Population Genetics

Question 1

genotype

Answer 1

pair of alleles an individual inherited from parents

Question 2

genetic fitness

Answer 2

determined by genotypes carried by an individual

Question 3

evolution

Answer 3

change in allele frequencies over time; does not work on genotypes directly

Question 4

genetic varriation

Answer 4

at any locus if there is genetic variation there are multiple alleles and the locus is polymorphic

Question 5

locus

Answer 5

location in genome

Question 6

phenotype

Answer 6

depends on genotype and enviornment

Question 7

frequency of alleles

Answer 7

must add up to one; frequency of allele is odds of picking genotype at random time of odds of picking that allele from within the genotype

Question 8

Hardy-Weinberg theorem states

Answer 8

1. the allele frequencies p and q will not change over time (after single generation, no matter what starting genotypes are the allele and genotype frequencies will not change if the assumptions are met)
2. The expected genotype frequencies of a11, a12, and a22 will be p^2, 2pq, q^2 respectively (assuming organism is diploid, locus= autosomal, only 2 alleles present, can extend equation to factor in other cases though)

Question 9

5 assumptions of Hardy- Weinberg theorum

Answer 9

1. Locus not under selection (all genotypes are equally fit)
2. No new migration occurs at the locus (no new alleles)
3. No migrants enter the populations (no new allele)
4. The population size is infinite (no genetic drift)
5. Individuals mate randomly (no inbreeding or assortative mating)

Question 10

domestic animal populations and Hardy-Weinberg theorem

Answer 10

domestic animal populations break all 5 assumptions but it is an excellent approximation to reality especially for majority of loci not under selection

Question 11

Using Hardy-Weinberg equation can prove that frequency of heterozygotes is highest

Answer 11

when p=q= 50%

Question 12

using hardy-weinberg equation can prove that rare allele are

Answer 12

almost always heterozygous; when p=.5 then half pop is heterozygous a12 (2pq=.5) and rest is either homozygous a11 (25%) or a22 (25%); p=.01 (a1 rare) freq(a12) is 1.98% and freq(a11) is 0.01% meaning 198x more likely that A1 is heterozygous than homozygous recessive

Question 13

Hardy-Weinberg law describes

Answer 13

equilibrium state of locus in a diploid population after 1 generation ( and every subsequent one)

Question 14

a11 a12 a22 same as

Answer 14

a11= AA
a12= AB
a22= BB
if easier to think of that way this is how it was described in power point

Question 15

Why are rare alleles hard to breed out of population

Answer 15

Rare allele almost never seen because if someone has it they’re usually heterozygous and ok, v rare that you end up with a someone actually expressing it; could use genetic testing to see who is carrier for it to make sure they don’t mate or at least don’t mate with another heterozygote

Question 16

Hardy-Weinberg with 3 alleles

Answer 16

Freq (A)=p ; Freq (B)= q; Freq (O)=r
Freq (AA)= p^2
Freq (BB)= q^2
Freq (OO)=r^2
Freq (AB)= 2pq
Freq (AO)=2pr
Freq (BO)=2qr

Question 17

Why is frequency (AB)= 2pq

Answer 17

bc we count AB and BA as same so mult by 2

Question 18

2 or more loci

Answer 18

unlinked loci (ie diff chromosome) then just mult independent events together bc diff chromosomes means these events aren’t linked this = linkage equilibrium

Question 19

when alleles at two loci tend to co occur they are in

Answer 19

linkage disequilibrium

Question 20

linkage disequilibrium

Answer 20

can occur if there is non-random mating (ie yellow labs tend to mate with yellow labs black labs tend to mate with black labs); can also occur if two loci are very close on same chromosome (ie there is physical linkage btwn the two)

Question 21

Haplotype

Answer 21

particular sequence of alleles along a chromosome (think half the genotype; have two sets of chromosomes one from mom one from dad and so at every locus have two haplotypes; haplotype is on actual chromosome molecule, can’t physically hold more than one allele at each marker than exists along it

Question 22

haplotype theory vs reality

Answer 22

in theory if three balletic markers there are 8 possible haplotypes (2x2x2=8) but in reality almost never see all possible hapoltypes; this is because to see all of them crossovers would have to occur btwn all markers in the haplotype but for many close markers there have been zero cross overs; can also loose haplotypes bc drift

Question 23

haploid diversity

Answer 23

higher in large and old populations; lower in small and young populations

Question 24

haplotype diversity and bottle necks

Answer 24

decides following a population bottleneck bc many are lost by drift during bottleneck can -> less fitness in subsequent generations

Question 25

recovery of genetic diversity

Answer 25

takes a v long time to replenish once lost, replenishes through accumulation of new mutations and recombination

Question 26

recombination

Answer 26

everyone gets diff pieces of chromosomes (maternal and paternal) but cousins and things can end up with identical pieces because certain things get chunked together

Question 27

ancestor vs present day Linkage disequibibrium

Answer 27

if ancestor has one super useful gene that everyone inherits and it becomes monomorphic will see this in everyone but will see diff chunks of same genes around it bc of recombination

Question 28

perfect linkage disequilibrium descprition

Answer 28

if you have hapolotypes and you know 3rd marker (looking at 4 variable sites total) and from 3rd marker know what will be at 4th marker with 100% certainty; linkage disequilibrium means correlated; 100% linkage = perfect linkage disequilibrium

Question 29

linkage disequilibrim definition

Answer 29

non random association of alleles at pairs of markers; will have different expected and observed frequencies if markers have linkage disequilibrium

Question 30

reporting linkage disequilibrium

Answer 30

always reported for a pair of markers; most common LD statistic is correlation coefficient r^2

Question 31

r^2

Answer 31

if = 0 then markers are completely unliked (PAB=PAPB); if they are in perfect linkage disequilibrium then it =1 (ie if you know genotype at A you also know genotype at B)

Question 32

farther apart two markers along a chromosome are the ___ linkage disequilibrium you expect to observe

Answer 32

less; ie things farther apart means less chance they are going to be linked together

Question 33

PAB PA PB

Answer 33

``` PAB= frequency(AB genotypes) PA= frequency(A allele) PB= frequency(B allele) ```

Question 34

what increases the distances at which we see high LDs

Answer 34

population size and history, founder events and bottlencekcs

Question 35

why are human LD values dropping to low levels are shorter distances between markers than dog breed populations

Answer 35

bc dog breed populations have had severe bottle necks recently and humans haven't; after bottle necks haven't been enough time for recombination to break up non random associations btwn markers in close proximity ie humans have had more time for things to be broken up leading to lower LD at things closer together

Question 36

across multiple dog breeds LD

Answer 36

decays quickly; few haplotypes within a breed across breeds there are many

Question 37

how does LD arise

Answer 37

when new allele is born it is in LD with entire chromosome; as it exists longer recombination will break it up from its friends and break LDs

Question 38

recombination

Answer 38

generates new combinations of alleles (new haplotypes) by crossing over; this erodes LD; more likely to occur for markers farther apart; LD between young (new alleles) is high (bc haven't been around long enough to be broken up yet) and is low between old alleles (unless under selection) (bc longer around means more time for recombination to split you apart)

Question 39

LD different in diff breeds

Answer 39

breeds with more bottlenecking have less genetic diversity

Question 40

decay of LD within populations

Answer 40

pure breeds have less genetic diversity than village dogs which have less genetic diversity than wolves (wolves have lowest LD bc most genetic diversity)

Question 41

LD and gene mapping

Answer 41

1. start with mapping in species or population in which LD extends long distances (millions of bps); requires relatively few markers and adequately covers the entire genome for genome wide association 2. Finish with mapping in species or population in which LD extends over short distances where fine mapping resolution will be higher (but depends on selective sweep) and where you may more readily identify the causal mutation

Question 42

haplotype diversity in part due to

Answer 42

population events such a bottle necks that most breeds have experienced

Question 43

LD is a correlation between allele states at markres

Answer 43

- genome wide association capitalizes on presence of LD to "cover" a genome with markers that assay "unshuffled" haplotype regions - long range LD hampers efforts to finely map mutations w/ in an associated interval - LD can be long or short range in diff populations and sometimes this is useful tool for mapping