Exam 2 Ch6-10 Flashcards
(195 cards)
1
Q
What founded the field of population genetics?
A
The Modern Synthesis
2
Q
A theory of evolution combining the ideas of Charles Darwin, mendelian genetics and statistics.
A
The Modern Synthesis.
3
Q
What founded the field of population genetics?
A
The Modern Synthesis.
4
Q
What are Darwin’s 4 postulates?
A
- Individuals within a species are variable.
- Some variation is passed to offspring.
- more young are born than can survive.
- individuals with favorable variations survive to reproduce. (non-random survival and reproduction.)
5
Q
Allelic variation exists among individuals?
A
Darwin postulate.
5
Q
Alleles are passed down Via meiosis and fertilization.
A
Darwin postulate.
6
Q
What is the definition of evolution?
A
The change in allele frequencies in a population over generations.
7
Q
evolution at the population level:
A
Microevolution.
EX: flies developing traits that make them more resistant to pesticides.
8
Q
What is Hardy-Weinberg equilibrium Principle?
A
This is a null model of how populations act when evolution is not occurring.
9
Q
What are the 5 things that occur for a population in HWE?
5 assumptions?
A
(No Evolution) No Changes in allele frequencies, These thing cause that.
1. Random mating/ No selection.
2. No Mutation
3. No Migration.
4. (infinitely) Large population size.
5. Diploid sexual organisms.
6. No Random Events or Genetic Drift.
10
Q
What is a group of interbreeding individuals and their offspring?
A
a population.
11
Q
What is a diploid organism?
A
One which inherits to copies of sister chromatids, one from mother, one from father.
12
Q
In a population 60% of gametes received A, remainder received a. What Proportion of genotypes will be aa?
How many Aa?
Assuming HWE.
A
aa: 0.16
Aa: 0.48
13
Q
What is the HWE equation?
A
q2+2pq+p2=1
14
Q
What is the point of using HWE since we know most of the assumptions are taking place?
A
- Can use it to show when evolution is not occurring.
- has specific testable assumptions which are violated then HWE conclusions will not hold.
- Good to use as the null “hypothesis.”
15
Q
All alleles stay in the gene pool for a population, what does this mean?
A
No migration.
16
Q
Can HWE equation be used to calculate allele and genotype frequencies of all populations?
A
No! Not all populations are in HWE.
17
Q
What does it mean if HWE is in disequilibrium?
A
That the HWE equation will not accurately predict genotype frequencies on it’s own.
If allele frequencies changed causing the disequilibrium then evolution is occurring, but this is not always the case.
18
Q
What type of equation is HWE?
A
A binomial equation.
19
Q
Test used to determine the probability of acquiring the results acheived?
A
Chi-Squared test.
20
Q
What are the 4 steps of a chi square test?
A
- Calculate allele frequencies observed.
- Use the frequencies observed to calculate expected frequencies of genotypes if the pop was in HWE.
- Use expected frequencies to calculate for expected individuals based on pop total.
- Chi Square test (O-E)2/E for each genotype and add the totals, this will give you the Chi Value. (2 alleles is 1 degree of freedom.)
21
Q
How many degrees of freedom for 3 alleles?
A
3.
22
Q
What must be heritable for evolution by selection to occur?
A
Phenotypic heritability.
23
Q
When allele frequencies are changing in a population what are the HWE violations that could cause this?
A
Selection
24
If in a population The genotype aa causes a deleterious recessive mutation (0.5%) survival rate, what will be the genotype frequency in the next generation 100 individuals?
Currently 200 individuals in HWE, where A frq= 0.6.
A=0.6, a=0.4.
(0.4)2=0.16
0.16 * 0.5=0.08
0.08 is frequency for survival out of 200 O.G. so, 0.08 * 200=16 (aa) surviving offspring.
16/100=0.16 is the new genotype frequency.
25
When given a survival rate for a genotype currently in HWE how can that be used to predict the next generation?
HWE can be used to find the allele and genotype frequencies.
Genotype frq * the survival frq= offspring frq.
Offspring frq * the OG Pop= # offspring in the next gen.
Once the total population calculated (all genotypes) you can then find the new allele and genotype frequencies.
Technically this violates conclusion #2: genotype frequencies will be given by q2, 2pq, p2 since we added in the survival rate.
26
What happens when an allele is strongly favored?
That allele will quickly increase in frequency and may even become fixed. Speed can depend on dominant Vs Recessive and OG frq
27
What does it mean when an allele fixates?
This is when an allele becomes homozygous for all of the population.
28
What are the 2 fundamental conclusions of HWE?
1. Allele frequencies are unchanging.
2. genotype frequencies will be given by q2+2pq+p2=1
29
How can selection violate HWE without changing allele frq?
In cases of selection such as over-dominance the allele frq do not change while genotypes frq do, this violates #2. genotype frequencies will be given by q2+2pq+p2
Also violates the non-random mating and inbreeding may also cause this.
30
What is the equation for degrees of Freedom?
Df=K-1-m
K= # of genotypes/ classes
m= the # of values (allele frq) we can calculate from the data. So if we can find a=0.4, we already know A=0.6 in a two allele system
31
Equation to determine # of possible genotypes from alleles available?
n*(n+1)/2
32
A mutation preventing infection of HIV (75% lethality) occurs in a population: r @ 1% frq. HIV has a 2% infection rate in the population. What is likely to happen after many generations and why?
(no intermediate advantage)
The allele frequency is likely to stay about the same, since it has such a low frequency the alleles are really only going to in the heterozygotes, in this case no advantage. EX: q2= 0.01*0.01=0.0001 Vs 2pq= 0.01*0.99=0.0099
33
What are the 2 things impacting allele frequencies?
initial frequencies and selection strength.
34
There is a deleterious allele in a population yet has not been lost due to selection, what is likely happening?
It is likely that the gene is rare, recessive and surviving in the heterozygous individuals, or hybrid vigor could be occurring.
35
A recessive deleterious allele is in a population starting at 0.5 frq, what is likely to happen?
(Hetero not affected)
The allele will likely slowly decrease in time until it is hidden in heterozygous individuals.
36
What are the S & W selection coefficients?
S: Strength of selection. (+1= strong & For, -1 against- die off.)
W: Fitness (ranges from 0-1) 0 is bad.
EQ: W=1+/- S
37
W//=1-S What does this mean?
What if S=1
Fitness (W) of recessive (//) minus the selection strength.
1-1=0 fitness (W) and that genotype would flat out die.
Selection against homozygous recessive.
38
W++=1-S
W+/=1-S
What does mean?
This is selection against both the hetero and homozygous Dominant genotypes, meaning the Phenotype is selected against.
39
What happens if an allele is advantageous dominant?
The allele will much more quickly reach fixation and have a concave graphical curve over generations.
(Concave: boer goat)
Vs how a recessive would reach fixation under similar selection (Convex)
40
What is hybrid Vigor or Over-dominance?
Heterozygote advantage.
41
What are two factors that maintain genetic diversity on a genotypic level?
1. Over-dominance within a population.
2. Frequency Dependent selection.
42
You study a loci in population of cats for E and e. When allele frequencies for E are initially >0.6 it goes to fixation, but lower than that and it is lost (e taking it's place) from the population. What could explain this?
Heterozygote disadvantage. (Pushes alleles to either loss or fixation.)
43
What will happen to allele frequencies in over dominance Vs under dominance?
Over- will reach an equilibrium. Under- will reach poles of fixation or loss, regardless of if recessive or dominant is more or less fit.
44
Within a population of fish they are either left or right mouthed. They attack from the respective side, over time the prey fish start to learn to be wary of the side they're mostly being bit on. What is this selective pressure?
Apostatic/ negative frequency dependent selection.
Maintains around the same alleles frequencies with up and down fluctuations.
45
What are "back mutations"? are they common, why?
When a mutated allele has a "return of function" mutation.
These are basically negligible due to chance of this happening being so rare. "Lots more choices for something to go Wrong Vs. Right."
46
Is Mutation on it's own enough to change HWE assumptions?
Not really, even high rates of mutation don't do much.
Needs selective pressures to really work.
47
Regarding Mutation Rate what is:
Pn
P0
m
Pn= Frq of A in particular generation.
P0= Frq of A in Gen 0
m= Mutation rate.
48
What is conjugation in bacteria?
Bacterial Sex.
49
What is the ultimate source of genetic variation?
Mutations.
50
What is the most common type of genotypic mutation?
Neutral- Synonymous, no change in trait produced.
51
What is the most common type of Phenotypic mutation?
Deleterious and selected against (usually.)
52
The tides of selection and mutation where mutations form, most deleterious and then are eliminated by selection.
The Mutation-Selection Balance.
53
What rate of deleterious alleles being eliminated (selected against.) is equal to the rate of creation by mutation.
Mutation-Selection Balance.
54
What is this?
q^= √m/s
equation for Mutation-Selection Balance
q^= equilibrium frq (usually given)
m- Mutation Rate
s- Selection coefficient. (0-1)
55
What would be the mutation rate required to achieve Mutation selection balance for a disease with an s=0.5 and q^=4
The known mutation rate is 0.1.
m=8, definitely not kept around by pure mutation, being affected by something else as well.
q^= √m/s
Wildy inaccurate #'s just to look at general use.
56
When the mutation rate cannot explain the higher frequency of a deleterious allele than would be expected what are other possible causes?
over-dominance, genetic drift, nat selection for linked genes, non-random mating, etc.
57
What kind of force is migration when it comes to populations?
a homogenizing force of populations within a species.
Not just homogenizing one population.
Makes populations more similar.
58
The movement of alleles among populations.
Migration. (not equivalent to season migration.)
59
Takes place through migration and is mediated through reproduction and vertical gene transfer?
Gene Flow, which can be dispersal of any life stage.
60
What is Vertical Gene transfer?
When alleles are passed down from parent to offpspring.
61
Movement into a population?
Immigration.
62
Movement out of a population?
Emigration?
63
When migration is occurring, what happens to the allele frequencies of the mainland?
NOTHING!! Mainland is presumed to be large enough, the effect of immigration to it is insignificant.
64
When migration is occurring, what happens to the allele frequencies of the Island?
They will become more like the mainland and changes allelic frequencies and can lead to evolution.
65
is Migration effectively one way?
Yes! "Back-migration" is insignificant.
66
Migration occurs and the allele frequencies change on an island, after this migration is cut off, & the population returns to random mating. What HWE conclusions are violated after one generation?
Only conclusion 1- no change of allele frequencies.
[conclusion 2 is only violated during migration since you will not be able to use the HWE equation (There will be excess of some genotype) until after the population returns to random mating.]
67
What does -P- Mean in migration?
(P-bar)
What happens to to this value after 3 generations?
The average allele frequency of q on the mainland.
This value remains unchanged, the mainland population is assumed to be large enough to not be affected by "back-migration."
68
What else does -P- go by?
P
69
What does the equation
P'=Pi-(Pi * m)+ Pm mean?
What does each variable mean?
This equation allows us to predict the frequency of an allele in the next generation when migration is occurring.
P'=. next gen allele frq
Pi= island frequency of prev gen
m= mutation rate
P= mainland allele frq- no change gen to gen.
70
On a mainland there are mostly Banded Snakes (B frq=0.9). These snakes regularly migrate to a nearby island full of un-banded (b) snakes.
after many generations the B allele frq on the island remains 0.2, why might this be?
There is likely selection acting against the the dominant phenotype of banding, the island could have a different environment that does not allow banded snakes to blend in well.
If there was no selection the banded allele would become fixed on the island and the two populations would be homogenized.
71
A value representing the variation in in allele frequencies among populations.
Fst
F "sub" t
Helps see how different populations are genetically distinct from each other.
72
What is the range for Fst, when does it mean at each end?
0-1
0= means no genetic difference between populations.
1 means complete genetic variation/ no overlap, could be due to isolation/ no genetic exchange.
73
Is migration a strong evolutionary force?
Yes, but only its affects on the islands.
74
How does gene flow affect genotype frequencies across population?
homogenizes.
75
What are 2 things small populations are prone to?
Genetic drift and therefore the extinction vortex.
76
What are 5 things that can be responsible for evolution at the population level?
Do they always cause evolution, if not give an example where it wouldn't.
1. Selection.
- Not always: over-dominance.
2. Genetic Drift, Yes.
3. Gene flow/ Migration, usually does, but if the mainland is the same as the island then it wouldn't.
4. Mutation.
- Not always- synonymous mutations, somatic (non-heritable.) mutations.
5. Non-random mating
77
When allele frequencies change just by chance.
Genetic Drift.
Evolution occurring by random chance.
78
Type of evolution that is not adaptive?
Genetic Drift.
79
Which HWE assuption does genetic drift violate?
(infinitely) Large Population.
80
Why can't HWE be used predict genotypes in small populations?
There is much more probability for the alleles to not unite in the same types of frequencies when compared to larger pops.
This failure to conform is only due to small size.
81
What is HWE based on?
Mathematical/ statistical probabilities.
82
What does ΔPi=m(P-Pi) mean?
This means the change in allele frequencies on island = migration rate times the mainland allele frq - island frq.
Can also be calculated by Pi'-Pi.
83
What does it mean if ΔP=0?
What two things could cause this?
This means that the allele frequencies are unchanging.
This can be due to m=0
or P-Pi=0 meaning the two populations already had the same allele frequencies.
Essentially evolution will not take place now.
84
If migration is cut off after however many generations, assuming no other HWE principles were violated, what will occur?
The changed allele frequencies will stop where they are and fall back into HWE genotypes.
85
What 2 conclusions are violated by genetic drift?
- Cannot Calc genotype frequencies based on HWE- disequilibrium.
- Allele frequencies change
- Small population.
86
In small populations what is likely to happen to the allele frequencies?
it is likely they will either be lost or go to fixation, this isn't really affected by the fitness of the allele, more the frequency, this is all just due to random probability.
87
Random discrepancy between expectations and actual results?
Sampling error.
88
Sampling error in production of zygotes within a population?
Genetic drift.
89
The result of a finite population size.
Genetic drift, occurs in all populations, just doesn't really affect larger ones much.
90
When a small group creates a new population?
Founder effect.
91
When random events cause a population to crash to a very low number?
Bottle neck effect.
92
Humans have hunted black rhino's to near extinction and they are now struggling regarding genetic diversity, what is this phenomena called?
A bottle neck effect, even though it is human caused it's "random" by which rhino's were in the wrong place at the wrong time.
93
What are the types of genetic drift?
Bottle neck and founder effects.
94
In finite population that aren't large what is likely to happen to the alleles?
How fast will it happen?
The alleles will either become lost or fixated over time, faster for smaller populations.
This also causes decline in heterozygosity.
95
When alleles fixate/ become lost what occurs genotypically?
Decline in heterozygosity.
96
Lets say in a small population there is are 2 alleles A-frq: 0.6 & a-frq: 0.4
Genetic drift occurs and randomly the A allele reach fixation within the population. How does this affect allele frequencies? The average allele frequency?
What was the probability of this fixation occurring?
A will change to 1 frq and a will change 0 frq
it doesn't affect average between the alleles though as (0.6+0.4)/2=0.5 & (0+1)/2=0.5.
The chance of this is was 60%.
(Sewall Wright showed the initial allele frq correlates with it's likelihood to reach fixation.)
97
A population of 16 flies goes through genetic drift, losing genetic variation, at the same rate as a population of 9, what is the smaller population called?
The effective population size.
98
Theory of genetic drift can make?
testable predictions about the behavior of alleles in finite populations.
99
What is mtDNA? what is the ploidy?
Mitochondrial DNA, usually haploid from the mother.
100
What is the inbreeding coefficient?
Equation?
Fis= (Hs-Hi)/ Hs
Hs: subpopulation/ expected heterozygosity.
Hi: Individual/ observed heterozygosity.
101
What is the Range of the Fis, what do the poles mean?
(-1)-(+1)
(-): excess heterozygosity.
(0): No inbreeding- value in correlation with HWE.
(+) some form of inbreeding is going on.
102
A measure of how likely it is the alleles in an individual are inherited and alike by descent.
The Fis inbreeding coefficient.
103
What does inbreeding lead to on a genotypic level?
Decrease in heterozygosity.
104
What are the 4 steps for finding the Fis? Fis= (Hs-Hi)/ Hs
1. Find allele frq
2. Use HWE to find expected heterozygosity (2pq), (frq) =Hs
3. Find observed Heterozygostiy (frq) =Hi
4. plug and chug. (S/E - i/O) /S/E
(Hs-Hi)/ Hs
105
level of differentiation among a set of populations
Fst
0-1
0= means no genetic difference between populations.
1 means complete genetic variation, could be due to isolation/ no genetic exchange.
106
What are the ranges for the Fst, Fis, W, S?
Fst: 0-1, 0=no genetic diff/ identical
Fis: (-1) - (+1), 0= no Inbreed, += inbred
W: 0-1, 0= die off
S: -/+ Selection strength (Affects what W represents.)
107
A measure of a populations behavior?
Ne
The effective population size.
108
What is the census Size?
N: The actual size of the population, not the effective size (Ne)
109
How do Ne and N relate to each other?
N>Ne
110
What are the 4 four primary factors that cause N>Ne?
1. Unequal Sex Ratio (referring to breeders of pop).
2. High Variance in Family Size- some individuals contribute no offspring.
3. Fluctuations in pop size over generations- individuals die for various reasons.
111
Ne=(4N-2)/(Vk+2)
Equation relationship regarding the effects of high variance in family size.
112
Ne=4Nef * Nem/ Nef + Nem
Equation relationship regarding the effects of unequal sex ratio. (Male-harem of females.)
em- male breeders
ef- female breeders.
113
Ne=t/sum:(1/Nei)
t= # of generations.
ei= effective size at ith generation.
Equation relationship regarding the effects of fluctuations in population sizes.
114
What occurs in Fst due to genetic drift?
It will increase since the populations are becoming more differentiated from each other.
115
What causes Fst to go up and down?
Fst up= Genetic drift
Fst down= Gene flow (migration)
116
What prompted the question of why is there so much variation observed within pops in nature?
Genetic drift removes variation within a population and occurs in all populations regardless of size.
117
What are the 2 theories proposed to answer why there is so much variation observed within populations despite genetic drift?
Neutral and Selectionist theories.
Neutral maintains that rate of evolution = neutral mutation rate.
Selectionist = Mutations are frequents and mostly (+) then selected for. Rate of substitution is determine by nat selection of (+) alleles.
118
What is the rate of evolution at the genotypic (single locus) Molecular level?
The rate at which new alleles created by mutation are substituted for other alleles already present.
(Would be if a population of (iA)(iA) suddenly got a (iB) and that allele took over.)
119
What is purifying selection?
Strong Negative selection.
120
There is evidence for neutral theory such as such there being a higher chance of deleterious mutations Vs (+), over all synonymous mutation had highest rates. What does this conclude regarding the rate of evolution?
The rate of evolution is greatest @ DNA positions that when altered will be synonymous, and the least likely to affect fitness.
121
When a mutant allele is produced that does not impact fitness what will determine the frequency?
Genetic drift, as it's Not acted on by selection.
122
What is DN?
What is DS?
Non-synonymous substitution rate.
Synonymous substitution rate
123
DN/DS <1?
When replacements are deleterious. (due to small non-synonymous mutation rate, likely to do deleterious dying out.)
124
How is neutral theory used?
Since it specifies the rates and patterns of sequence change that occur in absence of evolution, we can use it as our null hypothesis to prove possible natural selection.
125
DN/DS =1?
Neutral synonymous mutations.
126
DN/DS >1?
Replacements are advantageous. (due to higher non-synonymous mutations thriving and contributing to rate.)
127
What are Ex of positive selection promoting replacement substitutions?
- Plant (S) Alleles (determinant of self-incompatibility.)
- immunoglobuliins (immunity)
- MCH proteins (self/ non self recognition and immunity.)
128
What are Ex of positive selection of loci?
- Recently duplicated genes that have attained new functions.
- Loci involved W/ Sex determination.
- Species specific interactions between sperm and egg.
129
Are synonymous mutations exposed to selection?
They can be.
For example Codon Bias.
Hitchhiking- not direct exposure.
130
What is selective sweep/ hitchhiking?
When an allele undergoing positive selection drags along other nearby genetic polymorphisms that are in linkage disequilibrium, these can even be neutral or deleterious mutations and lead increased frq of them.
131
What is a polymorphism?
Refers to the existence of 2 or more distinct forms.
132
What is translational efficiency?
The efficiency/ speed at which a codon (part of mRNA) can translate for a protein. tRNA "reads the codon" to build the protein and may have binding affinity for certain codons.
133
What is Codon bias?
uneven usage of synonymous codons due to the advantage of one of the codons such as having more tRNA available for it, translational efficiency, more genomic content available for it. Mostly affects highly expressed genes.
134
What is the point of coalescence?
To look back within a populations Hx and examine the factors that may have led to todays allelic frequencies.
135
What allows phylogenetic Comparisons of species trees with gene trees?
Coalescence.
136
Is coalescence longer or shorter for a small population?
Shorter amount of time to look back on.
137
What is Panmixia?
Random mating.
138
What is non-random mating? Does it cause evolution?
When mates are chosen based on some particular trait/ phenotype.
Not by itself, great indirect effects though.
139
Random mating with respect to what is required for HWE?
Respect to locus of interest.
140
Individuals choose mates similar to themselves?
positive assortative, Non random mating.
(increases homozygosity, neg hetero.)
141
Individuals choose mates different from themselves?
Negative assortative mating, (Dissasortative mating.) non-random mating.
(increases heterozygosity.)
142
What is the most common form of non-random mating?
Inbreeding.
143
What is the most extreme form of inbreeding?
What are the ratios for homozygotes and heterozygotes for genes passed from a hetero parent?
Selfing.
0.25 homozygous for either allele.
0.5 for hetero.
144
What does selfing lead to an increase in?
Decrease in heterozygosity.
0.25 homozygous for either allele.
0.5 for hetero- halved every gen while homozygous are each gaining a quarter from that.
145
What does an Fis/ F of 0.5 mean?
Population is selfing.
146
What is r when it comes to inbreeding?
Coefficient of relatedness.
147
if one hetero parent produces two kin and each one gets A, what is the chance (if the two sibling mate.) to produce a homozygote?
So 0.5 chance of allele from parent (0.5 * 0.5).
Chance of the single allele from either sibling 0.5, (0.5 * 0.5)
so 0.25 * 0.25= 0.0625 chance of being identical by descent.
148
When inbreeding has reached a point that the deleterious recessive alleles are now starting to be expressed.
Inbreeding depression.
Reduction in fitness of a population due to homozygosity.
149
What kind deleterious allele is not affected by inbreeding depression? why?
Dominant deleterious, because they are expressed regardless if they're in the genotype, no hiding in the population.
150
What are 4 evolved mechanisms to avoid inbreeding?
- Mate choice.
- Self-incompatibility.
- Dispersal.
- Different phenologies of male amnd female organs.
151
if a population is unable to avoid inbreeding even with evolved mechanisms, what can we assume?
it is a small population/ endangered species.
152
What HWE conclusions can be also be violated due to non-random mating?
Cannot calc genotypes from alleles accurately.
153
What is mutational meltdown?
When the mutations within a soecies continue to build and build and start to cause fitness declines.
154
What 2 things combine to form extinction vortex?
Mutational meltdown and inbreeding depression.
155
What can be done for species in extinction vortex?
Forced introduction of new alleles, genetic diversity.
156
What are the five facets of an extinction vortex?
- Accumulation of mutations, leading to reduction in pop size.
- Increasing genetic drift with smaller pop size.
- Speed and fixation of deleterious mutations increases.
- Population size continues to decrease in response.
- Mutational meltdown.
157
What are 2 things that must be under stood to understand the significance of sex
- Microevolution at multiple loci
- linkage equilibrium/ disequilibrium.
158
What is an epistatic gene?
When 2 or more loci affect 1 trait.
159
Do genes exist in isolation?
No!
160
If the frequency of one allele has no affect on the other.
Linkage equilibrium
161
The two alleles are on the same chromosome and there fore can partially be used to predict the frequencies of one another.
Linkage disequilibrium.
162
Why might two alleles in linkage disequilibrium have a lower Vs higher chance of a recombination event?
The closer two genes are physically on a chromosome the less likely a recombination event will occur.
163
For a population in linkage equilibrium Chromosome genotype of one locus is?
Independent of of locus.
164
Non-random association between a genotype at one locus and another.
Linkage disequilibrium.
165
The frequency of a b chromosome also carrying a A or a is the same for each A, a.
Linkage equilibrium
166
What is the linkage equilibrium formula?
What does it mean if =0?
D=(gAB * gab) - (gAb * gaB)
if =0, linkage equilibrium.
167
are the frequencies of chromosomes always equal?
No, not when in disequilibrium.
168
Linkage equation in simple terms?
Frequencies of the (Dom/Dom * Rec/Rec) - (Frq of: Rec/Dom, Dom/Rec)
Example:
(AB) * (ab) - (Ab) * (aB)
169
How can the expected frequencies of the chromosome haplotypes be calculated?
Find the allele frequencies (no need to multiply since haplotype)
Multiply the allele frq for each allele to find the probability of a gamete (haplotype) receiving the specific alleles.
170
If a population is shown to be in linkage equilibrium what does this mean?
It means we can use HWE equation for each loci independently. Assuming no other violations present.
171
What admixture?
When two or more previously isolated group are now introduced leading to an increase in heterozygosity and therefore genetic diversity.
172
What are 3 reasons for linkage disequilibrium?
-The genes are physically linked
-Selection on multilocus genotypes
- Population admixture.
(We know this violates HWE at the singular loci level and that if in equilibrium totally we should be able to use HWE, the fact we can't is an indicator that the gene will not be in equilibrium with all other genes.)
173
if a gene is shown to be in equilibrium with another gene does that mean HWE will definitely work on each loci indepently?
Not necessarily, this does not conclude that either gene will not be linked or have interactions with other loci which could be under pressures that disrupt affect HWE equilibrium both loci.
174
What are ways to eliminate linkage disequilibrium?
- Sexual organisms
- meiosis
-cross over events
-outbreeding
175
What is outbreeding?
The mating of individuals not very related to each other, not the same as admixture: mixing of isolated populations.
This is because outbreeding can occur within a population.
176
What randomizes genotypes of loci with respect to each other?
Genetic recombination (no breaking things, just mixy mix.)
177
What breaks up old genotype combinations and creates new ones?
Meiosis. (chromosome literally taken apart to be put together later with other ones to Create new chromosomes.)
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if r=0 what does this mean?
0 recombination occurrence, genes are in disequilibrium and are also probably physically linked.
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what does D mean regarding multiple loci?
@ 0.25?
D represents the coefficient of linkage disequilibrium. 0.25 is the most extreme value meaning no recombination is taking taking place and the genes are strongly linked this will continue unless decay is at play.
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Why do we study disequilibrium?
Because if we don't we be assuming incorrect selective pressures on genes that are actually just linked and changing in frequency due to hitchhiking/ selective sweep.
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Are most loci in linkage equilibrium?
Yes mostly due to meiosis.
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What are the 3 cons of sexual reproduction?
Costly, Complicated, Dangerous.
(having sex requires organisms to have more vulnerable moments, takes a lot of energy, and species have a lot of complication for having sex think birds and how much effort the males put in for sex.)
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What is beneficial about the aphid reproduction cycle.
During summer months environmental factors cuase viviparous parthenogenesis of the female ants (easy time for ants to survive.) however when fall comes around the female ants are stimulated to start producing male ants (this is an XX-X0 sex determination) they are able to do this through a random loss of one x chromosome, by winter the ants will switch to oviparous sexual reproduction allowing for new genotypes to be put through selective pressure before summer again, this increase chances for species survival through winter.
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Sex is __________ due to genetic drift?
Beneficial.
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What is the meaning of muller's ratchet?
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A normal function group and a mutated (-) group both exist, due to genetic drift, the normal group does not reproduce and is lost.
What is this in terms of the significance of sex?
These are clicks up Muller's ratchet meaning future populations will have more mutation and likely lower fitness without further sexual reproduction.
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As Muller's ratchet clicks what occurs?
Accumulation of mutations and decreasing fitness, without change from this track this will lead to extinction vortex.
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What resets Muller's ratchet?
Sex, if no mutation group is lost, it can reformed through recombination.
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What is the optimum amount of mutation in sexual organisms?
None.
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How does sex affect Loci linkage?
reduces disequilibrium, brings values closer to D=0
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is Muller ratchet the only reason sex is beneficial?
No Muller's ratchets on it's own will not hold totally beneficial for sex since it so slow and dependent on population size.
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What explains benefits for sex in the short term?
Sex is beneficial to variable selection in changing environments. while asexual reproduction will always produce individuals adapted to a stable environment, that just doesn't happen, environments are ever changing and by having variable off spring there are greater chances some of them will find success in the changing environment.
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What is the Red Queen Hypothesis?
Species have to keep evolving just to stay in the same place.
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