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

F = Coefficient of inbreeding: probability that two alleles in an individual are identical by descent (both alleles are copies of a particular ancestor’s allele in some previous generation).

F increases as relatedness increases.

If we compare heterozygosity of inbred population Hf with that of a random mating population Ho relationship is

Hf = Ho (1-F)

Anytime F>0 frequency of heterozygotes is reduced and frequency of homozygotes naturally increases.

Calculating F. Need to use pedigree diagrams.

Example: Female is daughter of two half-siblings.

Two ways female could receive alleles that are identical by descent.

Fig 6.27a

Male Female Male

Female Male

Half-sibling mating

Fig 6.27b

Total probability of scenario is 1/16 + 1/16 = 1/8.

Inbreeding increases frequency of homozygotes and thus the probability that deleterious alleles are visible to selection.

In humans, children of first cousins have higher mortality rates than children of unrelated individuals.

Fig 6.28

Each dot on graphrepresents mortalityrates for a humanpopulation.

Mortality rate for children of cousinsconsistently about 4%higher than rate forchildren of non-relatives.

In a study of 2760 individuals from 25 Croatian islands Rudan et al. found a strong positive relationship between high blood pressure and the inbreeding coefficent.

Inbreeding depression 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.

Fig. 6.30

Migration: movement of alleles between populations.

Migration can cause allele and genotype frequencies to deviate from Hardy-Weinberg equilibrium.

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.

Lake Erie water snakes. Snakes range in appearance from unbanded to strongly banded.

Banding caused by single locus: banded allele dominant over unbanded.

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.

Fig 6.6

If selection favors unbanded snakes on islands why aren’t all snakes unbanded?

Migration introduces alleles for banding.

Fig 6.7

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

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 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.

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.

Fig 6.11

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.

6.12c

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.

Silvereyes colonized South Island of New Zealand from Tasmania in 1830.

Later spread to other islands.

http://photogallery.canberrabirds.org.au/silvereye.htm

6.13b

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.

Fig 6.13 c

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

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.

One survivor was heterozygous carrier of a recessive loss of function allele of CNGB3 gene.

Codes for protein in cone cells of retina.

4 generations after typhoon homozygotes for allele began to be born.

Homozygotes have achromotopsia (complete color blindness, extreme light sensitivity, and poor visual acuity).

Achromotopsia rare in most populations (<1 in 20,000 people). Among the 3,000 Pingelapese frequency is 1 in 20.

High frequency of allele for achromotopsia 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 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.

6.15A

6.15B

6.15C

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.

6.15D

6.15E

6.15F

Genetic drift produces steady decline in heterozygosity.

Frequency of heterozygotes highest at intermediate allele frequencies. As one allele drifts to fixation number of heterozygotes inevitably declines.

The Hardy-Weinberg model provides an idealized picture of how allele frequencies and genotype frequencies are expected to change over time in a large population.

The Wright-Fisher model is a similar model but applies to small populations.

The W-F model retains the assumptions of the H-W model except for population size and in the model only a small sample of gametes are drawn at random from the gene pool.

The small sample drawn mimics the effects of drift because allele frequencies in the sample can differ a lot from the starting gene pool.

We know that genetic drift leads to a loss of heterozygosity over time.

Alleles going to fixation naturally reduce the diversity of alleles in the population and without allelic diversity heterozygosity must decline.

In a Wright-Fisher population expected heterozygosity declines on average by a factor of 1/2N per generation, where N is population size.

When N is large 1/2N is very small so we expect heterozygosity to decline slowly. Conversely, with a small population 1/2N is large and heterozygosity will decline quickly as a result of drift.

Recall that F = Coefficient of inbreeding: probability that two alleles in an individual are identical by descent (both alleles are copies of a particular ancestor’s allele in some previous generation).

Also recall that two alleles can be identical in their genetic sequence (e.g. both A1), but if they did not come from the same shared ancestor they are not considered identical by descent.

Consider a gamete pool to which all parents contribute equally and from which offspring are produced by drawing two gametes at random.

With a population of N parents each contributing 2 alleles there is a total pool of 2N alleles.

Under these circumstances the probability of an offspring having two alleles derived from the same parental copy is 1/2N.

{Note the probability is not 1/2N * 1/2N because the first allele can be any allele and there is then a 1/2N chance it is the same as that first one}

The parental generation had a level of heterozygosity that we call Hparental.

Thus the offspring generations heterozygosity is

Hoffspring = [1 – 1/2N] * Hparental

See box 8.2 for derivation

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

Followed populations for 19 generations.

Population size kept at 16 individuals.

What do we predict will occur in terms of allele fixation and heterozygosity?

In each population expect one of the two alleles to drift to fixation.

Expect heterozygosity to decline in populations as allele fixation approaches.

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.

Fig 6.16

Frequency of heterozygotes declined steadily over course of experiment.

Declined faster than expected because effective population size was smaller than initial size of 16 (effective refers to number of actual breeders; some flies died, some did not get to mate).

Fig 6.17

Effective population size refers to the number of breeders in a population.

In many cases population size and effective population size may be quite different if most individuals don’t breed, if a few individuals produce most of the offspring or if there is a strongly biased sex ratio.

Templeton et al. (1990) Studied Collared Lizards in Ozarks of Missouri

Desert species occurs on remnant pieces of desert-like habitat called glades.

http://en.wikipedia.org/wiki/File:Collared-lizard.jpg

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

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.

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.

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

Repopulate glades by introducing lizards.

Burn oak-hickory forest between glades to allow migration between glades.

Another way in which populations may be exposed to the effects of drift is if the population experiences a bottleneck.

A bottleneck occurs when a population is reduced to a few individuals and subsequently expands. Even though the population is large it may not be genetically diverse as few alleles passed through the bottleneck.

Simulation models show a bottleneck can dramatically affect population genetics.

Next slide shows effects of a bottleneck on allele frequencies in 10 replicate populations.

The northern elephant seal (which breeds on California and Baja California) was hunted almost to extinction in the 19th century. Only about 10-20 individuals survived.

Now there are more than 100,000 individuals.

The northern elephant seal population should show evidence of the bottleneck.

Two studies in the 1970’s and 1990’s that examined 62 different proteins for evidence of heterozygosity found zero variation.

In contrast, similar studies of southern elephant seals show plenty of variation.

More recent work that has used DNA sequencing has shown some variation in northern seals, but still much less than in southern elephant seals.

Examination of museum specimens collected before the bottleneck have shown much more variation in these specimens than in current populations, which shows that the population was much more genetically diverse before the bottleneck.

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 and northern elephant seals.

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.

Lesser Prairie Chicken

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.

Fig 6.3

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.

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.

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.

FIG 6.31

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 strategy?

In 1992 prairie chickens introduced from other populations to increase genetic diversity.

Hatching rates increased to >90%.

Population increased.