An Easy 5 Points Is Available by Sunday 23 Feb, Midnight

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an easy 5 points is available by Sunday 23 Feb, midnight

The mid-term assessment survey (a quiz on Beachboard)!
Results from this help me to know how to adjust the class for
the rest of the semester, if needed. Please take the survey!

there are still spots available in one of the SI sections!
M/W/F 10-1050 am; contact Lena Vincent
(lena.vincent@csulb.edu)

second exam is in three weeks Tuesday 11 March!

so far...
you know where information is held in cells (DNA!), and how that
information is used to make or modify other key molecules of living
cells (proteins! carbohydrates! lipids!). You understand the
importance of genetic information in determining an organism's
structure and function.

you know how organisms replicate their genetic information and
distribute it to daughter cells. In addition, you know how those cell
division events (binary fission, mitosis, meiosis) fit into the processes
of asexual and sexual reproduction.

you understand the basics of how traits are inherited in sexual
reproduction, and how those inheritance patterns are related to
processes that happen in meiosis (e.g., segregation of alleles, and
independent assortment of chromosomes/traits)
remember the overall goals of the course?
I want you to leave this course with:
a basic understanding of the scientific method

a broad overview of the history and diversity
of life on earth, from ~4 billion years ago to
now

an understanding of the evolutionary
mechanisms by which that diversity arose

At this point we have enough background
knowledge to address this issue! That's what
we'll do for the next ~3 weeks.
1) a bit more about how how genotype affects phenotype...

2) what is evolution?

3) where does genetic variation in populations come from?

4) describing the genetic makeup of populations
allele frequencies
genotype frequencies

5) a "null model" for evolution: Hardy-Weinberg equilibrium

6) mechanisms of evolution:
mutation
gene flow
genetic drift
natural selection
nonrandom mating
today's goals
how does genotype affect phenotype?
so far we've seen mostly Mendel's examples, where there are two
clearly distinct alternative traits for each character, e.g.:

the phenotypic variation in these
cases can be described as "either-
or" of the distinct alternatives, or...
"____________ variation" (slightly
different definition than in second
lecture)

qualitative variation is usually
caused by allelic variation at a
single locus, like we've already
talked about.

at the population level,
such traits have a bimodal*
distribution

(*if there are only two alleles in the population)
example: purple vs. white flower color is caused by the two alleles
a pea plant has at the flower color locus)
another example: wet earwax vs. dry earwax in humans
wet, sticky, and
yellow or brown
(~50% lipid)
dry, crumbly,
and grayish
(~30% lipid)
another example: wet earwax vs. dry earwax
wet, sticky, and
yellow or brown
(~50% lipid)
dry, crumbly,
and grayish
(~30% lipid)
this is a simple either-or trait, with wet (W) dominant over dry (w)

we even know what locus is involved it's the gene for a protein
called ABCC11. ABCC11 protein is embedded in the plasma
membrane, where it transports molecules across the membrane.

W allele: ...ATT GCC AGT GTA CTC GGG CCA ATA TTG ATT ATA CCA...
... Ile Ala Ser Val Leu Gly Pro Ile Leu Ile Ile Pro ...

w allele: ...ATT GCC AGT GTA CTC AGG CCA ATA TTG ATT ATA CCA...
... Ile Ala Ser Val Leu Arg Pro Ile Leu Ile Ile Pro ...
many traits aren't "either-or", but instead vary along a continuum
the phenotypic variation in these cases can be described as
"______________ variation"

quantitative variation in a trait is usually caused when that trait is
affected by allelic variation at many loci

example: human body
height is affected by
alleles at ~180 loci!

at the population level,
such "polygenic" traits
often have a normal
(bell-shaped) distribution



allele frequencies


mutation
gene flow
genetic drift
natural selection
nonrandom mating
today's goals
what is evolution?
the term simply means "change"

but biologists use it most specifically as meaning:

changes in allele frequencies in populations over
time

(population = a group of organisms of the same species
living in the same area at the same time, and
interbreeding with each other)
what is evolution?
the term simply means "change"

but biologists use it most specifically as meaning:

time

(population = a group of organisms of the same species
living in the same area at the same time, and
interbreeding with each other)
if allele frequencies are to change over
time in populations, there needs to be
some genetic variation. What is the source
of genetic variation in populations?



allele frequencies


mutation
gene flow
genetic drift
natural selection
nonrandom mating
today's goals
where does genetic variation come from?
new alleles are formed by mutation: change in an organism's
nucleotide sequence

mutations are often (but not always) associated with DNA
replication events; in that case, mutations are basically copying
errors

there are many kinds of copying errors!
substitution of a single base in a gene (a "point mutation"). For
protein-coding genes, this may or may not have any effect on the
amino acids the gene codes for
AUC UCU GCU CCG
Iso Ser Ala Pro
AUC UCA GCU CCG
Iso Ser Ala Pro
AUC UAU GCU CCG
Iso Tyr Ala Pro
no change in
protein
change in
protein
there are many kinds of copying errors!
insertions or deletions: addition/loss of one or more bases in a
gene. If the gene codes for a protein, a number of bases that is not a
multiple of 3 is gained or lost, this results in a "frame-shift mutation",
changing all the amino acids in the protein!

AGC ACU GCU CCG
Ser Thr Ala Pro
multiple of 3; in this,
loss of an a.a.
not multiple of 3;
all a.a. change!
AGC ACU GCU CCG
Ser Thr Ala Pro
AGC ACU GCU CCG
Ala Leu Leu
some mutations don't actually affect the nucleotide sequence of
individual genes, but instead add or remove entire genes!

gene _______________ mistakes in
meiosis sometimes lead to duplication
of entire genes (or groups of genes),
so that a chromosome that previously
had one copy of some gene (e.g., actin)
now ends up with two or three or
more copies!

most mutations are copying errors... so it makes sense that
organisms that do more copying generate mutations more
frequently!

-- organisms that have very rapid generation times e.g.,
viruses, bacteria copy DNA for reproduction very frequently.
Thus in a given time period say, a year a population of
bacteria will have generated and passed on many mutations to
their offspring.

-- in contrast, organisms with long generation times (e.g.,
people) don't copy DNA for reproduction very often, so the total
number of mutations we generate and pass on per unit time is
relatively low.
are mutations good, or bad?

-- mutations sometimes have no effect on phenotype at all
(e.g., if they don't cause an a.a. change in a protein, or they
cause a change that doesn't affect tertiary or quaternary
structure) (these are called ___________ mutations)

-- mutations often have negative effects on phenotype (e.g.,
frameshift mutations are cause a protein to be nonfunctional,
and that is usually a problem)

-- mutations rarely have positive effects on phenotype
do mutations happen because an
organism/population/species "needs" them to deal with
some specific problem?

-- NO! Mutations arise randomly with respect to the "needs" of
the organism

E.g., if a population of fish is living in a pond that is warming from year
to year, any mutations that occur will be random with respect to
location in the genome. So the fishes will not have more mutations in
genes associated with thermotolerance (even though those beneficial
mutations which remember, are rare! in those genes might be
especially useful at the time!)
one other key source of variation: sexual reproduction

-- crossing over, independent assortment, and random
fertilization don't generate new alleles but they generate new
combinations of alleles, both within loci and among loci

-- the book uses a nice analogy here the proceses of sexual
fertilization don't make new alleles, but they "shuffle existing
alleles and deal them at random to provide [new] individual
genotypes"



allele frequencies


mutation
gene flow
genetic drift
natural selection
nonrandom mating
today's goals
evolution is:

time
if evolution is defined as change in allele
frequencies, we need to know how to
describe allele frequencies (and, it turns
out, genotype frequencies) so that we
can observe it...
describing the genetic makeup of populations
review: different forms of a gene are called alleles. A diploid
organism can have at most how many different alleles at a
particular locus?
review: different forms of a gene are called alleles. A diploid
organism can have at most how many different alleles at a
particular locus? TWO
but the population may
contain many more than two
alleles! The gene pool is the
sum of all copies of all
alleles at all loci in a
population.
what we need are some simple metrics by which to describe
gene pools, to see if they change from generation to generation...
how can we describe genetic variation in a population?
You could get an exact
count of allele freqs in
a popn... but to do that you'd
have to examine every
individual!

Normally we estimate popn
frequencies by taking a
random sample of individuals
from the popn

1) allele frequencies what is the proportion of a given allele
in a population?

how to calculate allele frequencies
(for the simplest case: only one allele at that locus in the popn)
(this population is monomorphic at this locus; that allele is said
to be fixed in the population)

say the allele present in the popn is

A (let's call its frequency p)

since there is only one allele, p must be equivalent to 1
(all alleles in the popn are A)

p
number of copies of A in the population
total number ofalleles at that locusin the population
(for a simple case: only two alleles at that locus in the popn)
(this popn is ________________ at this locus)

say the two alleles present in the popn are:
A (let's call its allele frequency p)
a (let's call its allele frequency q)

note: p + q = 1!

p
number of copies of A in the population

q
number of copies of a in the population
The possible genotypes are AA, Aa, aa
N
AA
= number of individuals of genotype AA
N
Aa
= number of individuals of genotype Aa
N
aa
= number of individuals of genotype aa
The total number of individuals in the population is
N = N
AA
+ N
Aa
+ N
aa

The total number of alleles at this locus in the population
is...?
Let p = frequency of allele A in the population.
Let q = frequency of allele a in the population.
p = 2N
AA
+ N
Aa

2N

q = 2N
aa
+ N
Aa

2N
note: p + q = 1!
since p + q = 1...

if you know p, you can figure out q!
q = 1 p

if you know q, you can figure out p!
p = 1 - q
two examples...
clicker question 3
You have 100 snapdragon plants growing in your garden.
68 of them are red (42 homozygous dominant, 26
heterozygous: hey, you must have done a bunch of test
crosses to figure that out!), and 32 are white (homozygous
recessive). What are the allele frequencies of R (red) and r
(white) in the population?

A. R=.90, r=.10
B. R=.33, r=.67
C. R=.55, r=.45
D. R=.75, r=.25
E. R=.67, r=.33
the allele frequencies of these two popns are identical... but how
those alleles are distributed among individuals is very different!
so... we need another descriptor of genetic variation in addition
to allele frequencies genotype frequencies!
how to calculate genotype frequencies

number of individuals with that

particular genotype in the population
total number of individuals in the population
frequency of
a particular
genotype
e.g. N
AA
=90/200 = 0.45

N
Aa
=40/200=0.2

N
aa
=70/200=0.35

these must add up to 1 too!
clicker question 4
84 of them are red (49 homozygous dominant, 35
heterozygous), and 16 are white (homozygous recessive).
What is the frequency of the heterozygous genotype in the
population?

A. 0.16
B. 0.32
C. 0.35
D. 0.49
E. 0.98
wait a minute... why do we care about this, again?

well, evolution is change in allele frequencies of populations over time...
so we clearly need to be able to measure allele frequencies if we want to
describe evolution happening.

genotype frequencies indicate how allelic variation is distributed among
individuals in the population; we'll see why that is important in a second.
To identify when evolution is occurring, we can quantify allele
frequency in a population over time! (but that takes time, and doesn't
help us understand what is causing the change)

Alternatively, we can use a mathematical model to predict what a
population should look like at one moment in time if NO evolution is
occurring. When evolution IS occurring, data from a real population
will not match the model's predictions! "Deviations" from the
predictions help us understand what is causing the change.



allele frequencies


mutation
gene flow
genetic drift
natural selection
nonrandom mating
today's goals
Hardy-Weinberg equilibrium
in a population of sexually reproducing organisms that is NOT
evolving, allele frequencies (by definition) do not change from
generation to generation

if no evolution is occurring, the different genotypes should appear in
frequencies that are easily determined from allele frequencies using a
simple mathematical model (the Hardy-Weinberg equation); these
genotype frequencies also should not change from generation to
generation

for a real population to be "in HW equilibrium" where predicted
genotype frequencies match real genotype frequencies in the
population, and we infer that no evolution is occurring five conditions
need to be met:

The HW equation uses a population's allele
frequencies to predict "equilibrium" (no evolution
occurring) genotype frequencies in that population
Conditions that must be met for a real population to
be in HWE:

1) there is no mutation

2) there is no gene flow (movement of individuals in or out
of the popn, or reproductive contact with other popns)

3) population size is extremely large (infinite, actually)

4) there is no natural selection (differential survival or
reproduction of individuals with different genotypes)

5) mating is random

(aside: probability in "individual-level" crosses)
-- we've already used probability
(and Punnett squares) to
estimate the chances of getting
particular genotypes in crosses
between two individuals, right?

-- in crosses between two individuals,
each parent can only produce gametes
that all carry one allele (if the parent is
homozygous at that locus), or gametes
where half carry one allele, and half
carry the other (if the parent is
heterozygous at that locus)

-- from those probabilities, one can easily calculate the probability of
getting offspring with particular genotypes in the offspring generation

-- the HW equation does exactly the
same thing, except at the population
level!

-- at the population level, the probability
of getting a gamete with one or the other
allele depends on allele frequency in
the population

-- if you know allele frequencies in the
parental population, you can estimate the
frequencies of each kind of gamete they
produce... and then you can easily use
probability to figure out chances of getting
particular genotypes in the next
generation... which is genotype frequency!

-- the book illustrates this with
what is basically a "population-
level" Punnett square

-- but it's easier to figure this out
using simple probability

Prob (C
r
C
r
) = p
2
= 0.8 x 0.8

Prob (C
r
C
w
) = p x q = 0.8 x 0.2

Prob (C
w
C
r
) = q x p = 0.2 x 0.8

Prob (C
w
C
w
) = q
2
= 0.2 x 0.2

-- remember that probabilities of all the possible outcomes of an event
have to sum to 1!

-- so, the HW equation for predicting equilibrium genotype frequencies
is this:

p
2
2pqq
2
1
frequency of
homozygous
dominant
frequency of
homozygous
recessive
frequency of
heterozygotes
you need to know this equation, and you need to be able
to work through word problems using it!!!

clicker question 5 (ungraded)
A randomly mating population of 100 dairy cattle
contains a recessive allele causing dwarfism. If there are
16 dwarf calves in the population, what is the frequency
of heterozygous carriers of the allele in the entire herd?
(Assume that the population is in HW equilibrium).
A. 16% (0.16)
B. 32% (0.32)
C. 48% (0.48)
D. 64% (0.64)
E. 96% (0.96)
clicker question 6 (ungraded)
20 are homozygous dominant, 20 are heterozygous, and
60 are homozygous recessive for flower color. Is this
population in Hardy-Weinberg equilibrium?

A. Yes
B. No
C. Not enough information given
wait why do we care about HW equilibrium, again?
-- HW equilibrium is where a non-evolving population should be! It
can only be there if the following conditions are met:

conditions for HW equilibrium
1) no mutation
2) no gene flow
3) infinite population size
4) no natural selection
5) random mating
wait why do we care about HW equilibrium, again?
-- HW equilibrium is where a non-evolving population should be! It
can only be there if the following conditions are met:

conditions for HW equilibrium
1) no mutation
2) no gene flow
3) infinite population size
4) no natural selection
5) random mating
known evolutionary mechanisms
1) mutation
2) gene flow
3) genetic drift
4) natural selection
5) nonrandom mating
so if a real population is not at HW equilibrium for a locus,
we know that one or more of those evolutionary mechanisms is
acting at that locus!

how the real population deviates from HW equilibrium also
gives us some insight into which mechanism is acting



allele frequencies


mutation
gene flow
genetic drift
natural selection
nonrandom mating
today's goals
mechanisms of evolution: mutation
1) mutation any change in the nucleotide
sequence of DNA

-- this is the ultimate origin of genetic variation!

-- mutation rates are usually low
~1 mutation per 10
9
base pairs per generation

Since human gametes contain ~3x10
9
base pairs, each human gamete
has ~3 new mutations; each zygote carries ~6 mutations. That seems
like a lot, but the human genome contains ~20,000 genes... so few new
alleles arise per individual per generation.

but... since the human population is ~7 billion, humans as a population
accumulate ~42 billion new mutations each generation!
mechanisms of evolution: mutation
1) mutation any change in the nucleotide
sequence of DNA

-- if mutation is occurring in a population, it doesn't actually cause
much deviation from HWE, because:

a) it's relatively rare the rate at which mutations arise is usually
pretty low

b) new alleles formed by mutation start out at extremely low
frequencies! Thus they have very little effect on e.g. predicted
mechanisms of evolution: gene flow
2) gene flow movement of genes among
populations
-- caused by migration of adult individuals among populations, or by
migration of gametes (that is, reproductive contact!) between two
populations

-- movements of
genes into a
population can
add new alleles
to that population,
or influence the
frequencies of
existing alleles.

-- gene flow between two populations tends to make them more similar to
each other; if there is enough gene flow, they become one gene pool!
mechanisms of evolution: genetic drift
3) genetic drift random changes in allele
frequencies from generation to
generation due to "sampling error"

-- if only a small subset of individuals from a population reproduce,
they are unlikely to contain alleles at the true population frequency,
just by chance

-- example: drift in
allele frequencies
in a small population
of plants
3) genetic drift

-- drift has more effect in small populations compared to large;
however, in populations of finite size it is always having an effect!

-- drift causes allele frequencies to change at random, often in
different directions from generation to generation

-- drift tends to
reduce genetic
variation: rare
alleles tend to
get lost!
3) genetic drift

an illustration of the effects of popn size on
drift... ten simulations of changes in allele
frequency due solely to chance in three popns:
20, 200, and 2000 individuals.
(Frequency of the allele starts at 0.5 in each case;
each line shows results from one simulation)

-- the allele gets fixed (frequency=1) or is lost
(frequency=0) only in the smallest population

-- allele frequency is much less variable in the
largest population
3) genetic drift

We often observe two special cases of genetic drift...
population bottlenecks a population that is reduced
dramatically in size usually loses genetic variation because
of drift
population bottlenecks a population that is reduced
dramatically in size usually loses genetic variation because
of drift
example northern elephant seals

-- before 1800s used to be very
abundant on west coast

-- in 1800s hunted for oil until
thought to be extinct in 1884

-- ~30 were rediscovered in 1892;
since then, the population has
recovered to ~200,000 animals

-- at the "bottleneck" of ~30, most of the genetic variation in the population
was lost; even now, the original genetic diversity has not been regained.

3) genetic drift

We often observe two special cases of genetic drift...
founder effects when a new population is started by just a few
immigrants, those immigrants usually carry only a random subset
of the variation in the original population

Lots of examples in human popns! E.g.:
-- in 1814, 15 British colonists founded a
settlement on the islands of Tristan da Cunha,
in the South Atlantic

-- by chance, one carried a recessive allele for
a particular form of blindness (retinitis
pigmentosa)
-- the frequency of that allele in the founding popn was MUCH higher than
that in the British population at large
mechanisms of evolution
next time: natural and sexual selection!

essential vocabulary
qualitative variation

quantitative variation

polygenic traits

normal distribution

evolution!

population

mutation

point mutation

insertion/deletion

frame-shift mutation

gene duplication
gene pool

allele frequency

fixed

monomorphic

polymorphic

genotype frequency

Hardy-Weinberg
equation, equilibrium

gene flow

genetic drift

sampling error

population bottleneck

founder effect

study questions
define the word "evolution"

where does genetic variation in populations come from?

are mutations typically beneficial, neutral, or harmful?

do mutations arise in response to the "needs" of an organism, or
randomly in a population?

how many alleles can be present at a locus in a diploid individual,
vs. in a population of diploid individuals?

be able to calculate actual allele and genotype frequencies when
given data about a population!

can two populations have the same allele frequencies, but different
genotype frequencies?
study questions
how can we use the Hardy-Weinberg equation to identify cases
where evolution is or is not occurring?

what are the conditions that a population must meet to be in HWE?

understand how to use the HW equation to solve word problems!

mutation can change allele frequencies in a population, but not very
much why not?

why does gene flow between two populations tend to make them
more similar to each other?

what is genetic drift, and why does it cause allele frequencies to
fluctuate randomly? Why does it affect small populations more than
large populations? And why does it tend to reduce genetic
variation?

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