Small populations and genetic drift

Small pops and bottlenecks

• small pops often the result of a bottleneck effect

• defined as a decrease in pop size

  • may last from one gen to many gens

  • size and duration of the bottleneck are extremely important

• ex. black-footed ferret

• reduced to fewer than 100 individuals

• most endangered spp have been bottlenecked:

  • endangered = small pop size by definition

Ex. of bottlenecked species

• arabian oryx

• european bison

• indian rhino

• California condor

• Whooping crane

• Size of the bottleneck: the more individuals lost, the greater the immediate loss of genetic variation.

Bottlenecks and genetic variation in seals

• comparison of genetic variation in six seal species for a panel of the same 24 microsatellite loci.

Genetic drift and random sampling of alleles

• genetic drift: chance changes in allele frequency that result from the sampling of alleles from generation to generation in a finite pop

• the finite number of alleles transmitted to progeny will be an imperfect sample of the allele frequencies in the parents

• allele frequencies will change, variation will be lost

• violates HW assumption of infinite pop size

Genetic drift and pop size

• small pops drift more than large pops

Drift ex - we assume that none of the 3 alleles A1, A2, and A3 has a selective advantage

Random sampling of gametes: the kid on the right got A1 from both parents.

Differential reproduction due to chance.

Genetic drift and bottleneck duration

• generation interval is the average age of reproduction - used instead of years

Size and duration of the bottleneck

• severe bottleneck, large initial loss of alleles

• loss of alleles thru drift more likely in small pops

• long bottleneck duration, loss of alleles more likely than short bottleneck duration

• changes in the genetic structure of a pop due to random sampling of alleles and differential reprod of adults

• results in:

  • loss of genetic diversity (fixation)

  • random changes in allele frequencies

  • differentiation among pops

Expected loss of heterozygosity due to drift in one gen:

• proportion of heterozygosity remaining after 1 gen = 1 - 1/2n

• pop size: 2, 10, 25, 50, 100

• proportion heterozygosity remaining: 75%, 95%, 98%, 99%, 99.5%

• issue: bottlenecks usually last for multiple gens

  • (1-1/2N)^t

  • so even a pop maintained at n=500 will retain only 95% of its diversity for 50 gens

• NB: Rate at which genetic variation is lost following genetic drift depends on the locud

• Diploid: -1/2N

• Haploid = -1/N

• Maternally inherited plastid/mtDNA = -1/N_f

Loss of allelic diversity

• allelic diversity is another way to measure loss of genetic variation

• expected loss of heterozygosity:

  • insensitive to sample size, comparisons between pops or spp more meaningful

  • insensitive to effects of bottlenecks - 75% retained even thru an extreme bottleneck of 2 individuals

  • expectation is (1-1/2N) regardless of the number of alleles present and their frequencies

• 2 individuals possess a max of 4 different alleles, so a lot of variation can be lost if many alleles are present at a locus in a pop

• difference between H and A is greatest in small pops

• effect of bottleneck on number of alleles depends on numbers and frequencies of alleles

  • E (A’) = A - ∑ a j=1(1 – p_j)^2N

• where A is the initial number of alleles, pj is the frequency of the jth allele, N=number of individuals, E(A’) is the total expected number of alleles remaining

• Ex: 1 locus, 2 alleles, frequencies of 0.9 and 0.1, bottleneck of 2 individuals

• E(A’) = 2 - (1 - 0.9)^4 - (1 - 0.1)^4 = 1.34

  • if both allele frequencies were 0.5 E(A’) = 1.88

  • rare alleles are likely to be lost during bottlenecks

  • loss of rare alleles has little effect on heterozygosity

Founder effect

• special case of genetic drift

• founding new pops with a small number of individuals will cause changes in allele frequencies and loss of genetic variation

Fitness effects of genetic drift: changes in allele frequence

• changes in allele frequency likely in small pops

• may increase frequency of harmful alleles

• harmful alleles usually recessive

• continually produced by mutation but kept at low frequencies by selection

• in small pops, drift can cause harmful alleles to be fixed

• selection less effective in small pops

Bottleneck of 2 individuals

• most rare alleles lost

• any allele for which one of the 2 fouunders is heterozygous will be found in new pop with a frequency of 25%

• most loci in 2 founders will not carry a harmful allele but every individual carries harmful alleles at some loci

• can’t predict which harmful alleles will increase in frequency

• but can predict that several harmful alleles that were rare will be found at higher frequencies

• ex. dalmations

  • few founders

  • susceptible to kidney stones bc excrete high amounts of uric acid

  • due to a recessive allele at a single locus

Fitness and drift: loss of allelic diversity

• drift has a greater effect on allelic diversity than on H if many alleles at a locus

• Mhc loci highly diverse and related to disease resistance and immune response

• bottleneck of 2 individuals: dozens to hundreds of alleles reduced to a max of 4

• small pops more susceptible to disease epidemics

Fitness and drift: inbreeding

• increased homozygosity

  • relatives tend to have the same alleles

  • if they mate together, likely to be homozygous

  • recessive harmful alleles expressed

• reduced heterozygosity

  • lose any heterzygote advantage