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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. Migration. Consider Continent-Island migration model.

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chapter 7 migration genetic drift and non random mating
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.
migration
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.
empirical example of migration s effects
Empirical example of migration’s effects
  • Lake Erie water snakes. Snakes range in appearance from unbanded to strongly banded.
  • Banding caused by single locus: banded allele dominant over unbanded.
slide4

http://animaldiversity.ummz.umich.edu/site/accounts/pictures/Nerodia_sipedon.htmlhttp://animaldiversity.ummz.umich.edu/site/accounts/pictures/Nerodia_sipedon.html

lake erie water snakes
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.
lake erie water snakes1
Lake Erie water snakes
  • If selection favors unbanded snakes on islands why aren’t all snakes unbanded?
  • Migration introduces alleles for banding.
slide8

Fig 6.7

A unbanded, B+C some banding, D strongly banded

lake erie water snakes2
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).
genetic drift
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.
genetic drift1
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.
genetic drift2
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.
empirical examples of sampling error founder effect
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.
founder effect in silvereye populations
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/silvereye-460.jpg

founder effect in silvereyes
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.
founder effect in silvereyes1
Founder effect in Silvereyes
  • Norfolk island Silvereye population has only 60% of allelic diversity of Tasmanian population.
founder effect in human populations
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.
slide22

Pingelap Atoll

http://people.brandeis.edu/~msitzman/docs/pingelap_large.html

founder effect in human populations1
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.
founder effect in human populations2
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 (<1 in 20,000 people). Among the 3,000 Pingelapese islanders the frequency is 1 in 20.
founder effect in human populations3
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.
effects of genetic drift over time
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.
conclusions from simulations
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.
conclusions from simulations1
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.
empirical studies on fixation
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
buri 1956 study
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?
buri 1956 study1
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.
buri 1956 study2
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.
buri 1956 study3
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).
allele fixation in natural populations
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.
templeton et al 1990
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.
templeton et al 19901
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.
templeton et al 19902
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 >66% of glades contained no lizards.
templeton et al 19903
Templeton et al. (1990)
  • What conservation measures could be taken to assist Collared Lizard populations?
templeton et al 19904
Templeton et al. (1990)
  • Repopulate glades by introducing lizards.
  • Burn oak-hickory forest between glades to allow migration between glades.
non random mating
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.
inbreeding
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?
inbreeding1
Inbreeding
  • In each generation the proportion of heterozygous individuals in the population will decline.
inbreeding in california sea otters
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.
inbreeding in california sea otters1
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

inbreeding in california sea otters2
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.
inbreeding in california sea otters3
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)
inbreeding in california sea otters4
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
inbreeding in california sea otters5
Inbreeding in California Sea Otters
  • If otter population in H-W equilibrium, genotype frequencies should be
    • SS = 0.6* 0.6 = 0.36
    • SF =2*0.6*0.4 = 0.48
    • FF = 0.4*0.4 = 0.16
  • However actual frequencies were:
    • SS= 0.485, SF= 0.212, FF =0.303
inbreeding in california sea otters6
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.
general analysis of inbreeding
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.
general analysis of inbreeding1
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 particularancestor’s allele in some previous generation).
  • F increases as relatedness increases.
general analysis of inbreeding2
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 F>0 frequency of heterozygotes is reduced and frequency of homozygotes naturally increases.
general analysis of inbreeding3
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.
slide63

Calculating probability that two alleles in an inbred individual are identical by descent

Male

Female

Male

Half-sibling mating

Male

Female

Fig 6.27a

general analysis of inbreeding4
General analysis of inbreeding
  • Total probability of scenario is 1/16 + 1/16 = 1/8.
inbreeding depression
Inbreeding depression
  • Inbreeding increases the frequency of homozygotes and thus the probability that deleterious alleles are visible to selection becausean individual will receive two copies of the deleterious allele.
  • In humans, children of first cousins have higher mortality rates than children of unrelated individuals.
slide67

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

inbreeding in humans
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.
inbreeding in humans1
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 1400’s-1700’s)
inbreeding in humans2
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.
inbreeding depression1
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.
inbreeding depression in plants
Inbreeding depression in plants
  • Inbreeding depression best studied in plants.
  • Can experimentally produce inbred and outbred plants easily.
inbreeding depression in plants1
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.
slide76

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)

inbreeding avoidance
Inbreeding avoidance
  • Many mechanisms to avoid inbreeding have evolved. Include:
    • Dispersal.
    • Genetically controlled self-incompatibility.
    • Mate choice.
small populations and inbreeding
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.
population genetics and conservation of prairie chickens
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.
conservation of prairie chickens
Conservation of Prairie Chickens
  • In 1960’s habitat protection measures introduced and population increased until mid 1970’s.
  • Then population collapsed. By 1994 <50 birds in two populations in Illinois.
conservation of prairie chickens1
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.
conservation of prairie chickens2
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.
conservation of prairie chickens3
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 < 40% hatch rate.
conservation of prairie chickens4
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.
conservation of prairie chickens5
Conservation of Prairie Chickens
  • Conservation strategy?
conservation of prairie chickens6
Conservation of Prairie Chickens
  • In 1992 prairie chickens introduced from other populations to increase genetic diversity.
  • Hatching rates increased to >90%.
  • Population increased.
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