Random fixation and loss of heterozygosity Frequency of heterozygotes decreases over time, as alleles drift towards fixation or extinction - all else being equal (no selection, etc), the frequency of heterozygotes should fall in every generation We can talk about “heterozygosity” as an average across all genes, and across all individuals in a population - at what % of loci are you heterozygous? - what is the average % for individuals in your population? More genetic diversity (polymorphism) usually means more heterozygosity... usually.

Random fixation and loss of heterozygosity Frequency of heterozygotes decreases over time, as alleles drift towards fixation or extinction - all else being equal (no selection, etc), the frequency of heterozygotes should fall in every generation - given by the relationship Hg+1 = Hg 1 - 1 where N = population size 2N amount of heterozygosity in this generation amount of heterozygosity in the next generation

Random fixation and loss of heterozygosity The frequency of heterozygotes should fall in every generation - given by the relationship Hg+1 = Hg 1 - 1 where N is population size 2N You are trying to maintain a group of 50 endangered llamas. How much will heterozygosity decrease in one generation? Hg+1 = Hg 1 – 1 = Hg 1 – 1 2(50) 100

Random fixation and loss of heterozygosity The frequency of heterozygotes should fall in every generation - given by the relationship Hg+1 = Hg 1 - 1 where N is population size 2N You are trying to maintain a group of 50 endangered llamas. How much will heterozygosity decrease in one generation? Hg+1 = Hg 1 – 1 = Hg 1 – 1 = Hg (99/100) = Hg (0.99) 2(50) 100 Heterozygosity in the next generation (Hg+1) will be 99% of heterozygosity now (Hg)

Random fixation and loss of heterozygosity The frequency of heterozygotes should fall in every generation - given by the relationship Hg+1 = Hg 1 - 1 where N is population size 2N You are trying to maintain a group of 50 endangered llamas. How much will heterozygosity decrease in one generation? Hg+1 = Hg 1 – 1 = Hg 1 – 1 = Hg (99/100) = Hg (0.99) 2(50) 100 thus, despite your efforts to arrange random matings, heterozygosity will decrease by 1% per generation. NO MATTER WHAT YOU DO.

Random fixation and loss of heterozygosity Heterozygosity decreases in every generation, but more slowly in large populations - the faster an allele disappears due to drift, the more quickly you lose heterozygosity

Random fixation and loss of heterozygosity tested experimentally by Buri with fruit flies   - started 107 replicate populations each with 8 boy + 8 girl flies - all flies were initially heterozygotes for a brown eye color allele (bw/bw-75) - each generation, out of all offspring, 16 were chosen to start the next generation - monitored for 19 generations

Random fixation and loss of heterozygosity Expected result: - no selective advantage, so bw-75 allele should drift to fixation 50% of the time and be lost 50% of the time - heterozygosity should decrease over time   Results after 19 generations: - in 30 populations, bw-75 allele was lost - in 28, it was fixed

Random fixation and loss of heterozygosity Heterozygosity could also be directly scored by eye color - decreased every generation, as predicted by theory - actually decreased faster than expected, as though N = 9 flies (not 16)

Genetic bottlenecks & the founder effect A bottleneck is a dramatic reduction in the number of surviving individuals in a population A “founder effect” is a special form of bottleneck that occurs when a new population is founded by a small number of individuals, who come from a larger, ancestral population Both are special cases of genetic drift, when a random sample of alleles is effectively taken from the large starting population, either by the survivors of a die-off, or founders of a new population

Genetic bottlenecks & the founder effect Both are special cases of genetic drift, when a random sample of alleles is effectively taken from the large starting population, either by the survivors of a die-off, or founders of a new population When a new population is started by a few survivors or initial colonizers, their genetic make-up will largely determine the allele frequencies as the young population grows 2 signatures of a bottleneck or founder event:  reduced genetic diversity: a small group of founders won’t carry all the alleles present in the population they came from  shift in allele frequencies: if founders happened to carry rare alleles, those will be over-represented in the new population (relative to the original, large population they came from)

Genetic bottleneck 2 signatures of a founder event:  reduced genetic diversity: a small group of founders won’t carry all the alleles present in the population they came from - California now has ~ 125,000 Northern elephant seals - seals were hunted down to ~30 individuals in the 1800s, then grew to 350 by 1922, when they were protected - sequencing one region of mitochondrial DNA revealed only 2 variable (polymorphic) positions out of 300 base pairs of DNA - in contrast, the southern elephant seal (never hunted under 1000 animals) has 23 variable positions in the same region

Founder effect 2 signatures of a founder event:  reduced genetic diversity: a small group of founders won’t carry all the alleles present in the population they came from  shift in allele frequencies: if founders happened to carry rare alleles, those will be over-represented in the new population (relative to the original, large population they came from)   example: Pennsylvania Amish carry allele for a rare form of dwarfism, at a frequency of 7% - only present at 0.1% in most populations - one of original 200 founders had the recessive allele - consequence: way more Amish dwarves than you’d expect

Genetic drift and Elephant tusks 98% of 174 female elephants in the Addo National Park lack tusks - population was reduced to 11 individuals by hunting, until protected in 1931 - at that point, 50% of females lacked tusks - near loss of female tusks is likely a result of genetic drift, following population bottleneck females w/ tusks proportion of population size

Genetic drift and Elephant tusks 98% of 174 female elephants in the Addo National Park lack tusks - Alternative hypothesis: ivory hunters imposed strong selection against tusks - if tusklessness were a recessive trait, what would you expect to happen to the frequency of tusklessness since the population was protected? Why? females w/ tusks proportion of population size

Drift vs. Selection n = 10 individuals n = 100 n = 1,000 n = 10,000 100 50 % of helpful allele - introduce a helpful allele that gives you a 5% fitness boost - initially, allele is present at a frequency of 5% What happens to the frequency of that good allele over time?  in small populations, good alleles are often lost due to drift  in large populations, selection is stronger than drift, so good alleles rise in frequency until they fix

Variation in natural populations When scientists started measuring protein variation in natural populations, they were surprised by how much polymorphism there was – about 25% of loci have multiple alleles visible by gel electrophoresis, in a wide range of species Why is there so much variation at the molecular level? Why hasn’t the most advantageous allele become fixed in a population

Variation in natural populations Why is there so much allelic variation in natural populations? 2 opposing theories: Neutral theory: most allelic differences don’t make a difference to fitness; they neither hurt nor help the organism - most mutations are bad (make the protein worse) so they are rapidly removed by selection (we never see them) - mutations that survive are neutral (make no difference) - may become fixed by genetic drift (chance, not selection) 

Variation in natural populations Why is there so much allelic variation in natural populations? Selectionist theory: natural selection maintains genetic diversity, because most alleles are beneficial under some set of circumstances Selectionists argue, there’s no way you’d see so much variation unless it was important (even if only under rare circumstances) Mutations may be favorable when colonizing a new environment, or if conditions change a lot year-to-year

“Nearly Neutral” Theory Neutral theory had some problems - predicts that large populations should have more genetic diversity, but they don’t Ohta proposed her nearly neutral theory to better explain observed results from nature: - most mutations are slightly deleterious (a little bad for you) - in large populations, selection will eliminate alleles that confer lower fitness over time - in small populations, a bad allele may rise to a high frequency by genetic drift before it gets wiped out by selection

“Nearly Neutral” Theory Ohta proposed her nearly neutral theory to better explain observed results from nature In nearly-neutral model, the relative power of selection vs. drift on new mutations depends on population size - a better explanation of empirical results, but harder to test predictions because population size is tough to determine Basic argument of both Neutral and Nearly-Neutral models is that selection acts against most mutations that cause protein variants In contrast, selectionists argue that selection often favors certain mutations, which keeps them hanging around and promotes genetic diversity or variability

Neutral or Selectionist? One way to test these theories is to look at th number of silent vs. non-synonymous substitutions over a given region of DNA   are silent point mutations in DNA (no effect on phenotype) more common or less common than non-synonymous changes? Negative selection: amino acid substitutions are less common than silent DNA substitutions (change is bad) Positive selection: non-synonymous amino acid substitutions are more common than silent substitutions

Polymorphic sites 1: DNA changes Some positions are polymorphic (different nucleotides are found) between some of the species - a single nucleotide is fixed within each species Other positions are polymorphic within one species, but are otherwise fixed among species

Polymorphic sites 2: amino acid changes S or T V or F different amino acids can occur at a site within one species different amino acids can be fixed between species

Normally, most substitutions that survive to be detected are silent 1. DNA – 17 polymorphic sites 2. amino acid – 4 polymorphic sites (= non-synonymous changes) When non-synonymous changes pile up faster than silent changes (given that codons differ in whether one mutation can change the amino acid), it indicates positive selection is acting to quickly fix mutations before they get lost to drift

Neutral or Selectionist? Evidence for positive selection suggests selection is driving the rate at which mutations are fixed as proteins evolve Smith & Ayre-Walker (2002) compared ratio of non-synonymous (dN) to synonymous (dS) substitutions within 2 Drosophila species, and between the two species, over the whole genome - found many sites where there were more non-synonymous changes between the species than within either species - indicates that selection favored differences between species - they estimated 45% of amino acid differences between the 2 species had been fixed by positive selection

Neutral or Selectionist? Begun et al. (2007) found amount of polymorphism was correlated with recombination rate across Drosophila simulans genome Different regions of the genome can differ in how often crossing over occurs – some places have more, others less Some genes are more polymorphic than others (have more alleles) Neutral theory predicts no relationship between amount of genetic polymorphism (# of alleles) and how often crossing over happens  Why does selectionist theory predict a correlation?...

Neutral or Selectionist? Selection favoring one allele will also tend to drag alleles at nearby or linked loci to high frequency if selection strongly favors “big C” allele of the C gene... ...it will also tend to favor “B” and “D” alleles, if they happen to be linked to “C” on a chromosome A B C D E F a b c d e f

Neutral or Selectionist? Selection favoring one allele will also tend to drag alleles at nearby or linked loci to high frequency if selection strongly favors “big C” allele of the C gene... A B C D E F ...all these alleles will be lost, unless they can get onto the “winning team”  i.e., any chromosome with a C allele a b c d e f

Neutral or Selectionist? in regions of high recombination, linked loci can escape the effects of selection on nearby genes  crossing over “breaks up the team” Even if selection strongly favors C allele... alleles of other genes can cross over onto C chromosomes A B C D E F a b C d e f a b c d e f In regions of high recombination, many alleles at linked loci can “hitchhike” onto chromosomes with favorable alleles, and thus survive selection  greater overall polymorphism

Neutral or Selectionist? Begun et al. (2007) found amount of polymorphism was correlated with recombination rate across Drosophila simulans genome in regions of low recombination, linked loci can’t escape the effects of selection on nearby genes if selection strongly favors “big C” allele of the C gene... A B C D E F a b c d e f ...all these alleles get lost  The correlation is strong evidence that selection acts on alleles all the time, across the whole genome  Supports selectionist theory, not neutral theory