Biology 108 - Exam 2

Population size dictates the ________ .

strength of genetic drift

What can we estimate?

Effective population sizes for real populations

There is a balance between _______ .

the loss of variation due to drift and new mutations

Genetic drift causes ______ .

neutral genes to evolve in a "clock-like" manner

The binomial distribution

can model the probability of getting a particular number of “A” alleles in the next generation

The expected variance in allele frequency due to one generation of drift is:

V = (pq) / 2N (variance of the binomial distribution)

The standard deviation is an _____ .

approximation of the magnitude of expected change in allele frequency in the next generation

Both the ________ and _________ of the ___________ are _________ .

magnitude, variance, change in allele frequency, proportional to population size

How can we estimate the size of real populations?

go out and count every single individual, use a mark-recapture approach, call the count of all the individuals in the population the “census size” (Nc)

The census size is often ______ as the “N” of the actual gene pool.

not quite the same

Every individual may ______ to the gene pool.

not contribute

The population size may be ________ .

fluctuating to some extent through time

Effective population size Ne

The number of breeding individuals in an idealized population that would show the same amount of genetic drift as seen in the population being studied

We can use the _______ to estimate Ne!

relationship between variance and N

We can measure _______ using ______ .

variance in allele frequency for a population, temporal
sampling

Estimating Ne by temporal sampling makes ______ .

many assumptions about the populations/alleles

Why does estimating Ne by temporal sampling make many
assumptions about the populations/alleles?

the allele you are measuring is drifting neutrally, often difficult/impossible to be sure of neutrality, 4-fold degenerate sites are a common choice for “neutral” alleles

Knowing Ne size allows you to ______ .

estimate many other key parameters; strength of genetic drift, times when populations/species split, mutation rates

New mutations _______ .

constantly arise and increase variation

µ (“mu”)

the mutation rate for a single locus, probability of a new mutation each generation per haploid genome (gamete), number of alleles that occur each generation that will eventually fix

The per-generation probability that a gamete or offspring has an allele ______ .

is different from the parental genome at a particular locus

At least some mutations are _____ neutral.

not

Mutations with large fitness effects can ___ .

easily overcome drift

Mutations with small fitness effects _____ .

can’t easily overcome drift

When drift is weaker (larger Ne), _______ .

smaller effect mutations can overcome it

Recessiveness causes ______ .

the average selective effect of traits to be small

Many genetic diseases are the ______ .

result of drift in small populations

Amish populations show ____ .

unusually high allele frequencies for alleles related to dwarfism (Ellis–van Creveld syndrome), Angelman syndrome, and various metabolic disorders

In the long term, drift causes the ______ .

eventual fixation of one allele

The total number of NEW mutations each generation is _____ .

proportional to population size

2N

number of haploid genomes per diploid individual

2Nµ

number of new mutations every generation

initial frequency

the probability that a neutral allele will eventually fix

New mutations appear in ____ .

single copies

1/2N

probability that a new mutation will eventually fix

Populations accumulate fixed differences at a _____ .

constant rate

“Neutral Theory of Molecular Evolution”

populations/species accumulate fixed differences at a constant rate like a “molecular clock”, most mutations that differ between populations/species are neutral

We can use the molecular clock to ____ .

date how long two species have been isolated

K=2μT

# fixed differences (K) between 2 species that separated from one another T generations ago

Non-neutral mutations evolve at _____ .

non-neutral rates

Most of the genome is ______ .

not particularly functional

When populations become geographically isolated, _______ .

they evolve differences in allele frequencies

Genetic diversity is _____ .

hierarchically structured

We can summarize variation at ____ .

multiple loci or a single locus

Summary Statistics

metrics (usually single values) that summarize/describe some attribute of a set of observations

Two forms of heterozygosity:

Observed heterozygosity (Hobs or Ho), Expected heterozygosity (Hexp or He)

Observed heterozygosity is just the ______ .

proportion of heterozygous genotypes

Expected heterozygosity is the _____ .

number of heterozygotes expected under HW Equilibrium

We can use Hobs and Hexp to ______ .

quantify inbreeding

Inbreeding (f)

measure of the deficit of expected heterozygotes, ranges from zero (no inbreeding) to one (no heterozygotes), undefined when p or q = 0, often elevated due to sibling matings and/or selfing (e.g. in plants)

We often want to ________ for a ______ .

quantify genetic variation, whole sequence

Example of interbreeding problem

Watterson’s theta

number of polymorphic sites

Nei’s theta (pi)

mean expected heterozygosity per nucleotide

How much variation do we expect to see in a sequence?

at equilibrium between drift and selection, both π and θ are expected to be equal to the “population scaled mutation rate”

We can use _____ to ______ in the ________ .

summary statistics, visualize diversity, genome

We can use ______ to ____ that might be _____ .

patterns of diversity, identify loci, evolving rapidly (or slowly)

Species are composed of ______ .

multiple populations

We can measure variation ______ .

both within and between populations

We are often interested in how populations _____ .

differ in diversity or allele frequencies

FST tells us _____ .

how much genetic variation is within populations compared to the total population

Evolutionary processes affect FST in various ways such as:

genetic drift causes FST to increase, selection (e.g. because of different environments) increases FST, gene flow decreases FST

FST tends to increase with ____ .

geographic distance between populations

We can compute FST along the ____ to _____ involved in _____ .

genome, identify loci, local adaptation

We can visualize genetic variation ______ .

within and between populations in various ways

Principal Components Analysis ______ .

compresses genotypes at many loci in a 2-D plot

Populations cluster together because of _____ .

close proximity, intermixing, and shared genetic history

Why can it be difficult to identify groups of individuals that cluster together (like humans)?

there are very small differences between populations

natural selection

change in allele frequency due to differential survival or reproduction of genotypes (fitness) with differing phenotypes

Selection is ______, but can be _________ .

non-random, overwhelmed by drift in small populations

What did Rosemary & Peter Grant perform in the Galapagos?

identified genes and SNPs strongly associated with beak size using FST

Selection causes ______ .

changes in the frequency of both phenotypes and alleles

“Selection for” a trait causes _________ .

both it and its allele(s) to increase in frequency

“Selection against” a trait causes _______ .

both it and its allele(s) to decrease in frequency

No evolutionary force other than _________ causes adaptation!

natural selection

Differences in fitness are the ________ .

ultimate cause of all natural selection

Fitness

quantitative measure of how much an individual with a particular phenotype or genotype will contribute to the next generation on average

What are the 2 types of fitness?

absolute and relative

Absolute Fitness

number of fertile, surviving offspring of an individual or a particular genotype

Relative Fitness

fitness of a genotype relative to the genotype with the highest fitness in the population

We can use _______ to represent _________ .

coefficients, differences in fitness between genotypes

What are the coefficients that represent differences in fitness between genotypes?

“W” = relative fitness of a genotype, “s” = the selection coefficient, “h” = the dominance coefficient

What does the selection coefficient tells us?

relative fitness of “aa” vs “AA”(i.e. how much “worse” aa is)

What does the dominance coefficient tells us?

how fitness is modified in heterozygotes

In sufficiently _____ populations, if there are ______ between genotypes , _________ .

large, fitness differences, selection will always occur

Unlike genetic drift, ______ is _____ .

natural selection, predictable

Natural selection tends to ______ .

reduce genetic variation

Strong selection can _____ .

severely deplete genetic variation

In general, selection can only act when ______ .

Nes > 1

Even ______ can change ________ given long time scales.

VERY weak selection, allele frequencies

The predator cannot _______ so the _____ .

“see” the genotype, phenotype is the target of selection

Selection on alleles is a result of ______ .

selection on phenotypes

Most of the time, selection is quite _____ , but can be _____ .

weak (s<

Some lineages evolved to have _______ x higher fitness than their ancestors
in the presence of ___ !

~10,000, antibiotics

We can directly mathematically model changes in
_______ due to _____ .

allele frequency, selection

We can use mathematical models to _____ .

predict the outcome of evolution

We can visualize ______ using the metaphor of a ______ .

adaptative evolution, “fitness landscape”

Why do we use basic mathematical equations to model selection?

make predictions about evolution, build intuition for how selection works in real populations, much faster than performing simulations

model of natural selection

defines absolute and relative fitness for each genotype, using A/A as the standard

(model of natural selection) How will allele frequencies change due to selection?

w is the probability of survival from zygote to adult (viability)