozygotes declined steadily over
  course of experiment.
• Declined faster than expected because effective
  population size was smaller than initial
  population size of 16 (effective refers to number
  of actual breeders some flies died, some did not
  get to mate).

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Fig 6.17
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Allele fixation in natural populations

• Templeton et al. (1990) Studied Collared Lizards
  in Ozarks of Missouri
• Desert species occurs on remnant pieces of
  desert-like habitat called glades.

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Templeton et al. (1990)

• Human fire suppression has resulted in loss of
  glade habitat and loss of crossable savannah
  habitat between glades. Areas between glades
  overgrown with trees.

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Templeton et al. (1990)

• Based on small population sizes and isolation of
  collared lizard populations Templeton et al.
  (1990) predicted strong effect of genetic drift
  on population genetics.
• Expected low genetic diversity within
  populations, but high diversity between
  populations.

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Templeton et al. (1990)

• Found expected pattern. Genotype fixation common
  within populations and different genotypes were
  fixed in different populations.
• Lack of genetic diversity leaves populations
  vulnerable to extinction.
• Found gt66 of glades contained no lizards.

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Templeton et al. (1990)

• What conservation measures could be taken to
  assist Collared Lizard populations?

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Templeton et al. (1990)

• Repopulate glades by introducing lizards.
• Burn oak-hickory forest between glades to allow
  migration between glades.

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Non-Random mating

• The last of the five Hardy-Weinberg assumptions
  is that random mating takes place.
• The most common form of non-random mating is
  inbreeding which occurs when close relatives mate
  with each other.

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Inbreeding

• Most extreme form of inbreeding is self
  fertilization.
• In a population of self fertilizing organisms all
  homozygotes will produce only homozygous
  offspring. Heterozygotes will produce offspring
  50 of which will be homozygous and 50
  heterozygous.
• How will this affect the frequency of
  heterozygotes each generation?

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Inbreeding

• In each generation the proportion of heterozygous
  individuals in the population will decline.

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Inbreeding in California Sea Otters

• Because inbreeding produces an excess of
  homozygotes in a population deviations from
  Hardy-Weinberg expectations can be used to detect
  such inbreeding in wild populations.

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Inbreeding in California Sea Otters

• Sea otters, once abundant along the west coast of
  the U.S., were almost wiped out by fur hunters in
  the 18th and 19th centuries.

photo www.turtletrack.org
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Inbreeding in California Sea Otters

• California population reached a low of 50
  individuals (now over 1,500). As a result of
  this bottleneck, the population has less genetic
  diversity than it once had.

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Inbreeding in California Sea Otters

• Population is still at a low density and Lidicker
  and McCollum (1997) investigated whether this
  resulted in inbreeding.
• They determined genotypes of 33 otters for PAP
  locus, which has two alleles S (slow) and F (fast)

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Inbreeding in California Sea Otters

• The genotypes of the 33 otters were
• SS 16
• SF 7
• FF 10
• This gives approximate allele frequencies of S
  0.6 and F 0.4

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Inbreeding in California Sea Otters

• If otter population in H-W equilibrium, genotype
  frequencies should be
• SS 0.6 0.6 0.36
• SF 20.60.4 0.48
• FF 0.40.4 0.16
• However actual frequencies were
• SS 0.485, SF 0.212, FF 0.303

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Inbreeding in California Sea Otters

• There are more homozygotes and fewer
  heterozygotes than expected for a random mating
  population.
• Having considered alternative explanations for
  deficit of heterozygotes, Lidicker and McCollum
  (1997) concluded that sea otter populations show
  evidence of inbreedng.

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General analysis of inbreeding

• Self-fertilization and sibling mating are the
  most extreme forms of inbreeding, but matings
  between more distant relatives (e.g. cousins) has
  the same effect on the frequency of homozygotes,
  but rate is slower.

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General analysis of inbreeding

• F Coefficient of inbreeding probability that
  two alleles in an individual are identical by
  descent (this means both alleles are copies of a
  particular ancestors allele in some previous
  generation).
• F increases as relatedness increases.

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General analysis of inbreeding

• If we compare heterozygosity of an inbred
  population Hf with that of a random mating
  population Ho the relationship is
• Hf Ho (1-F)
• or expressed in H-W terms the expected frequency
  of heterozygotes in an inbred population would be
  Hf 2pq (1-F)
• Anytime Fgt0 frequency of heterozygotes is reduced
  and frequency of homozygotes naturally increases.

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General analysis of inbreeding

• Calculating F. Need to use pedigree diagrams.
• Example Female is daughter of two half-siblings.
• There are two ways the female could receive
  alleles that are identical by descent.

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Calculating probability that two alleles in an
inbred individual are identical by descent
Male
Female
Male
Half-sibling mating
Male
Female
Fig 6.27a
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Fig 6.27b
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General analysis of inbreeding

• Total probability of scenario is 1/16 1/16
  1/8.

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Inbreeding depression

• Inbreeding increases the frequency of homozygotes
  and thus the probability that deleterious alleles
  are visible to selection because an individual
  will receive two copies of the deleterious
  allele.
• In humans, children of first cousins have higher
  mortality rates than children of unrelated
  individuals.

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Each dot on graph represents mortality rates for
a human population. Mortality rate for children
of cousins consistently about 4 higher than rate
for children of non-relatives.
Fig 6.28
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Inbreeding in humans

• Royal families have been particularly prone to
  inbreeding.
• In Ancient Egypt because royal women were
  considered to carry the royal bloodline the
  pharaoh routinely was married to a sister or
  half-sister.

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Inbreeding in humans

• The most famous example of a genetic disorder
  exacerbated by inbreeding is the Hapsburg jaw or
  Hapsburg lip severe lower jaw protrusion .
• (Hapsburgs were the ruling family of Austria and
  Spain for much of the 1400s-1700s)

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Inbreeding in humans

• Extensive intermarriage of close Hapsburg
  relatives occurred.
• The last of the Spanish Hapsburgs, Charles II
  (1661-1700) had such severe jaw protrusion he
  could not chew his food properly.
• Charles II also had a large number of other
  recessively inherited genetic problems that
  caused physical, mental, sexual and other
  problems. Charles was infertile and the last of
  the Spanish Hapsburg kings.

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http//en.wikipedia.org/wiki/Charles_II_of_Spain
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Inbreeding depression

• Inbreeding depression (reduction in fitness
  caused by inbreeding) also documented in studies
  of wild animals.
• E.g. Great Tit. Two studies show that survival of
  inbred nestlings is lower than that of outbred
  individuals and that hatching success of inbred
  eggs is lower than that of outbred eggs.

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Fig. 6.30
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Inbreeding depression in plants

• Inbreeding depression best studied in plants.
• Can experimentally produce inbred and outbred
  plants easily.

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Inbreeding depression in plants

• Patterns to emerge from studies
• Inbreeding effects are clearest when plants are
  stressed (competition, under pest attack, grown
  outdoors).
• Inbreeding effects most often show up later in
  life cycle. (Appears maternal effects i.e.
  contributions from the mother to the offspring
  e.g. provisioning of seed mask effect
  initially).
• Inbreeding depression varies among family
  lineages.

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Fig 6.29
Open bars first year data. Filled bars second
year data. Coefficient of inbreeding
depression is measure of how much inbreeding
reduces values for various parameters.
Waterleaf (a biennial plant)
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Inbreeding avoidance

• Many mechanisms to avoid inbreeding have evolved.
  Include
• Dispersal.
• Genetically controlled self-incompatibility.
• Mate choice.

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Small populations and inbreeding

• In small populations inbreeding may be
  unavoidable.
• Even with random mating, a small population that
  stays small and receives no immigrants will
  become inbred.
• Major problem for rare species such as California
  sea otters.

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Population genetics and conservation of Prairie
Chickens

• Two hundred years ago Illinois covered with
  prairie and home to millions of Greater Prairie
  Chickens.
• Steel plough allowed farmers to farm the prairie.
  Acreage of prairie plummeted and so did Prairie
  Chicken numbers.

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Lesser Prairie Chicken
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Conservation of Prairie Chickens

• In 1960s habitat protection measures introduced
  and population increased until mid 1970s.
• Then population collapsed. By 1994 lt50 birds in
  two populations in Illinois.

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Fig 6.3
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Conservation of Prairie Chickens

• Why did prairie chicken populations decline even
  though available habitat was increasing?
• Prairie destruction reduced numbers of birds and
  isolated the populations from each other.

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Conservation of Prairie Chickens

• No migration between populations.
• Small populations vulnerable to genetic drift and
  inbreeding depression.
• Accumulation of deleterious recessive alleles
  (genetic load) can lead to extinction of small
  populations.

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Conservation of Prairie Chickens

• Problem exacerbated when exposure of deleterious
  mutations further reduces population size and
  increases effectiveness of drift. Extinction
  vortex.
• Prairie chickens showed clear evidence of
  inbreeding depression. Egg hatching rates had
  declined dramatically by 1990 lt 40 hatch rate.

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FIG 6.31
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Conservation of Prairie Chickens

• Illinois Prairie chicken populations showed less
  genetic diversity than other populations and less
  genetic diversity than they had in the past.
• Illinois birds 3.67 alleles per locus rather than
  5.33-5.83 alleles of other populations and 5.12
  of Illinois museum specimens.

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Conservation of Prairie Chickens

• Conservation strategy?

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Conservation of Prairie Chickens

• In 1992 prairie chickens introduced from other
  populations to increase genetic diversity.
• Hatching rates increased to gt90.
• Population increased.