EXAM 2 Flashcards
founded the field of population genetics
use of mathematical theory and hypothesis testing which are components of scientific inquiry
modern synthesis
Darwin’s postulate 1 restated in population genetics terms
allelic variation exists among individuals
Darwin’s postulate 2 restated in population genetics terms
alleles are passed down from parent to offspring (through meiosis and fertilization)
Darwin’s postulate 3 restated in population genetics terms
more young are born than can survive
Darwin’s postulate 4 restated in population genetics terms
some allelic combinations are more fit than others (these can survive to reproduce more often) based on allelic variants
change in frequency of alleles in a population over generations
new definition of evolution
evolution at the population level, the level at which evolution acts
microevolution
a null model for the behavior of genes in a population, specifies what will happen to frequencies of alleles and genotypes
applies to all diploid sexual organisms
Hardy-Weinberg Equilibrium
group of interbreeding individuals and their offspring
adults produce gametes
gametes combine to make zygotes
zygotes grow up to become next generation of adults
population in HWE
HWE- tracks the fate of _____ across generations in a population
find out if particular alleles become more or less common over time
mendelian genes
imagine 60% of eggs and sperm received allele A and 40% received allele a
frequency of A allele in the gene pool = 0.6, and the a allele= 0.4
when egg and sperm meet what proportion of genotypes will be AA?
60% egg will be A, 60% sperm will be A
0.6 X 0.6 = 0.36
so 36% of zygotes will have genotype AA
imagine 60% of eggs and sperm received allele A and 40% received allele a
frequency of A allele in the gene pool = 0.6, and the a allele= 0.4
when egg and sperm meet what proportion of genotypes will be aa?
0.4 X 0.4 = 0.16
16% will be aa
imagine 60% of eggs and sperm received allele A and 40% received allele a
frequency of A allele in the gene pool = 0.6, and the a allele= 0.4
when egg and sperm meet what proportion of genotypes will be Aa?
0.6 X 0.4 X 2 = 0.48
(Aa = 0.6 X 0.4, aA = 0.4 X 0.6 therefore multiplied by 2)
48% homozygous
what is the trick to know your genotypic frequencies are correct?
they should add up to 1
determine frequencies in the next generation
multiply the heterozygote proportion by 1/2 and add this to the homozygote proportion
if a population is in Hardy Weinberg equilibrium it will never ____ regardless of starting frequencies
evolve
allele frequencies are in equilibrium and are the same as the first generation
numerical example shows what in HWE?
p+q =
1
Frequency of allele A
(AA, AB, BB)
p
Frequency of allele B
(AA, AB, BB)
q
HWE equation 1
p^2 +2pq + q^2 = 1
HWE equation 2
(p+q)^2 = p^2 +2pq+ q^2
individuals homozygous for dominant
p2
individuals heterozygous for both alleles (EX N and n)
2pq
individuals homozygous for recessive
q^2
the allele frequencies in a population will not change generation after generation
conclusion 1 of HWE
if the allele frequencies in a population are given by p and q, the genotype frequencies will be given by p^2, 2pq, and q^2
expected values
conclusion 2 of HWE
there is no selection and all members contribute equally to the gene pool
HWE assumptions 1
there is no mutation
no new alleles are created
HWE assumptions 2
there is no migration
all alleles stay in the gene pool
HWE assumptions 3
there is an infinitely large population size
no random events = no genetic drift
HWE assumptions 4
panmixia
mates are chosen randomly
HWE assumptions 5
allows prediction of genotypic frequencies given allele frequencies
allele and genotypic frequenciess will not change as long as the assumptions are met
why use HWE?
HWE phenotypic example with dominance
polydactyl cats is from an autosomal dominant trait caused by a variant
polydactyl cat example: if a population of 100 cats has 60 polydactl and 40 normal individuals. Then the frequencies of polydacryl and normal phenotypes are:
0.60 and 0.40
by having explicit assumptions (HWE) the violations of assumptions can be used to determine which forces are causing
disequilibrium or evolution
a change in allele frequency over time, allele frequencies do not change in a HWE population and therefore it does not have:
evolution (in terms of HWE)
what happens when assumptions are broken
no selection
no mutation
no migration
large population size
random mating
differential reproductive success
individuals with particular phenotypes survive to reproduce more than others
Cavener and Clegg used two alleles for alcohol dehydrogenase locus (Adhf and Adhs) to break down alcohol at different rates. They maintained two populations of flies spiked with alcohol and two controls without alcohol
determined genotypes at each generation with random samples.
empirical study of drosophila
in the empirical study of drosophila, which populations appeared to be in Hardy Weinberg equilibrium where the alleles did not change
control populations
in the empirical study of drosophilia populations under seletion pressure showed a decline in:
Adhs allele
the populations evolved in the study of drosophila because of selection which favored:
better ability to break down alcohol
allele frequencies do nto change but genotype frequencies cannot be calculated by HWE
conclusion 2 being violated
Pregnant women are more susceptible to malaria
invades the placenta
Causes placental inflammation and usually death of the child
*Influences placenta development and inflammation
*SS and SL produce more of the protein than LL
Malaria season (76 infants SS=16,SL=50,LL=10)
malaria example of selection
test if HWE holds or is broken, how to determine whether the difference between the actual genotype frequencies and HWE expected genotype frequencies is significant
chi-squared test
X^2 = sum (observed – expected)^2 /expected
Chi-squared equation
frequency of allele 20% 1/4 of people with genotype +/+ or +/delta32 die before reproducing
all delta32/delta32 individuals survive
after 40 gens (1000yrs) the delta32 allele is nearly 100%
(graph with an upward slope increase and leveling of at 1.0)
CCR5-delta 32 model 1
frequency of allele 20%
HIV infection rate less than 1%
all delta32/delta 32 individuals survive
after 40 gens (1000yrs) the delta32 allele is still at 20%
selection is too weak to cause a large change in allele frequencies
(graph with a horizontal line at 0.2)
CCR5-delta 32 model 2
frequency of allele 1%
1/4 of people with genotype +/+ or +/delta32 die before reproducing
all delta32/delta32 individuals survive after 40 gens (1000yrs) the delta32 allele is still at 1%
most copies of delta32 would be heterozygotes and hidden from selection
(graph with horizontal line at 0.1)
CCR5-delta 32 model 3
two alleles + and l
individuals with genotype +/+ or +/l are normal
individuals with genotype l/l do not survive
this is a recessive lethal allele
Flour beetle selection example
in the flour beetles with the l locus because they have ____ expect populations to evolve to lower l frequencies
lower fitness
flour beetle selection ex: frequency of allele l dropped as expected but was not eliminated altogether
l frequency over 12 generations
if recessive is common, evolution is rapid
when recessive is rare, evolution is very slow
when rare, the recessive allele is usually hidden from selection- the allele is maintained even if it is negative toward the population
dominance and allele frequency interaction
selection coefficient: fitness of an allele, ranges from 0-1
w
selection coefficient: strength of selection of an allele
gives strength of selection on homozygous recessive phenotype
amount of strength against the phenotype
s
selection in favor of the phenotype
positive S
selection against the phenotype
negative S
w++ = 1 - s, w+l = 1 - s, wll = 1
negative selection on dominant phenotypes
the fixation point of selection, a mechanism of evolution
genetic drift
when one allele is dominant and one is recessive _____ is equal to that of one kind of homozygote
heterozygote fitness
changes rate of evolution
eventually one allele may become fixed and the other is lost
heterozygote fitness is intermediate to two homozygotes
different evolutionary outcomes are produced
heterozygote fitness is superior or inferior to homozygotes
heterozygote has an advantage over homozygote
fitness advantage for homozygote
overdominance
example with drosophila melanogaster
single locus
homozygotes for V allele viable
homozygotes for L allele lethal
initial V allele frequency is 0.5
initial L allele frequency is 0.975
Rate slowed and viable allele reached equilirbium at 0.79
what happens to the lethal allele
lethal should decrease in frequency overtime but not completely disappear
what is present in the drosophila melanogaster example of selection
meaning heterozygotes have higher fitness than either homozygote
this maintains genetic diversity
benefits of heterozygosity outweighs the benefits from the homozygotes
Heterozygote superiority or Overdominance
heterozygotes may have lower fitness than either homozygote
so the homozygote is preferred over heterozygote
under dominance
compound chromosomes
C(2)
normal chromosomes
N(2)
if Wc(2)C(2) how many survive
0.25
if Wc(2)n(2) how many survive
0
if Wn(2)n(2) how many survive
1
reduces genetic diversity within a population by pushing alleles to fixation
heterozygote inferiority
for the second example with fruit flies: Within the population, it is _____ diversity but outside it is ______ diversity
eliminating, maintaining
in this graph: heterozygote has the advantage of fitness increases and moves towards an optimum in the middle- increase diversity, to get the most heterozygotes in a population you need the most mix of alleles
overdominance graph
in this graph: homozygote has the advantage -fitness will increase and reduce diversity
under dominance graph
in nature, selection changes over time this maintains genetic diversity
frequency-dependent selection
fish that attack other fish for food by attacking them from behind grabbing their scales and darting away
perissodus microlepis (scale-eating fish)
left-handed and right-handed determines which side of the fish its mouth will be which allele is dominant and which is recessive
right always attack the left side
left always attack the right side (means for selection depending on preferred side)
right-handed (dominant)
left-handed (recessive)
in frequency-dependent selection, the population is always evolving for a ____ frequency of rarer type because it is a more successful predator and is more fit, leaving more offspring
higher
when one form becomes more popular and common the other decreases- selection and fitness changes
oscillating effect
introduces new alleles into a population, not a potent evolutionary force alone
mutation
model mouse population mutation example: The frequency in the new population is calculated by
calculating how much A is lost
mutation can cause evolution but it usually happens
slowly
____ alone cannot cause great changes in allele frequencies but it is still important in evolution
but
in combination with selection it can be a potent evolutionary force
mutation
studied a strain of E. coli incapable of conjugation, the mutation is the only form of genetic variation
frozen ancestors are compared with the newer generations to see which is better in fitness
fitness and cell size increased in response to natural selection (occurred in jumps)
mutations caused bacteria to divide faster and increase in size
lenski’s E. coli study
when the rate of deleterious alleles being eliminated by selection quals rate of creation by mutation
mutation-selection balance
when mutation is low and selection is high
q hat is low
when mutation is high and selection is low
q hat is high
in the q hat equation for deleterious recessive allele equilibrium m is the ____ and s is the ____
mutation rate, selection coefficient
cystic fibrosis example: CTFR causes chronic lung infection and few individuals survive the disease this is because a ______mutation occurs
loss of function
if the selection coefficient is ____ then the mutation rate is not high enough to maintain the recessive allele
strong
researchers discovered cystic fibrosis still has a high frequency because it is maintained by _____ meaning it is not selected against
heterozygote advantage
cystic fibrosis is maintained by
mutation and overdominance
the movement of alleles among populations
migration
transfer of alleles from one gene pool to another gene pool of a different population
gene flow
movement into a population
immigration
movement out of a population
emigration
model of migration that has two populations, mainland and island
migration of alleles to the continent is insignificant
migration of alleles to the island could have a large impact on allele and genotype frequencies
gene flow is effectively one-way
one-island model
in the one-island model gene flow changed the
allelic frequency
population of the island
Pi
migration rate
m
population of the mainland or source
p
Lake Erie water snake example is an example of ____ because the unbanded allele is not fixed and diversity is maintained on the island
migration
given enough time gene flow will make two populations more _____
similar
early succession species, each island has different aged individuals, seed dispersal by wind or water, eventually will die off when outcompeted by another species
red bladder campion
when there is no similarities between the population and they are completely different Fst=
1
when the populations are the same or identical Fst=
0
in Fst ____ values represent more variation in allele frequencies
larger
extremes have _____ diversity
more
intermediate populations have _____ diversity
less
genetic drift is also known as _____ and this violates the idea that an infinite population is assumed in HWE
random chance
_____ populations do not work for HWE
smaller
genetic drift 10 zygote example: this example did not work because it (small size)
broke both HWE conclusions
because of drift, one allele can rise to ____ over time
fixation
random discrepancy between theoretical expectations and actual results can be called ____
also known as genetic drift when involved in the production of zygotes
sampling error
a small group of individuals start a new population and allelic frequencies are by chance different from the source population, by chance not all alleles will be represented (ladybug example)
founder effect
the Pennsylvania Amish have a higher frequency of dwarfism and polydactyl recessive alleles due to the
founder effect
random events cause a population to crash to a very low level, many alleles are eliminated from the population, the remaining population has different allelic and genotypic frequencies than the beginning
bottleneck effect
low genetic diversity of cheetahs due to several mass extinction events is an example of
bottleneck effect
when a population goes to fixation ____ also declines because of genetic drift (important if trying to manage an endangered species) a
also a good measure of diversity in a population
heterozygosity
demonstrated that the probability of fixation for a particular allele is the same as its original frequency
(EX if the initial frequency of an allele is 0.8, 80% will drift to fixation)
sewall wright
a study in the ozark mountains where a specific type of lizard exists because it can thrive in the desert like habitat
Templeton’s natural study of Crotaphytus lizards
average number of alleles per loci
allelic richness
a collection of genes that tend to be inherited together
haplotype
fraction of loci that have at least two alleles with frequencies above 0.01
genetic polymorphism
two measures of genetic diversity used in youngs study of plants
genetic polymorphism and allelic richness
genes that have more alleles show more ____ in a population
diversity
proportion of the variance in the subpopulation contained in an individual, also known as the inbreeding coefficient
Fis
differentiation among a set of populations
Fst
total expected heterozygosity among all populations
Ht
when an Fst value is small and closer to 0 it means the populations are relatively _____
similar
the size of an idealized population that would lose genetic diversity at the same rate as the actual population
effective population size
three primary factors of effective population size
unequal sex ratio
high variance in family size
fluctuations in pop size over generations
effective population size equation (unequal sex ratio)
Ne=4(Nef)(Nem)/(Nef+Nem)
variance in family size
Vk
effective population size equation
(variation in family size)
Ne= (4N-2) / (Vk + 2)
effective population size equation
(fluctuation in population size)
where t=number of generations
Nei=effective size in the ith gen
Ne=t/sum of (1/Nei)
effective population size
Ne
advantageous mutations are very rare and most mutations are selectively neutral
neutral theory
advantageous mutations are more common, rate of substitution determined by natural selection on advantageous mutation
selectionist theory
negative selection (synonymous)
purifying
positive selection (nonsynonymous)
diversifying
there is a higher rate of substitutions with ____ or silent mutations (neutral theory graph)
synonymous
____ is the greatest at DNA positions that, when altered, are least likely to affect function and therefore least likely to alter the organism’s fitness (support for neutral theory)
rate of evolution
when replacements are deleterious
dn/ds < 1
when replacements are neutral
dn/ds=0
when replacements are advantageous
dn/ds>1
codon usage random vs nonrandom, it is often nonrandom, highly expressed genes
codon
can lead to an increase in frequency of neutral or even deleterious genes
hitchhiking (selective swap)
a method that allows the calculation of effective population size in previous generations using phylogenetic comparisons, estimate what our ancestral populations would have been by using genetic drift
coalescence
___ mating is necessary for conclusion 2 of HWE to hold
random
non random mating, females choose males with a particular phenotype
assortative mating
individuals choose mates similar to themselves, increase in homozygosity decrease in heterozygosity
positive assortative mating
disassortative mating, individuals choose mates different from themselves, increases heterozygosity
negative assortative mating
most common type of nonrandom mating, mating among genetic relatives, increases homozygosity at all loci
inbreeding
in the case of inbreeding homozygous can only produce
homozygous
in the case of inbreeding heterozygous can produce (frequency of heterozygote is halved in every generation
half homozygote, half heterozygote
we cannot predict allele frequencies from ____ frequencies
genotype
probability that two alleles in an individual are identical by descent, coefficient of inbreeding
F
signifies 100% homozygote
f=-1
the population is panmictic
f=0
some kind of inbreeding is occurring
f>0
the population is selfing
f=0.5
entire population are homozygotes, locus is fixed for one allele
f=1
to calculate F in terms of probability just
multiply each probability for both populations then add those final probabilities together
exposure of deleterious alleles as homozygotes, loss of function mutations are usually hidden as heterozygotes, increased frequency at which deleterious alleles affect phenotypes
inbreeding depression
as a plant grows it is more likely to ___ when it is created from selfing
die
mortality rate in inbreeding individuals is ____ than those who are distantly related
higher
mate choice, self incompatibility, dispersal, different phenologies of male and female organs
mechanisms to avoid inbreeding depression
small populations cannot avoid
inbreeding
this population was reduced to a very low number because of hunting and habitat destruction, the population, isolated from other puma populations, problems of migration, genetic drift, and non-random mating all causing them to become extinct
Florida panther example
synergistic effects on drift, population size, and accumulated mutations
mutational meltdown
mutational meltdown and inbreeding depression combined result in a
extinction vortex
Accumulation of deleterious recessives leads to reduction in population size
Effectiveness of genetic drift is increased
Speed and proportion of deleterious mutations going to fixation increases
Population size decreases more
conservation genetics
sex is beneficial due to genetic drift
hypothesis 1 to why sex is important
sex is beneficial due to variable selection in changing environments
hypothesis 2 to why sex is important
disrupted by sex because it disrupts the accumulation of mutations (lack of recombination heightens mutation and resets the rachet), proves the first hypothesis
Muller’s Rachet
the world is changing so much individuals need to evolve to keep up, proves the second hypothesis
red queen hypothesis
the frequency of one allele does not affect the frequency of another allele, they are not close together on the genome, therefore they do not get inherited together
linkage disequilibrium
in linkage disequilibrium, one locus can predict or influence the evolution of another due to
genetic linkage
predicts how tightly loci are linked
physical distance between one another
linkage disequilibrium is created by
genetic drift, population admixture, selection on multi-locus genotype
linkage disequilibrium is eliminated by _____ because of meiosis, crossing over (genetic recombination) , and outbreeding
sex
rate of linkage disequilibrium decline is proportional to the
rate of recombination
clegg study: documented decay of linkage disequilibrium in fruit flies maintained populations for 50 generations, linkage disequilibrium ______ with sexual reproduction
declined to almost zero
as the rachet clicks, overall fitness ___ due to the accumulation of mutations
decreases
trematodes eat the snail gonads so that they have 0 fitness, hypothesis 2 on why sex is important, Lively found higher sexual proportion in areas with high trematode infection
trematode and snail example
inherited as dominant and recessive, each genotype has one phenotype
mendelian traits
polygenic, multifactorial, continuous
each phenotype is determined by many genes, often these genes are unknown
quantitative
examines discrete genotypes
allele and genotype frequencies of populations
population genetics
examines continuously distributed phenotypes
mean and variance of populations
individuals phenotypic values
quantitative genetics
most traits are ____ and determined by multiple genes in our genome
suppressed
traits that show continuous variation
ex) human height, cheetah sprint speed, flower size
quantitative traits
used for quantitative traits to understand the variation in a population
descriptive statistics
quantitative traits often occur in a
normal distribution
one allele masks another
dominance
alleles combine to create a phenotype
additive
separate loci interact to create a phenotype
epistasis
uses for quantitative genetics
measure heritable variation
measure differences in fitness
predict evolutionary response to selection
statistical creation that identifies a particular region of the genome as containing a gene associated with the trait of interest
QTL
if statistically significant ____ will be found in QTL mapping
these are indicated spikes on an LOD graph
neutral markers
linkage example with mice
cross two homozygotes for two different traits- F1 gen will be heterozygous for both, when f1 gen reproduces you will have a mix of alleles, to determine trait of interest backcross F1 gen with a parent
how often the traits were shuffled in the progeny
used to make linkage maps
frequency of recombination
map distances between markers is calculated in
centimorgans
if neutral markers appear significantly more often than chance with certain phenotypic values a____ that is linked to the marker may be affecting the trait
QTL
long odds ratio
plots for each phenotypic trait
likelihood that there is a QTL linked to the particular neutral marker
LOD score
in an LOD score anything that surpasses the ____ of 95th percentile, indicates linkage
threshold
if QTLS are detected it
indicates that a locus in the region affects the phenotype, which exact locus is still unknown
what can you use to test if a particular gene in the region affects the phenotype?
knock out mutations or CRISPR
QTLs are mapped in which fields
agriculture, biomedicine, evolution
P= G + E what is G
value determined by genotype
P= G + E what is E
value determined by environment
phenotypic variation
Vp
genetic variation
Vg
environmental variation
Ve
measuring heritable traits equation
Vp=Vg+Ve
if you know the heritability and the selection differential you can predict the
evolutionary response
what distribution is common for quantitative traits
normal
evolutionary response equation
R=H^2S
R=H^2S what does R=
predicted response to selection
R=H^2S what does H^2=
heritability
R=H^2S what does S =
selection differential
multiple genes are contributing to the genotypes
polygenic
three patterns of selection
Directional
Stabilizing
Disruptive
fitness increases with the value of a trait, shift in heritable phenotype frequency in a consistent direction
directional selection
individuals with intermediate values of a trait have highest fitness means the population stays the same, curve narrow
stabilizing selection
individuals with extreme values of a trait have highest fitness
disruptive selection
fitness graph for directional selection
a constant increase from o
fitness graph for stabilizing selection
normal distribution favor intermediate
fitness graph for disruptive selection
