Population Genetic - Drift Flashcards

Question

If our highest probability outcome is to get the same allele frequency, why does this result in evolution? (If we end up stabilizing around 50:50 -- why do we get evolution)

Answer 1

* In a single generation, the ”on average” part doesn’t matter – there’s only one round of zygote selection * Any sampling errors (deviation of a subset from the true population values) stick * Even if started at p = 0.5 --> THEN The population is restocked at the new value of p = 0.35 TEHN you sample another 20 gametes BUT you are sampleing from p = 0.35 and then might get p = 0.4

Answer 2

It’s not directional -- p can go up or down -- and we can’t know the direction or magnitude of the change from one generation to the next --> there is no analytical ∆p equation for drift!

Answer 3

If start at p = 0.6 -- when sampling gametes -- most often get back to p = 0.6 - Getting back to p = 0.6 is the most likley outcome BUT in experiment it only occured 18% if the time MEANS that 82% of the time get something other that p = 0.6 --> 82% of the time get chnage -- the liklihood of statying at 0.6 is low even though it is the most common outcome - 82% of the time = get chnage in allele frequencey - Standrad error = can avergae how far you are for subset sample size

Answer 4

You can look at the probability of chnage even though you can't know if P will increase or decrease or the magnitude of chnage BUT you can get probability that P will chnage ***There is no dP equation for drift

Answer 5

If we sample cards (52 cards) with replacmemnt (can choose a card more than once) -- at the end it is inevtiable that you will go to fixation for one card END -- inevitable you will only get one crad - end will get a singole crad all 52 times - You don't know which crad but know you will fix for one card * Sampling with replacement (so that you restock the deck each round) – you will inevitably end up with a single card at the end * This happens because each time one is missed from sampling error, it’s gone for good * Variation is lost through time When know that you will end up with a single crad but we can't know for sure which card that will be --> Means that dirft will tend towards fixation in the long one but don't know which allele that will be

Answer 6

When sampling pools a finite number of times = eventually get fixation for one allele - Means sampling errors are important -- critical affect = when lose sometuing = lose it for good - Each time one is missed from sampling error, it’s gone for good Means that dirft will tend towards fixation in the long one but don't know which allele that will be Affect of drift = genetcually decrease -- every time misample something and soemthing is not representaed = that copy is lost = lose variation

Answer 7

When lose something = lose it for good == when you lose that varaition (when go to fixationf or allele) you lose varaition for good - If varariation gets lost = varaition decrease END = fix for one allele

Answer 8

Every copy of each allele has equal probability of going to fixation (Probability of any one copy of A or any one copy of A is equally likley to reach fixation) - In a given population, each individual allele segregating in the population has an equal probability of being the one that goes to fixation eventually (Doesn't mean that p and q alelles are equally likley to go to fixation -- means individual copies of alleles in the gamete pool are equally likley to go to fixation) - If have 20 copies of an allele in a population then porbvility of any one copy if allele going to fixation is 1/20 IF P = 0.6 and q = 0.4 --> NOt equally likeley for p or q ro be fixed BUT each individuakl copy has the sameprobability Each copy in the gamate pool has the same probability Example -- if have 20 copies of an allele -- each copy has a 1/20 chance of going to fication IF p = 0.6 and q = 0.4 --> Probaboliyu pf P OR q going to fixation is Mutaually exclusive - One copy pf p or one copy of q Since ME (one copy of P will go to fixation or a different copy of P will go to fixation) - P(One copy of P going to fixation) OR P(Andifferent copy of P going tp fixation) = 1/20 + 1/20 -- since have 12 copis of P (the probability of any one copy going to fixation is mutation exulsive) -- add all 1/20 = get 12/20 = 0.6

Answer 9

Probability pf P OR q going to fixation is Mutually Exclusive ALSO -- ME for one copy of P OR a different copy of P to go to fixation

Answer 10

P = 0.6 and q = 0.4 --> porbaility of P going to fixation = 60% and q going to fixation is 40% (because probability of any one copy gping to fixation is 1/20 and ME = can add individual orobabilities together) --- The probability being 0.4 is ONLY for the starting generation --> As soon as the allele frequncey chnages due to drift that porbabiloity resets THEN if P = 0.45 and q = 0.55 NOW probability of P going tp fixation is 45% and Probability of q going to fixation is 55%

Answer 11

Probability of P or Q going to fixation = equal to the frequncey of P or Q in the popultion BUT only in that starting point -- IF chnage frequncey then that chnage sticks around and change probability

Answer 12

Probability of P or Q going to fixation = equal to the frequncey of P or Q in the popultion BUT only in that starting point -- IF chnage frequncey then that chnage sticks around and change probability

Answer 13

As soon as the allele frequency changes due to drift, that probability resets Example -- if start with p = 0.4 IF the sampling error going to the next generation causes the frequcncey to chnage to p = 0.55 - NOW the proabbility of blue going tp fixation has gone from 0.4 to 0.55 NOTE: There was nothing intrinsic about blue that made it less likely to go to fixation in the last generation

Answer 14

Larger populations – or more specifically larger numbers of zygotes being produced between generations in those populations – produce less sampling error = less drift - Larger sample size = smaller sample error - Larger population = apprach getting back same allele frequncey - As popultion size gets vigger = get ckoser to starting allele frequencey - If you lose a little bit of varaition = negligible drift in large population BUT in small popultion this can cause a large amount of change (Just as a larger sample size gives us more accurate results in statistics) Have inverseley proportional relationshio between popultion size and afefct of drift (Smaller = higher affect of drift)

Answer 15

Drift is a stronger evolutionary force in small populations (harder for NS to recon with) - True for small popultions that stay small for many generations (like rare or endagered species) AND it is also true for events in large popultions that cause temperary popultion reductions - True in popultions that are small and stay small AND true in otherwise large popultions that go through period of population contraction

Answer 16

Affect of drift stays around even after gets larger again

Answer 17

1. Founder events 2. Bottlenecks Cause otherwise large popultion to go through contraction BOTH have short lived stage of small popultion

Answer 18

A new popultion is derived from a small number of individuals drawn from a large ancestral population - Start popultion derived from small amount of individuals Ex. A small numver of people go to colonize islands - The allele frequncey of the new popultion has lots oif drift = very different allele frequncey (frequcney is very different than ancestral population)

Answer 19

A population’s history is marked by one or more generation of very small population size before regrowth

Answer 20

Bottle neck = not starting new popultion -- have a popultion that already exists -- popultion is already in a fixed place that THEN goes through a collapse and then bounces back FOR BOTH -- the effect of drift while in small popultion size carries over even if the popultion goes back to a larger size

Answer 21

Village of Salinas in a remote part of Dominican Reprublic - Population of 4300 in 1970s - Founded 7 generations ago by much smaller number of people - At founding = had very little immigration into area -- mostly had gene pool from families who settled there - In the founding = had disproportional representation -- tracked back to know guy that had kids with 4 women = became over represented in the gene pool --> The guy happened to be a carrier for 5-alpha-reductase-2 (Phenoype in homozygous = have malfunctioning copy of sex hormone in utero (Have testrone --> DHT -- DHT is the type of Testrone that the fetus responds to) -- have malfunctioning copy of sex hromone -- they are mot mkaing the right version of testrone -- without the mascularization cue = fetus developes as female -- have XY --> Have XY individual with female genetelia -- presents as female even thoough XY - Stay presenting as female until bodu begins repsonding to testrone at puberty and swicth -- born as anatomical female and swutch - Everyone was used to it in female -- 1% of girls swicth at puberty to males

Answer 22

Make testrone differentley/res[ond to testrone differentley --> difference in detecting testrone DHT is the version the hormone that really triggers external masculinization during development

Answer 23

10% of popultion = has the allele --> 1% of XY have this phenotype - 10% maintained -- how is this mainatined

Answer 24

Is maintained fior unique allele solsey becvause of random over represenattion in founder event? -- YES NOT mainatined due to mutation-selection balance --> selection had nothing to do with the intial rise in frequncey (the man didn't even have the phenoytype) - The high prevemlance of this gene in Slainas (over 1/10 men are cariers) is just due to hustorical happenstance Have kids with 4 women in small popultion ti start with --> that over representation is maintained even though popultion grew to sevral thousands of people

Answer 25

Because the founding population was small, each person had a large chance of contributing disproportionately to future generations --> One of these people, Altagracia Carrasco, did have a disproportionate effect and it had consequences later on -- Carrasco had children with at least four women –and his genes rose in frequency in the population Carrasco -- He was also a carrier for a mutation in the gene for 5- alpha-reductase-2

Answer 26

* This version of the enzyme functions poorly * Its role is the convert testosterone to dihydrotestosterone (DHT) * DHT is the version the hormone that really triggers external masculinization during development * Result: XY individuals that are homozygous for this allele are born with female external anatomy - but switch and develop male genitalia at puberty * The allele frequency in Salinas is >0.1 * Over 1% of genetic males exhibit this condition

Answer 27

Drift can lead to increased frequencies of deleterious allles -- in small popultions this effect can be dramatic

Answer 28

Founder events can have negitive consequnceys for the populations

Answer 29

Founder effects can be useful in studying human genetics --> The effects of rare allles are hard to study in larger popultions even if they have large effects BUT rare alles can be studies in smaller popultions with higher frequncey due to found effects - Reason populations on remote areas = hotbeds for geentoc studyes --> random increase in rare alelles = now frequcnet ebough to track raye and because they rise randomly to high allele frequencey because founder event - Can now track genetic basis for rare traits ***Genetic mechanisms behind a number of human conditions have been identified because the alleles behind them have drifted to high frequencies is small isolated populations - Can study mutations because the phenotypic affects that are usually uncommon occur more and more often because of founder effects Remote islands with known founding histories like Tristan da Cunha have been hotbeds of human genetic research for that reason ***Remote islands with known founding histories like Tristan da Cunha have been hotbeds of human genetic research for that reason

Answer 30

Reason populations on remote areas = hotbeds for geentoc studyes --> random increase in rare alelles = now frequcnet ebough to track raye and because they rise randomly to high allele frequencey because founder event - Can now track genetic basis for rare traits ***Remote islands with known founding histories like Tristan da Cunha have been hotbeds of human genetic research for that reason

Answer 31

Bottlenecks have similar effects as founder events -- capturing random events that have long term consequences in popultion long after rebound - Even if have complete rebound the effects still stick around BUT NOW -- not based on starting poplation NOW have existing popultion

Answer 32

It takes a lot of time to build up varaition --> If that is wpied out (like from bottle neck or founder events) = wipe out million of years of varaitionand will take millions of years to get that varaition again ***Strong drift in historical events can instantly undue the work of natural selection and thousands of generation’s worth of mutation accumulation

Answer 33

Many the populations of many marine mammals have very low genetic diversity, even if current populations seem large and stable Most marine animals had a really big bottle neck -- Now they are OK but they had a bottle neck Northern Elephant seals -- - People drive them almost to extciction -- in 1880s ther were less than 30 left --> most of the breedng popultion was wiped out = almsot went extcit) - NOW they are back to 100,000 but the strength of drift when in low popultion size sticks around --> NOW only 2 allels in mitocondria genome (loss of varaition) = low varaition because population crash - Only the varaition from the small popultion gets passed down = ONLY get varaition from 28 inidviuals when small popultion size SLIDES ON SEALS: * In the 1880s (about 12 generations ago) they were only 20-30 left * That bottleneck locked that random variation in place from there forward * Now, those 100,000 individuals only carry two mitochondrial haplotypes

Answer 34

Low genetic diversity -- that effect stays even after the popultion increases in size - effect of drift when small popultion stciks around *** Strong drift in historical events can instantly undue the work of natural selection and thousands of generation’s worth of mutation accumulation - when in low popultion size sticks around loss of varaition = low varaition because population crash --> low varaition + effect of drift when small popultion stciks around - Only the varaition from the small popultion gets passed down = ONLY get varaition from 28 inidviuals when small popultion size ***Many the populations of many marine mammals have very low genetic diversity, even if current populations seem large and stable

Answer 35

Many (most) species do not exist as a single continous gene pool -- they are subdivided into seperate pools across space - There are cases of species NOT in subdivsion popultions BUT most are - They are vaiarble across space = doesn't amke sense to treat as one gamete pool Ex. Balck baers in upstate NY do not form a cohesive reproductive popultion with the black bears in florida - Doesn't it make sense to make one gamete pool across all North America because there are baers in florida that are not likley to mate with baers in adirondacls == have subdivisions populations of species

Answer 36

Subdivided = different = important to treat them seperatley 1. Subdivided population can differ due to differences in selection pressures and the mutations that occur in one but not the others - Difference in selection pressures - Difference in mutations --> have different amounts of genetic varaition -- it would be hard to get mutations from one subpopultion to another 2. But they are also bound to differ from each other due to drift - In subdivided populations, random changes are inevitably going to accumulate between them - They are bound to have differences due to drift -- error in one popultion = bound to be different than error in the other popultion = change the subdivided popultions to be difefrent even if they started at the same frequncey ***They are vaiarble across space = doesn't amke sense to treat as one gamete pool Ex. Balck baers in upstate NY do not form a cohesive reproductive popultion with the black bears in florida - Doesn't it make sense to make one gamete pool across all North America because there are baers in florida that are not likley to mate with baers in adirondacls -- have subdivisions populations of species

Answer 37

But they are also bound to differ from each other due to drift - In subdivided populations, random changes are inevitably going to accumulate between them - They are bound to have differences due to drift -- error in one popultion = bound to be different than error in the other popultion = change the subdivided popultions to be difefrent even if they started at the same frequncey

Answer 38

Looking to see the number of populatioons that have the same allele frequncies ALL start at p = 0.5; q = 0.5 - founding population of heterozygous Drosophila subdivided into 107 different populations and maintained at constant population size for 19 generations (each generation they cut back down top 16 individuals) - The frequency of the allele (which coded for eye color -- medielian traiot) was monitored at each step along the way (looked at phenoyype and could get ghenotype) As they go through time the disrabution chnages - Looked at frequncey class over each generation END = get fixed for P = 0 or P = 1 - Inevtiable outcome = lose varaition and get foxation - When hit point of fixation = other allele is gone for good - By Gen 19 – over ½ of the populations had become fixed for one allele of the other. - Variation within individual populations is decreasing Was perfectley even between p = 0 and p = 1 - There was a 50/50 chnace at the start tp fix for one of the alleles (50% fix for p and 50% chnace fix for 1) and get 50/50 split between fixing for p or fixing for q = get a 50:50 avegragse alle frequncei across all of the popultions = close to p = 0.5 - Over all of the frequncies across all popultions get back to p = 0.5 -- even thuough varaitioon within the popultion is lost Variation within popultin is lost BUT varaition across popultions is maintained

Answer 39

Variation within popultin is lost BUT varaition across popultions is maintained -- By producvt of probability based drift starting out - Within popultion varaition decreases BUT maintain varaition across subdivide popultion - Because stochastic = mainatin across popultions Allele frequncey across all popultions = still around 0.5 -- dirft decreased varaition within popultions but moantained varaition across popultions But the probabilities of which allele goes to fixation work out such that genetic variation in maintained among populations at the starting allele frequency

Answer 40

Lost from the population for good

Answer 41

We have 30 fixed for p = 0 and 28 fixed for p = 1 (50/50) -- The rest of the populations are uniformly distributed in the across the rest of the range - Was perfectley even between p = 0 and p = 1 - There was a 50/50 chnace at the start tp fix for one of the alleles (50% fix for p and 50% chnace fix for 1) and get 50/50 split between fixing for p or fixing for q = get a 50:50 avegragse alle frequncei across all of the popultions = close to p = 0.5 Allele frequncey across all popultions = still around 0.5 -- dirft decreased varaition within popultions but moantained varaition across popultions - But the probabilities of which allele goes to fixation work out such that genetic variation in maintained among populations at the starting allele frequency

Answer 42

Start with p = 0.4 --> and subdivide into 10 smaller popultions - Porbability in each popultions = 60% blue and 40% red -- same for all populations (smae proabbility for each one) MEANS 40% on average end red and 60% end blue fixation = IN THE END the avergae varaition will stay the same - Varaition across popultions is mainatained BUT the varaition within popultions is miantained - Axross subdivided popultions = have varaition - Within = lose varaition (Fix for one allele) - When divide into sub-popultions -- each sub popultions strats as the same as sancestrla popultion -- each sub popultion starts with 40% red and 60% blue --> Each subpopultion has 40% chance of fixing for red and 60% chance for fixing for blue --> Each will lose varaition because each will fix for an allele BUT each will fix for different alelle (Because stochastic) so across population mainatins varaition - Since each have the same 0.4 chnace and 0.6 chance --> the most likley outcome is that 0.4 fix for red and 0.6 will fix for blue = maintain varaition across popultions BUT within popultions fiox for one allele (p is either 1 or 0) = lose varaition within popultsions BUT among popultions you still have p = 0.4 and 1 = 0.6 (Still have 60% red and 40% blue-- becaus eexpect 60% of subpopultions to fix for red and 40% of subpopultions to fix for blue) They will all fix for one allele = lose varaition BUT they will fix for different alles = across popultions they keep the varaition - Each popultions has the same probability of fixing for red or blue allele at the start (0.4 chnace of red and 0.6 chance of blue) -- the most likley outcome is that 40% of then fix for red and 0.6 fox for blue --> within popultions p will be 0 or 1 BUT among the popultions p will stay 0.4

Answer 43

Heterozygosity - Use the expected # of heterozygous NOT the observed number

Answer 44

Metric for diversiity --> Genotypic frequency of heterozygotes in the population -- It is the expected frequency of heterozygotes given the allele frequency and assuming HWE - Use the expected # of heterozygous NOT the observed number - Allows us to quantify the loss of variation within populations - Quantify varaition in terms of heterozygosity ***Drift = stochastic --> probability of chnage in alelle frequenceies will occir based on Start in popultions -- FIRST = need to quantofy the loss of variation H = 2pq -- Heterozygosity = epxected frequncey pf heterozygotes given allele frequncdey (Measure of varaition in popultions)

Answer 45

2pq H = 2pq IF p = 0.4 --> Heterozygosity = 2 X 0.4 X 0.6 = 0.48 H = 0.48 IF p = 0.15 --> q = 0.85 H = 0.255

Answer 46

There is more varaition in p = 0.4 than p = 0.15 -- more even mix (cloer to 0.5 and 0.5) = more heterozygoues - If no go fixation = heterozygotsity decreases = less varaition P = 0.4 --> H = 0.48 Q = 0.85; P = 0.15 --> H = 0.255

Answer 47

H = 2pq -- use epxcted number of heterozygotes Example -- If p = 0.4 Heterozygosity (H) = 0.48 ^^ (2 X 0.4 X 0.6) 0.48 = Heterozygosity -- gives alleleic varaition in popultions --> expected number of heterozygote sbased on allele frequncey

Answer 48

Drift = inevitable in population less than infantite in size -- any popultions drift is always there ***Drift = based on Stnadrad error in gamete pool --> Smaller sample = more error - Change then sticks --> get new allele frequncey

Answer 49

Drift = based on standrad error in gamate pool -- error that you don't have the same allele frequncey

Answer 50

Inevitable outcome = loss of varaition over time --> Now chnage in varaition in gene pool for good Lose within subpopultion varaition --> decreases within subpopultion Maintain varaition acriss subdivided popultion -- because stochastic = mainatin varaition acriss popultions

Answer 51

q = 0.85 --> p = 0.15 H = 2 X 0.85 X 0.15 = 0.255 As allele frequncey os more polairized (closer to 1 and 0) = heterozygosity decreases

Answer 52

As allele frequcneies are more polarized (As p/q get closer to 0 and 1) = heteropzygosity decreases - Peak of varaition = when have 50:50 (P = 0.5; q = 0.5) When closer to even amount (Closer to 50:50) = increase varaition (Because increase in H and H is a measure of varaition) P = 0.4 (more 50:50 split) = higher H = more varaition p = 0.15 (more polarized) = Lower H = Less vraaition

Answer 53

Sum of the expecte dfrequncey of each individual heterozygites -- sum of the types of heterozygotes expected frequnceies

Answer 54

We can look at how Heterozygfosity is distubuted

Answer 55

Peak = 0.5 --> Highest H value when we have 2 alleles in the population - IF we start with a popultion with all Heterozygotes --> expected frequncey stays the same IN a two allele system expected Heterozygotsity is highets (Most amount of varaition is highest) at p = 0.5

Answer 56

F we start with a popultion with all Heterozygotes --> expected frequncey stays the same - If have all heterozygotes the observed H mighy be 1 BUT we use the expcted number of Heterozygotes = H will still be 0.5 (Even if observed is 1 -- if we strat with all Aa theb p = 0.5 --> then expected is 0.5 -- H is 0.5 NOT 1) - Use expecetd values for H NOT observed

Answer 57

Relationship is based on average decline in H between generations at a given population size – not deterministic - We can acalculte the average expected decline in H between popultions-- calculating the most likley H (pribabilistic) - Shows how popultion shize affects varaition --> Knowing that in the end we will always lose varaition Hg+1 = Hg [1 - 1/2N] --> Gives chnage in H in next generation - Hg = Heterzygosity of current genertion - Hg+1 = Heterozygosity in next generation - N = popultion size ***ONly parameter is popultion size Results: As N Increases = Avgerage chnage in H decreases - As N Increases = 1/2N gets small = less change in H over time because you are closer to being 1 (if 1/2N is smaller -- 1-1/2N stays closer to 1 because you are substracting a smaller numebr from one) -- If 1 - smaller number = 1 Times the current H = stays close to current H ***We are likley to decrease in H from one generation to the next IF go from p = 0.6 --> p = 0.5 - H is increaseing BUT avergae trend will be to lose varaition ober time -- on avergage = lose varaition --> Losing varaition is the most likley outcome for each generation - Doesn't mean that lsoing varaition is what will happen - We know we will lose varaition BUT we don't know what it will be but we can predict what is most likley

Answer 58

IF go from p = 0.6 --> p = 0.5 - H is increaseing BUT avergae trend will be to lose varaition ober time -- on avergage = lose varaition --> Losing varaition is the most likley outcome for each generation - Doesn't mean that lsoing varaition is what will happen - We know we will lose varaition BUT we don't know what it will be but we can predict what is most likley

Answer 59

Because we are thinkning about alleles NOT individuals --> The individuals in popultions are diploid = 2N for gamete pool

Answer 60

As N Increases = Avgerage chnage in H decreases - As N Increases = 1/2N gets small = less change in H over time because you are closer to being 1 (if 1/2N is smaller -- 1-1/2N stays closer to 1 because you are substracting a smaller numebr from one) -- If 1 - smaller number = 1 Times the current H = stays close to current H As population size increases, the average change in heterozygosity decreases (1 minus a smaller fraction)

Answer 61

Hg+1 = Hg [1- 1/2N] Hg+1 = 0.5 [1 - 1/(2 X 1000) = 0.49975 - HERE = we get a number that is slightley less than 0.5 -- expect small Sampel errow making 1000 zygotes = lose a little genetic varaition but not much We are likley to decrease in H from one generation to the next

Answer 62

SHOWS -- as you decrease N = Larger average chnage in H - At N = 1000 --> have small change in H THESE = NOT showing the actual outcome -- it is shwoing the Avgerage oucome across all possibel ouctomes - Avergae H from Probability N Zygotes --> Avergae their H

Answer 63

NOT showing the actual outcome -- it is shwoing the Avgerage oucome across all possibel ouctomes - Avergae H from Probability N Zygotes --> Avergae their H

Answer 64

Can't in humans BUT we can in other organisms -- plants do it (have self-fertalization) Can you have H = 0.25 in 1 indivdiuals if have 2 alleles --> NO -- BUT the H we calaculate is the averahe outcome NOT the actual outycome - SInce diploid --> single individual -- H = 0.5 --> H = 0 -- THEN have 0.5 + 0/ = 0.25 ---> Have will be 0.5 and 1/2 will be 0 and take average

Answer 65

We can look at the effect of drift through time - Before = we were just looking at one generation - Heterozygostity is lost after many generations (Alleleic shake up but to drift over time) TO make it for across generations = Had T expeonent -- add t to generations HERE = we assume that the popultion size is the same across multiple generations Hg+t = Hg [1 - 1/2N]^t t = numbver of generations

Answer 66

Hg+t = 0.5 [ 1 - 1/ (2X 100)]^10 Hg+t = 0.4755 We expect a >0.1 shift across time -- average change in allele frequnceies = >0.1 across 10 generations due to drift itself - Affect of mutations = needs more gernations to have allele freuqncey chnage BUT gere = have substantaial frequcey change HERE Even with a population of a 100, over 10 generations, we’re expecting an average allele frequency shift of over 0.1

Answer 67

Affect of mutations = needs more gernations to have allele freuqncey chnage BUT With drift = have substantaial frequcey change in shorter amount of time With drift -- even with a population of a 100, over 10 generations, we’re expecting an average allele frequency shift of over 0.1

Answer 68

We can graph how popultion's genertic varaition should decay within popultions over time --> We can make a graph tp make predictions about how genetic varaotions hould decay over time GRAPH -- RED = actual data Dotted line = prediction for avergae H chnage in 19 generations for popultion of 16 - Prediction of 16 -- Expect loss in h at the rate in the graoh THEN confront the prediction with data from experiment These two lines are slightley different -- because dirft is probabiolistic - The prediction for 16 doesn't hold up that much Results: H Decreased faster than expected given the popultion size of 16 - Some b ehaved as expected (fized for P = 0 or P =1) --> overall P = 0.5 across the generaytion - BUT the loss of varaition happened faster than expected -- the data matches a theroetical prediction based on population size of 9 ratehr than a popultion size of 16 - KNow that thyere were actually 16 indiviuaks in each generation but drift axross genertaion occured fatser than exoected DRIFT = faster than cencus popultion --> This is very common

Answer 69

Confronting models with data from the real world

Answer 70

We can make a plot that shows the expected decline in genetic diversity through time for a given popultion size

Answer 71

Gives expected line in expriements -- when look at real data vs. expected data for chnage in H over time To get the line = need to have N the same (Keep the same popultion size BUT change t) Plots the decline in H iover time Keep N the same -- only chnage T ONce find data = can plot the points -- gives expected line - Do prediction for how popultion will behave then test the hypothesis

Answer 72

Often occurs much fater than epxcted (like in dropshilla experimnet) - Populations often druft faster than we would epxect based on their true popultion size -- instead they dirft at the rate of a smaller population Drift = often occurs faster than censeus popultions -- common --> often occurer faster thna expcted based on popultion size itself - Because often dirft is based on teh effective popultion size rather than the true/cecus size

Answer 73

Census -- actual popultion size -- true popultion szie (Ex. in dropshilla experiment = 16) Effective popultion size -- The popultion size expected to match the realized rate of drift DRift = based on Ne (Ne is smaller than N)

Answer 74

The popultion size expected to match the realized rate of drift - Ne = # of indiviuals actually reproducimng in popultion - Actual indovdiouals contributing to the gene pool that we are misampling from DRift = based on Ne (Ne is smaller than N) Example -- Efefctive popultion size in dros[hila expeirment = 9 -- only 9 breeding indidviaiuls on average --> 9 indidvuals on average reprdoucing (7 do not) - 16 = cencus size - 9 = Ne

Answer 75

Because of 3rd postulate of NS --> Varaition in popultion ins S/R even if unrelated to phenotypes/genes - JUst have varaition in S/R (doesn't need to vary at as a function of a triat] If dirfting at N --> All indiviaual probability of S/R = 1.0 -- dorft at N = drifyoing at the actual counyd of Indiodvuals (Census popultion size) - Dirfting at N = everyone has probability of 1 - Phenotype is not affecting proibabiliyu Vs. Drifting at Ne (Effective popultion size) - HERE = 60% chnace of reproduction --> NOT per phenotype (Still uniform distrubution across all phenotypes) BUT all have probability of 60% = not all S/R - Actual breeding popultions = NOW subset of overall popultions --> NOT all repriduce = # of indiviualks reproducing = Ne DRift = based on Ne (Ne is smaller than N = more dirft = drift occurs faster in most popultions than epxected) - Because variation in S/R = drift occurs more powerfully than if it was just based on census size alone

Answer 76

Comes back to our nearly universal postulate for natural selection: not everyone gets to survive and reproduce (even when that’s unrelated to genotype) Not everyone participates in reproduction (without regard for their phenotypes or genotypes) - Different than selection -- because in selection not everyone contributes to the next generation BUT it is due to their traits -- HERE = the probability of participation is uniformly distrbuted just at a level lower than the actual popultion size - Here = not varying as a fucntion of genotype/phenotype Because variation in S/R = drift occurs more powerfully than if it was just based on census size alone

Answer 77

We will just look at sex ratio --> Sex ratio makes a big difference in effective popultion size Equation -- Ne = 4NmNf/(Nm + Nf)

Answer 78

The sex ratio of individuals participating in reproduction makes a big difference in effective population size = affects the rate of genetic drift - Big skew in sex ratio = affects N vs. Ne - N vs. Ne = very affected by if there is a big difference in males vs. females = affects the rate of drift

Answer 79

1. Polygamy -- One male + many females - Very common in nature 2. Polyandry -- One female + multiple males - Less common in natire but sometimes is still very important Throughs off the sex ratio = affects the rate of genetic drift

Answer 80

Example -- rate of drift in popultion starts the same In mating popultions 1 Bull = mates with 25 females If have 500 in popultions --> 250 femnales -- if have 1:25 mating ratio --> only 10 males mate 250 females (50:50 sex ratio) --> only 10 males mate - IN mating popultion only have 10 males and 250 females -- sampling acros 250 females + smapling across 10 males = very little varaition Equation: Ne = 4NmNf/(Nm + Nf) Nm = # of mating males Nf = # of mationg females Ne = 4 X 10 X 250/ (10 + 250) = 38.5 - 38.5 = much smaller than 500 --> Sex ratio throughs off Ne a lot ***Sex ratio throughs off Ne a lot

Answer 81

If N = 500 (much bogger) = varaiotion stays for a while If N = 38.5 (Ne = 38.5) = much more drift occurs = lose varaition much faster

Answer 82

If we chnage ratio to 1:5 --> NOW have 250 females and 50 males Ne = 166.78 -- Still much less than 250 ***STill a serious concern for conservation

Answer 83

We expect genetic variation to decrease within populations, but not among populations – we can compare those two levels

Answer 84

Compoare the within popultion varaition to the between sub popultion varaition - Look at varaition iwthin popultions vs. varaition between popultions to see how much drift has gone on - We can quantify the degree of genetic differentiation that drift has caused between these populations by examining heterozygosity within and between them Compare Observed vs. expected value to see how effective dirft i

Answer 85

Example -- eaisest to look at 2 sub popultions of the same species - Look at the varaition loss within the popultion and compare that to the exoected between popultions - Look at varaition iwthin popultions vs. varaition between popultions to see how much drift has gone on We can quantify the degree of genetic differentiation that drift has caused between these populations by examining heterozygosity within and between them Start = find H within each popultions and take avergae of H of the two popultions - Start by calculating the expected Heterozygosity within both populations and taking the average Population 1 H = 2pq P = 0.35 H = 0.455 Population 2 P = 0.8 H = 2pq = 0.32 THEN avergae varaition within the popultions -- take Average of both H H pop 1 + H pop2/ 2 = 0.455 + 0.32/2 --> Hs = 0.38756 Hs = Average H across the two popultions THEN -- We need tp turn to finidng the expected H if this was one big connected popultion --> Do so by combing the allele frequncies and Calculate H as before - Now we need H if one popultions --> Exopected H based on the avwerage allele frequcnies across the popultions - Find H if you take an avergae of the allele frequncies - If we assume equal popultion size = combined allele frequencey os just the average of the two Find Average P = 0.35 + 0.8/ 2 = 0.575 --> combine the alelle frequncies if in one popultions - Average alelle freqincey (assuming that they have teh same p[opultion szie) -- get alelle frequncey if they were one popultion - Means that if all of the indiovdiuals belongs to the same big popultion -- the allele frequcney would be o = 0.575 --> now we can use this to calculate the expected H across all popultions THEN find H with teh Average P --> Ht = 0.489 (2 X 0.575 X 0.425) - Gives you the expected H across all popultions THEN -- we can use these numbers to quantify the degree of magnbitude of genetic difference between the popuotions using FST index - Now look at the difference between the two - Divide by the total amount of varaition in popultion Hs = should always be equal to or smallter than Ht FST = Ht-Hs/Ht FST = 0.489 - 0.388 = 0.489 FST = 0.207

Answer 86

Hs = for sub popultion (Find each H for each popultion and take Average of H) Ht = H in total popultion (Suing Average allele frequceny) - Find avergae of P or Q and then find H based on Average P or Q

Answer 87

Populations A - Have no varaition within the popultions BUT compare to the varaition between popultions - HERE -- no varaition within popultions --> ALL varaition is between popultions P1 = 0 P2 = 1 Hs = 0 Ht = 0.5 - All of the varaition is between the popultions -- none of the varaition is within the popultion -- all of the varaition is exists between popultoons FST = 1 Population B P 1 = 0.52 P2 = 0.48 HERE -- Most of the varaition is within popultions --> there is little vraaition between popultions - Here there is the same amount pf varaition within as there is between popuoltions Hs = 0.4992 HT = 0.5 FST = 0.0016

Answer 88

FSt = indicates how close the popultions are from having drifted to fized differences from each other FST = between 0-1

Answer 89

FST = 0 --> No difference in allele frequncey between popultions - - Most of the varaition is within popultions --> there is little vraaition between popultions - Can teat as one population -- little variation between subpopulations FST = 1 -- Popiultion is fixed for allele = ALl of the varaition is between popultions - All of the varaition is between the popultions -- none of the varaition is within the popultion -- all of the varaition is exists between popultoons

Answer 90

FST = used very often --> Why calculate it Example 1 -- baer survivorship population - If we are hunting baers in Florida = we might wnat to know how they connected they are to baer popultion in other places --> if have differences = might have to say they are different BUT if FST = 0 --> They you can treat them at one population - Little genetic varaition between them = treat as one popultion Example 2 -- Used in epidemialogy --> Have a certain parasite that causes disease - Have a parasite that causes diseae + a vector (Parasite gets to misquitos and masiquiotes infect people) --> If want to control the disease = might need to think about popultion of parasite + vesctor popultion - Might have 2 popultions a a new variant of drug resistant nematodes --> need to know how worries are you that they will go to the other popultion -- might look at genetic differences between popultions + look for the same thing for masquitos - Quation = are they sepearet or is the FST LOW -- Look to see IF the two popultions are genetically differemt IF FST is low = the popultions are more in contact with each other

Answer 91

Drift = very strong evolutionary force in small popultions -- BUT in large populions ir may still be important over long time scales driving a constnat chnage at nuetral loci ***Drift = largley driven by popultin size - Different popultion size = affects the rate of drift - Smaller popultions -- drift occurs more rapidly

Answer 92

For a long time biologicsts thought No because genetic affect in large popultion is Subtle but not the case --> In any non-infinate popultion dirft occurs in background and see affect in the genome --> We know becayse we see change at. nutral loci

Answer 93

We know because we can see chnage in nuetral loci ***Drift in large popultions dirves constant change at nuetal loci If only selection = should only have to do with things that affect fitness but since doesn't affect fitness = can't be selection = we know drift cuases chnage in large popultions

Answer 94

Neural means selection is nuteral -- not associated with fitness = no selection - By nuetral we mean alelleic chnages with no fitness consequcnes -- not everything has an efefct on fitness --> Many phenotypes (even gentic oenes) = doesn't affect lifetime reproductive sucess = close to nuetral in popultion - Not everything matters for survival and reproduction -- many phenotypes (even ones with strong geentoc compeonents are neutral) -- espcailly in modern humans Example -- Height --> is the number of hids any one person is going to have vary as a function of hieght -- NO = nuetral trait - If only selection = should only have to do with things that affect fitness but since doesn't affect fitness = can't be selection = we know drift cuases chnage in large popultions

Answer 95

Chnages to DNA sequcne that do not affect peptide strucrture in coding region -- have synonmous codon chnage - In codon table --> Most amino acids (Exceot Trp and Met) = are readundant (Multiple codes specifiy the same amino acid) - Know it is nutral when change in DNA but have the same Amino acid = same Primary structure = same protein = no affect on phenotyoe There are a lot of varaints -- most varaints that are like this --> Can't affect phenotype = NS can't act = chnage in ferquncey MUST be due to drift

Answer 96

Varaints that are nutral at the molecular level -- with drift = focus on neutrality at the molecular lebvel They found this in 1960s -- realized once they looked at varaition on molecular level --> Sequcne proetin and then got DNA varaints --> HERE = there is no domiant or recssuve because no affect on phenotype

Answer 97

They found this in 1960s -- realized once they looked at varaition on molecular level --> Sequcne proetin and then got DNA varaints --> FOund that there was a lot of varaintion = At odds with the idea that NS drived all the varaintionn bevause the bulk of the varaition is nuetral = NS cam't act on it

Answer 98

The idea of long-term drift in large populations being an important evolutionary forces came about when were able to start observing variation at the molecular level – and some of it seemed odd if differences were driven by selection

Answer 99

Drift = Function of population size a larger population = expected allele frequency change = weak force in larger population --> Why should we care in a large population

Answer 100

For a long time they didn't thnk drift was important in a large popultion THEN when looking at the molecular level = they found controdictions to idea that drift isn't acting in large popultions When looking at the molecular level they found that most varaition within/between species = selectivley nuetral --> no affect on phenotype = can't affect surviva/reproduction = not chnaging due to natural selection = due to something else causinhg nuetral to change

Answer 101

When looking at the molecular level they found that most varaition within/between species = selectivley nuetral --> no affect on phenotype = can't affect surviva/reproduction = not chnaging due to natural selection = due to something else causinhg nuetral to change

Answer 102

With drift we focus on neutrality at the molecular level

Answer 103

The idea of long-term drift in large popultions being an important evolutionary force came about when we were able to start observing varaiation at the molecular level and some of it seemed odd if difefrences were driven by selection

Answer 104

Synonymous mutations -- nutral mutation --> means you get the same Amino Acid Mutation were if you change nucleotide sequence = can still specify the same amino acid = the secondary and tertiary structure is the same = function is the same = change to DNA that can't affect genotype - Still herediatry change in coding region

Answer 105

Genetic code = redundant --> can make Amino Acid by specifying more than 1 codon --> if you change nucleotide sequence = can still specify the same amino acid = the secondary and tertiary structure is the same = function is the same = change to DNA that can't affect genotype

Answer 106

Sequence genome -- variation = mostly changes that don't affect phenotype --> changes that don't affect Amino acid = don't affect phenotype A lot of varaition in protein coding regions = synonomous mutations (Within and among species)

Answer 107

How would this varaition build if Natural selection can't see it (no difference in S/R if can't make a phenotype) ANSWER: due to druft

Answer 108

Issue with varaition = how would neutral varaiation build if NS can't see it ANSWER -- can build due to drift - Change is due to drift NOT due to Natural selection

Answer 109

Thought that varaition can build due to drift in large popultions id all popultions had bottleneck events over time ISSUE = this doesn't scale up with what we see in nature (not seen in fossil record)

Answer 110

Change in code that leads to different amino acid

Answer 111

Constant rate -- Nuetral varaition appears to build at a constant rate Varaition builds in clocklike reptative rate

Answer 112

Varaition builds in clocklike reptative rate --> Variation builds in regular constant fashion = suggests it is NOT bottleneck

Answer 113

1. Not seen in fossil record 2. Does not match the clocklike fashion that we see

Answer 114

Done through nulceotide substitution (Mutation + Substitution) AND drift Some mutation goes to fixation because of drift

Answer 115

New varaition enters popultion as mutations but its converted tp varaition between popultions or species by substitition - Some mutation goes to fixation because of drift = mnucelotide substitution - Some new mutations randomly drift to fixation Substiution = fixation of one allele in plavce of other

Answer 116

Because of drift (In mutation and substitution)

Answer 117

Start = all yellow --> THEN have a mutation that drives a new alelle = get green Green = new variation - When you get the green eacvh copy of each allele has equal probability of going to fixation due to drift - THE green = can go to fixation HERE = have mutations + substitution --> When get all green DUE TO DRIFT = have substitution event -- no longer have the ancestral yellow only have the new green - No one allele is favored just have random change --> can get fixation of the new mutation

Answer 118

Fixation of one allele in plavce of other

Answer 119

Strength of drift = varies as a function of popultion size BUT mutation rate doesn't vary BUT the number of mutations does vary with popultion size - Number of new nuetral alleles in each popultions = 2nv Number of mutations increase as N increases Probability of any one alelle going to fixation = 1/2N (each alelle has equal probability) - 2nv = increases with N - 1/2N = decreases with N As N increase (popultion size increases) = probability of any one allele going to fixation decreases - As N increases = have more mutations but each one is less likley to drift to fixation (probability of going to fixation decreases as N increase) MEANS that the probability of getting a mutations AND the probability of that mutation going to fixation: 2Nv X 1/2N = v -- 2N cancles out = just get v as drive of nuertal substiutution in generation - Each generation the number of new mutations that are destined to become substititions --> 2nv X 1/2N = v -- population size cancel out completley Popultion size affects the affect of drift + the affect of number of mutations --> decrease of affect of drift = counteracted by number of mutations that as v increases as N increases -- effective population countercat of net result In small popultons = each allele has a higher chance of going to fixation VS. In large popultions more alelles come into existances --> The effect of popultion size balances out perfectley = only based on nuetral mutation rate = can occur in larger popultions

Answer 120

2nv -- get the number of new mutations in generation (Mutation rate times the number of gene copies in the population) v = rate of mutation N = number of allele copies

Answer 121

v = drives of nuertal substiutution in generation

Answer 122

Popultion size affects the affect of drift + the affect of number of mutations --> decrease of affect of drift = counteracted by number of mutations that as v increases as N increases -- effective population countercat of net result

Answer 123

1. New mutations 2. Drift BOTH vary as a function of N

Answer 124

Small populations = make new alleles but higher probability of going to fixation

Answer 125

The expected rate of nuertal substibution by drift is equal to the mutation rate In small popultons = each allele has a higher chance of going to fixation VS. In large popultions more alelles come into existances

Answer 126

In small popultons = each allele has a higher chance of going to fixation VS. In large popultions more alelles come into existances --> The effect of popultion size balances out perfectley

Answer 127

The effect of popultion size balances out perfectley = rate is ONLY based on nutral mutation rate --> if we assume that the mutation rate stays constant over time then this shjould result in constant clocklike rate of nuetral evolutionary chnage - Mutation rate = the same through time = expect to build constantly over time = get constant rate

Answer 128

Relationship with time since ancestor + rate of mutation building

Answer 129

We can look at time of divergenge using more data --> look at time based on mutation --> drift change builds in constant clocklike way

Answer 130

Because nonsynomous mutation have effect on fitness = we expect far fewer of them to be neutral BUT some are nuertal and we expect these substitutions to accumulate too just at a slower rate Rate = gives us a null expectation for coding region differences should accumulate in the genome

Answer 131

Synomous = nuetral Nonsynomous = can be efefctvley nuetral (might not change protein in important way = doesn't affect phenotype) BUT the nuetral ones occur at a lower rate than synomous Expect synomous and non-synomous to build at different rates - Non-synomous rate = lower -- get more synomous per unit of time than non synonomous because all synomous are nuetral Looking at the rates = allows us to build a null model for expevctations for coding diferences should accumalte in the genome - Can see if constsint change is based on idea that something is driven based on dirft -- gives evidence that NS is driving change

Answer 132

Expect to have a lower rate of nuerral non-synomous mutations than synomous mutations because some of the non-synomous have an effect

Answer 133

Looking at the rates = allows us to build a null model for expevctations for coding diferences should accumalte in the genome - Can see if constsint change is based on idea that something is driven based on dirft -- gives evidence that NS is driving change - At a given amount of accumulated neutral differentiation (amount of time separating species) - we should have an expected ratio of synonymous to nonsynonymous substitutions across the genome --> Selection favoring non-synonmous mutations should throw things off this expevctations (we can infer that patterns are the result of positive sel;ection by idetofying deviations from this ratio with higher than expected non-synonmous substitutions ratyes being driven by NS) - We expect this ratio to be pretty similar across the genome for sites that are evolving neutrally (with synonymous substitutions outnumbering nonsynonymous ones) IF not drift ratio of synomous to nonsynomous = allows us to have evidence that NS is driving change When looking at the rates = can get ratio of synomous vs. nonsynomousover seperating over time diverging = deviations form ratio = indicative that natural selection is driving chnage - Deviations from ratio = chnage is not due to drift = NS can be in process - (we can infer that patterns are the result of positive sel;ection by idetofying deviations from this ratio with higher than expected non-synonmous substitutions ratyes being driven by NS)

Answer 134

Example -- BRCA1 gene (Gene heavily implicated in breast cancer) --> Appears to have been under string postive selection relativley recetley -- because the ratio of Non-synomous:synomous is > than 1.0 - Looking at the ratio -- shows that most of the ratios are below 1 for most species until humans and chimps - Humans and chimps = have many non-synommous mutations compared to expectation of drift --> chnage = due to natural selection in common ancestor of humans and chimps Change see Natural selection is occuring nased on deviations from ratio based on drift alone = NS acted to shape varaition

Answer 135

MCR1 gene in plumage color --> see 1:1 correlation between degree of sexual dymorphism and degree of natural selection acting on the gene

Answer 136

Because of population size and body size of organisms