Lec 4 Flashcards
Population genetics
How and why allele frequencies change over time
Types of Variation: Phenotypic variation
To be heritable, this has to be genetically based
Types of variation: Non-genotypic variation
NOT heritable and plays NO role in evolution
I.e. derived from environmental factors
The DNA molecule: The source of genetic variation
Variation is stored in the form of DNA (or RNA)
A unit of DNA that is responsible for a particular trait is called a gene
Different versions of one gene are called alleles
The DNA molecule
DNA is a polymer - a macromolecule made from repeating units called nucleotides
Nucleotides contain a phosphate group, a nitrogenous base and a five-carbon sugar called deoxyribose
There are four types of nitrogenous bases in DNA - adenine (A), guanine (G), cytosine (C), and thymine (T)
DNA usually exists as a tightly-associated double-stranded molecule joined by hydrogen bonds
Structure of a genome
Genes are DNA sequences that code for proteins
Intergenic regions (“introns”) are stretches of non-coding or “junk” DNA
Most of the genome is non-coding DNA
Diploid organisms have pairs of homologous chromosomes: from mom, 1 from dad
Information flow
DNA -> (transcription) pre-mRNA -> (splicing) mRNA -> (translation) protein -> phenotype
From DNA to proteins
Coding regions (“exons”) are the part of the DNA that gets TRANSCRIBED and codes for proteins
For natural selection to operate, genetic information in DNA must have an effect on an organism’s phenotype
Transcription
DNA -> RNA
1) RNA synthesis is complementary and antiparallel to the template strand
2) New nucleotides are added to the 3’-OH group of the growing RNA, so transcription proceeds in a 5’ -> 3’ direction
3) The nontemplate strand is not usually transcribed
Translation
mRNA -> protein sequence
Each strand of RNA codes for amino acid
Relationship between codon triplets and amino acids
20 different amino acids with sequences specified by mRNA
Most amino acids can be coded by more than one nucleotide triplet
The third codon position is often “degenerate” or redundant
For example: GCA, GCG, GCC, and GCU all code for alanine
Proteins are the main functional elements in living organisms and are responsible for most biological processes including:
Catalyzing chemical reactions
Conferring rigidity to biological components
Altering the permeability of the cell membrane
Participate in the process of cell signaling and signal transuction
Making the wrong protein or altering protein structure can have __________ effects on phenotype
Major
Epigenetics
Major advance over the last several decades
Epigenetic inheritance refers to heritable mechanisms that alter gene expression without changes to the DNA sequences
In the cell, DNA is wound around histones
DNA must be “unwound” for transcription to take place - the promoter region is inaccessible and genes are not expressed when wound around histones
How tightly DNA is packaged around histones is moderated in part by methylation - the addition of a methyl group to a C-G base pair
Methylation reduces RNA polymerase binding and decreases transcription
Heritable patterns of methylation are important for cell differentiation (e.g. formation of different cell types)
Also responsible for DEVELOPMENTAL PLASTICITY - effects of environment on organism’s phenotype
Early life environment seems to affect gene expression, leading to phenotypic differences
MOST of this variation is reset each generation, but some components of epigenetics are heritable
Allele
Variant of a gene or particular sequence of DNA
Genotype
Combination of alleles at a particular locus
Locus
Any particular location on a chromosome, can be big or small
Outcome of genotype is _________
phenotype
Phenotype is what you see
There are 23 chromosome pairs:
1 each from maternal and paternal side
Form of DNA determines trait of tasting PIC or not tasting it
Alleles are represented by letters: Capital - dominant, lower = recessive
In order to get a recessive phenotype from two parents with dominant phenotype, the parents must be ______
Heterozygotes
The dominant trait (is, is not) always the most common trait
is NOT
Dominant allele may not be common in the population (i.e. polydactyly)
An allele (does, does not) have to be a gene
Does NOT
It can be ANY part of DNA that differs between individuals. So, if one individual has an A at a particular locus in an intron, and another individual has a T at that locus, we can refer to those as different alleles - even if they are not in genes, and even if they are only one nucleotide
Uppercase vs. lowercase letters referring to alleles
Do NOT always mean that one allele is dominant
A and a used to refer to different alleles at a locus, but do NOT assume that A is dominant
A does NOT refer to nucleotide adenine
Sometimes call different alleles A1 and A2, B and b, C1 and C2, CONVENTION is to call them A and a
A locus is:
a) A location in the genome
b) A particular genotype
c) Different genetic variants
d) A particular phenotype
a) A location in the genome
An allele is:
a) A gene
b) Any part of the DNA sequence that varies between individuals
c) A particular phenotype
d) A particular genotype
b) Any part of the DNA sequence that varies between individuals
Mendelian Genetics and Modes of Transmission
Gregor Mendel was an Austrian monk who looked at laws of inheritance and crossbreeding; contemporary of Darwin
1) Begin with purple-flowered and white-flowered plants
2) Self-fertilize for several generations to ensure that each breeds true (i.e. that each was homozygous)
3) Cross purple and while plants
4) Results: ALL F1 plants have purple flowers (purple = dominant, white = recessive)
5) Allow F1 plants to self-fertilize
6) Results: 3/4 of F2 purple, 1/4 white; F1 had to have been heterozygotes
Mendel’s Laws derived from experiments: Law of Segregation
Every individual possesses a pair of “factors” [genes] for any particular trait, and that each parent passes a randomly selected copy of only one of these “factors” to its offspring
- Offspring must receive genetic material from BOTH parents, or he would not have found white flowers in the F2 generation
- Each parent has 2 copies of these factors (what we now call 2 copies of a gene - 2 alleles - at a particular locus, or region of the genome)
- The 2 factors separate with equal probability and only one copy goes to each gamete (sex cells)
- Some gene variants are dominant over others
Mendel’s Laws derived from experiments: The Law of Independent Assortment
Which allele is passed down to the next generation at one locus is independent of which allele is passed down at another locus
- Mendel also experimented with other traits like seed shape
- The allele passed down at one locus (e.g. flower color) is INDEPENDENT (not influences by) the allele at another locus (e.g. seed shape)
- Today we know that story is more complex
Mendel’s laws give us the MECHANISM for inheritance (Darwin did NOT know why offspring resembled their parents)
Blending vs. Particulate Inheritance
Darwin and his contemporaries envisioned inheritance as a blending process
However, blending removes variation
Under a blending scenario, the F1 generation has an intermediate phenotype between the two parentals, AND the F2 generation is also intermediate
Mendel’s experiments showed that inheritance is a particulate process, which preserves variation over time
Phenotypes CAN be blended, but ____________ remains particulate with ______________
Inheritance; co-dominant alleles
Which observation(s) are evidence for particulate inheritance vs. blending?
a) F1 generations have intermediate phenotypes
b) F2 generations have parental and intermediate phenotypes
c) Alleles at different loci sort independently
d) Phenotypic variation is influenced by the environment
b) F2 generations have parental and intermediate phenotypes
Punnett square
Predicting phenotypes
What are the eye colors of the two black boxes?
a) Brown, brown
b) Blue, blue
c) Blue, brown
d) Brown, blue
d) Brown, blue
Darwinian + Mendelian Genetics
The source of variation was a big challenge for Darwin - why did individuals vary within a population?
The MODE of inheritance was also a huge problem for Darwin - he knew traits were transmitted from parents to offspring, but he didn’t know how
Darwin speculated that characteristics of the parents were blended - like mixing paint - as they passed to the offspring
But if that was true, how could a single fortunate change be spread through a species
The Modern Synthesis: Mendel + Darwin
During the early 20th century, genetics provided definitive answers to these questions
The combination of Darwinian ideas about selection with modern Mendelian genetics gave rise to neo-Darwinism or the Modern Synthesis
The Modern Synthesis: Individuals Vary
DNA is the unit of inheritance; phenotypic variation is caused by genes
Mutation during DNA replication creates new alleles or new genes
This is the SOURCE OF VARIATION Darwin wondered about
Individuals have different combinations of alleles and therefore have different phenotypes - this is why individuals vary
The Modern Synthesis: Offspring Resemble their Parents
Genetic variants (alleles) are the cause of variation in phenotypes
Individuals pass their alleles on to their offspring - this is why offspring resemble their parents
In sexually reproducing organisms parental alleles are recombined into unique combinations
This is in part why resemblance between parents and offspring is not pergect
The Modern Synthesis: The individuals with alleles best suited to their environment survive
In most generations, more offspring are produced than can survive
The individuals that survive and reproduce the most are those with the alleles and allelic combinations best suited to their environment
The Modern Synthesis + Darwinian Evolution
Alleles that increase the ability of organisms to survive and reproduce increase in frequency from one generation to the next, causing populations to evolve
With enough time, genetic change through mutation and natural selection leads populations became distinct species
The modern synthesis paved the way for the modern study of evolution
Today we can study natural selection operating at the level of phenotype and the genotype
This overarching evolutionary framework shapes all aspects of biological research
The sources of variation
Darwin postulated that variation exists naturally and some of this variation is heritable
Mendel confirmed that many of these variations are passed to the next generation intact
How are new variations produced? There are FOUR ways to introduce new genetic variants into a population
1) Mutation
2) Recombination
- Crossing over during meiosis
3) Migration
- Move individuals from one population to another
4) Lateral gene transfer
- Occurs primarily in bacteria
Mutation
Mutations are changes to the genetic material (either DNA or RNA)
Most mutations occur during DNA replication, but some occur by the action of other agents: radiation, chemicals
Somatic mutations cannot be transmitted to descendants in animals but may be passed on in other organisms
What is a mutant?
A mutant is an individual organism - or new genetic character - resulting from an instance of mutation
Mutation creates new characters or traits not found in the parental type
Types of mutations with evolutionary significance
Point mutations
- Synonymous
- Non-synonymous
Frameshift mutations
Inversions
Duplications
Chromosome re-arrangements
Polyploidy
Point mutations/single nucleotide polymorphisms (SNPs)
Changes in only ONE nucleotide
Can be transitions, transversions, insertions, or deletions
- Transitions = mutation from period to period (i.e. A-> G, C->T)
- Transversion = Mutations between different types of nitrogenous bases
Usually have SMALL phenotypic effects but in some cases can be loss-of-function mutations
Synonymous changes
Changes at degenerate bases are “synonymous” or “silent” - they don’t change the amino acid
Usually very SMALL to NO phenotypic effect
Non-synonymous changes
Changes at non-degenerate bases are “non-synonymous” or they change the amino acid
Nonsense mutations produce a stop codon that terminates translation
Larger phenotypic effects
Which of these mutations in the third codon position results in a non-synonymous change?
a) GCA -> GCC
b) CCU -> CCC
c) AAU -> AAG
d) UCU -> UCA
c) AAU -> AAG
Aspargine -> Lysine
Indels and Frameshifts
Indel is short for Insertions and Deletions
Insertions and deletions (indels) can have larger effects
If indel is a multiple of three, it is in-frame; if not, it causes a frameshift
Can have larger phenotypic effects, especially frameshifts
Inversions
180 degree flip of part of a chromosome
Can have large phenotypic effects
Detaches, flips in order, reattaches
Crossing over doesn’t work well when parts have been inverted
Duplications and Translocations have _______ phenotypic effects
LARGE
Duplication
A segment of the chromosome is duplicated
Translocation
Segment of a chromosome moves from one chromosome to a nonhomologous chromosome or to another place on the same chromosome (the latter not shown here)
Gene Duplications
They are the most common origin of new genes
The duplicated gene is not subjected to natural selection and is free to evolve
-One of the major sources of novelty in our genome
Multiple gene duplications produce gene families
Chromosome inversions and translocations
Chromosome re-arrangements affect linkage, can cause cross-over effects, and can produce supergenes
A supergene is a group of neighboring genes on a chromosome which are inherited together because of close genetic linkage
Inversions and translocations can have major effects because it affects linkage
Polyploidy
Whole chromosome duplication
Most common in plants
Is a well known mechanism of speciation
plants able to survive polypoloidy and actually create new species when undergoing polyploidy
Genetic Recombination
Crossing over occurs during meiosis, after chromosome duplication
Crossing over means that each gamete may have a unique genotype from the parent
-Important for “shuffling” variants
This is an important way that sexually reproducing organisms generate genetic variability in offspring
Which type of mutation is LEAST likely to have an effect on phenotype?
a) Inversion
b) Deletion
c) Synonymous mutation
d) Non-synonymous mutation
c) Synonymous mutation
What effects do most mutations have on fitness?
Slightly negative and neutral - most mutations are neutral or slightly deleterious
From an evolutionary standpoint, we classify mutations based on their
Fitness effect
Fitness effects
Typically neutral, beneficial, or deleterious
Mutations with _______ phenotypic effects are more likely to accumulate
Small
Mutations are mostly neutral or weakly deleterious
Mutations with _____ phenotypic effects are normally negative and rapidly eliminated by natural selection
large
In rare cases, mutations with large effects are ______ and those are strongly selected by natural selection
Beneficial
Fitness effects of mutations: Random generation
Mutations are NOT generated BECAUSE of their effect on fitness - this is not a directed process
Mutations are RANDOM, and then natural selection operates to remove or favor those mutations in a two-step process taht generates variation
The randomness of mutations was not always known
In 1943, Luria and Delbruck conducted an experiment to test whether E. coli can preferentially mutate to evolve resistance to a virus (bacteriophage), or whether resistance arose due to random mutations
Hypothesis 1 - Random mutation: prior to phage exposure, there would be a few resistant E. coli cells due to random mutation. After exposure, non-resistant cells would die and resistant cells would replicate and spread
Hypothesis 2 - Acquired, inherited resistance: When exposed to phage, all cells would be sensitive. Exposure would induce resistance mutations in some cells. This would be heritable, and would spread
Experimental setup
1) Inoculate nutrient broth with 50-500 phage-sensitive cells
2) Incubate and allow bacteria to grow to high density
3) Plate onto agar covered by large number of phage
4) Count number of colonies that appear after 24-48 hours
How to distinguish the hypotheses?
In any culture tube, the cells have arisen through cell division and are phylogenetically related
-Groups of cells in the tube will be related
Under the random mutation hypothesis, the resistant cells would have appeared in the nutrient broth, before phage exposure. If the mutation arose early and happened to spread in the culture, there would be many resistant individuals. If it arose late, there would be few
Numbers of resistant colonies will vary depending on when mutation arose
Under acquired resistance hypothesis, cells acquire resistance independently when they encounter the phage
Because there are very large numbers of cells, we would expect a similar number of resistant cells to arise on each plate
Predicts similar number of resistant colonies across plates
Evidence for random mutation
Luria and Delbruck constructed a mathematical model of these predictions, including a new distribution
They ran the experiment over and over
They kept finding dramatic variation in the number of resistant colonies among cultures, as predicted by random mutation that occurs independent of selection or the environment
Won the Nobel Prize for this and other achievements
Which statement correctly describes how mutations and natural selection interact?
a) Mutations generate deleterious mutations that are then always removed from the population by natural selection
b) The environment stimulates mutations, on which natural selection then acts
c) Mutations generate beneficial variants for the organisms, and natural selection acts on those variants
d) Mutations randomly generate genetic variants, and natural selection acts on those variants
d) Mutations randomly generate genetic variants, and natural selection acts on those variants
Mutation rates
Mutations randomly generate variation on which natural selection acts
If we want to predict how selection will work, we need to understand the rates at which mutations arise
These are typically SMALL
In humans, mutation rate is estimated at 1x10^-8 to 3x10^-8 per nucleotide per generation
The entire human genome is 3.1x10^9 (3.1 billion) nucleotides
That means 60-180 novel mutations per person
-NOT very many
Mutation rates vary ______-
a LOT
Very high mutation rates in RNA viruses
-Mutations accumulate in viruses, which is why we are able to map COVID already
A bit lower in DNA viruses
In cellular organisms, mutation rate per site increases with genome size
Mutation rates very in different parts of the _______, across different tissue types, among sexes, and among families
Genome
Fitness consequences of mutations
We saw an example of beneficial mutations with the Luria and Delbruck experiment
Such beneficial mutations fuel adaptive evolution
-Need randomly beneficial mutations to pop up
However - deleterious and neutral mutations are MORE common - Why?
Most traits have been under selection for a long time
-Mutations in coding sequence changes amino acids and therefore the proteins
Randomly disrupting these traits is therefore more likely to have negative consequences
Neutral or weakly deleterious alleles (those with small fitness effects) can persist in the population
-Ones that show up in third codon or non-coding region
Lethal or very deleterious mutations are quickly removed by natural selection
Fitness consequences of mutations to heat shock proteins in yeast
Generate many cells with different SNPs in the CODING region
Compete cells over time
Measure frequencies of each mutant
Infer fitness from frequency (higher frequency = greater fitness)
Tested at two temps: 25C (low temps), the protein is INessential, but at high temps it is essential to survival
At high temperatures, protein is essential to survival
What happens to the fitness consequences of mutations?
Mutations were more likely to be lethal at high temperatures
Thus, mutations in the protein have much more deleterious effects when the protein is necessary for survival
At 25C (low temperatures), what effect did most mutations in the heat shock protein have on fitness?
a) Positive
b) Negative
c) Neutral
c) Neutral
At HIGH temperatures, what effect did most mutations in the heat shock protein have on fitness?
a) Positive
b) Negative
c) Neutral
b) Negative
Do beneficial mutations arise to help organisms adapt to new environments? Why or why not?
NO, mutations occur randomly. Those that are beneficial for the environment will be SELECTED FOR, but the environment does not stimulate a mutation
Why do most mutations have neutral or deleterious fitness consequences?
Because they are changing things at a genetic level, and many times this is detrimental rather than helpful because genetic processes are very specific
Rediscovering Mendel
Mendel’s work remained obscurity for 35 years until it was re-discovered in 1900
-After re-discovery, his research was not immediately accepted
- The traits Mendel examined were discrete whereas most biological variation seems to be continuous
- Trait frequencies observed in nature were not consistent with frequencies under Mendelian inheritance
Discrete vs. Continuous traits
Discrete: One or another, no gradient
-i.e. Spiral direction is a discrete trait; can only go clockwise or counterclockwise
Continuous: Gradient, many variations
-i.e. skin color
Reginald Punnett
Punnett in 1908 showed several examples of traits that were subjected to Mendelian inheritance, including brachydactyly
G. Udny Yule’s criticism
If Mendel’s rules are correct, a heterozygous trait should be observed in a 3:1 ratio of dominant:recessive traits in a population
But, for example, brachydactyly does NOT occur in a 3:1 ratio in human populations - it remains rare
G. H. Hardy’s answer
Hardy (and Weinberg) developed a mathematical model to predict the POPULATION-LEVEL consequences of Mendelian inheritance
- It showed that Punnett’s examples of rare Mendelian traits, including brachydactyly, could be valid even though nothing close to a 3:1 ratio was observed
- It also showed that the frequency of an allele neither increases nor decreases simply because its effects are dominant or recessive
- In other words, dominant alleles do not replace recessive alleles over time
Population genetics
Study of genetic variation within populations
Involves the examination and modeling of changes in the frequencies of genes and alleles in populations over space and time
The study of changes in GENE and ALLELE frequencies over time and space => Evolution
Individual-Level Thinking
What gametes and offspring are produced, in what frequencies, from a given pair of parents?
Classic, or transmission, genetics focuses on how INDIVIDUALS are related to their parents
Population-level thinking
How do the characteristics of the population change over time as the result of evolutionary processes?
Population genetics focuses on groups of individuals =- specifically, groups of interbreeding individuals - and how characteristics of these groups change over time
Central questions we will ask with population genetics
How do allele frequencies change over time in the absence of natural selection?
How can we build a model of natural selection?
how do mutation, natural selection, nonrandom mating, and migration affect allele frequencies in a population?
Quantitative vs. Qualitative Predictions
A key component of population genetics is making quantitative predictions about evolutionary processes
To do this, we build models for how allele and genotype frequencies change over time
Models (in science)
Models are TOOLS for representing, visualizing, and studying complex processes or phenomena that cannot be directly measured
Can be mathematical, statistical, or verbal/illustrative
Every model has underlying ASSUMPTIONS: the conditions under which a model is true
By examining and altering the assumptions of models, we can make PREDICTIONS about real processes
Models approximate reality - they do not replicate it
An important component of any model is an estimate of uncertainty - how confident are you that your model is accurate
The more complex the process, the more challenging it is to model
Everything we do in population genetics is based on models: The Modern Synthesis
Early 20th century
RA Fisher, JBS Haldane, and Sewall Wright used mathematical models to connect Darwin’s theory of natural selection to Mendelian genetics
Showed that natural selection can change allele frequencies
Developed broad mathematical explanation how allele frequencies change at a single locus
Demonstrated effects of genetic drift and inbreeding on small populations
Annotation of alleles and genotypes in this course
A and a will be used to indicate different alleles, NOT adenine or denoting which is dominant/recessive
Population genetic models tend to be ______ for simplicity when modeling how allele frequencies change through time. This means we only have two alleles per locus
Di-allelic
Any particular locus can ONLY have 2 alleles
Allele frequency (f)
How COMMON an allele is in a population
f is determined by counting how many times the allele appears in the population and dividing by the total number of copies of the gene
f = number of specific allele/total number of alleles
The Hardy-Weinberg Model
AKA Hardy-Weinberg equilibrium
Primary NULL MODEL FOR EVOLUTIONARY BIOLOGY
Tells us how allele and genotype frequencies change over time in the absence of evolutionary processes like natural selection
This gives us a baseline against which we compare our observed data - if our data don’t match the model, then some other process is operating
Suppose that a single trait at a single genetic locus is encoded by a pair of alleles
In the absence of evolutionary processes
-How will the frequencies of these alleles change over time?
- How will the frequencies of the different genotypes change over time?
- In other words, what will happen to the frequencies of these alleles and genotypes due to the dynamics of chromosomal segregation and gametic fusion alone?
A quick refresher: what is the frequency of the RED allele in this population?
a) 10/20
b) 6/20
c) 14/20
d) 10/10
c) 14/20
Count each red allele and divide by total number of alleles
We’re interested in the frequencies of genotypes and alleles so we can measure how and why they vary
What if we only know the frequency of alleles?
We can PREDICT genotype frequencies from allele frequencies, but we have to make some ASSUMPTIONS
Random Mating
All individuals have equal probability of mating allele frequency in males = allele frequencies in females
Remember: We are going to call our alleles a and A, or A1 and A2 - these are the same thing!
We imagine that parents contribute gametes to a single large gamete pool; then pairs of gametes are drawn at random to form new offspring
To PREDICT the genotypes of the offspring, we need to figure out the PROBABILITY that an individual offspring is a homozygote (A1A1 or A2A2) or a heterozygote (A1A2 or A2A1)
This probability is the change that we reach into our gamete pool and “pull out” an A1, and then reach into our pool and pull out another A1 (sampling with replacement)
Chance that OFFSPRING has A1A1 genotype =
fA1 x fA1 = (fA1)^2
What is the change that an individual offspring has an A2A2 genotype?
A) fA2fA1 +fA1fA2
B) fA1 x fA2
C) fA2 x fA2
D) fA2
C) fA2 x fA2
Chance that OFFSPRING has A2A2 genotype =
fA2 x fA2 = (fA2)^2
Chance that OFFSPRING has A1A2 genotype =
fA1fA2 + fA2fA1 = 2fA1fA2
Expected genotype frequencies under random mating; the probabilities must sum to 1
(fA1)^2 + 2fA1fA2 + (fA2)^2 = 1
p^2 + 2pq + q^2 = 1
Here, p^2 means an individual with a pp genotype, q^2 has a qq genotype. This is the same as an A1A1 or aa or AA or A2A2 genotype - we are jsut distinguishing between 2 different alleles at a locus, and then indicating the frequency of homozygotes and heterozygotes
Random mating (does, does not) change the allele frequencies in a population
Does NOT
We are just reshuffling alleles into homozygotes and heterozygotes each generation
hardy-weindberg Equilibrium
After ONE generation of random mating, allele and genotype frequencies in a population will remain contant over time in the absence of other evolutionary influences
Under HWE, genotype frequencies will add up to 1
The Hardy-Weinberg Equilibrium: Conclusions
Conclusion 1: Allele frequencies in a population will not change over time (if our assumptions of random mating are met)
Conclusion 2: If the allele frequencies in a population are given by A1 and A2, the genotype frequencies will be given by A1^2, 2A1A2, and A2^2
Conclusion 3: If no other processes are operating, populations will reach HWE in one generation
Population genetics is the study of _____ in allele frequencies in populations
Changes
What does it mean that the expectation is that allele frequencies in populations DO NOT CHANGE over time?
We study agents that cause deviations from HWE and change allele frequencies between generations
What are assumptions of Hardy-Weinberg Equilibrium?
1) No selection
2) No mutation
3) No migration
4) Large population
5) Random mating
What are assumptions?
Assumptions are the conditions under which a model is valid
The Hardy-Weinberg Model
When all the assumptions of the HWE are met, allele frequencies do not change from one generation to the next - there is not evolution
If allele frequencies DO change among generations, then our assumptions are VIOLATED and one of these other processes is occurring
HWE is a baseline expectation with NO evolution; evolution studies the DEVIATIONS from HWE
5 Agents of Evolutionary Change
1) Mutation
2) Gene flow
3) Non-random mating
4) Genetic drift
5) Selection
Cause allele frequencies to change over time
Which of these statements is NOT a conclusion of the Hardy-Weinberg Model?
a) The allele frequencies in a population will not change only if the original allele frequencies are 60% and 40%
b) If the frequencies of alleles in a population are p and q the genotype frequencies are p^2, 2pq, and q^2
c) The genotype frequencies can be calculated based on the allele frequencies
d) The allele frequencies in a population will not change over time
a) The allele frequencies in a population will not change only if the original allele frequencies are 60% and 40%
Why are mutations at degenerate codon positions often considered “silent”?
a) Because they have positive effects on fitness
b) Because they are unlikely to affect the phenotype
c) Because they lead to changes in the amino acid in a protein sequence
d) Because they have negative effects on fitness
b) Because they are unlikely to affect the phenotype
What is the frequency of the blue allele in this population?
a) 7/10
b) 12/20
c) 8/20
d) 5/20
c) 8/20
Which statement correctly describes how mutations and natural selection interact?
a) Mutations generate deleterious mutations that are then always removed from the populations by natural selection
b) The environment stimulates beneficial mutations, on which natural selection then acts
c) Mutations randomly generate genetic variants, and natural selection acts on those variants
d) Mutations generate beneficial variants for the organisms, and natural selection acts on those variants
c) Mutations randomly generate genetic variants, and natural selection acts on those variants
Based on the information provided, what is the phenotype of the individual in the black box?
a) Small
b) yellow
c) Big
d) Green
d) Green
In a population under Hardy-Weinberg equilibrium, you measure the frequency of p (or A or A1) to be 0.3. Based on the figure above, what is the frequency of q (or a or A2)?
a) 0.7
b) 0.8
c) 0.4
d) 0.5
a) 0.7
What is the genotype in the black box?
a) Aa
b) aa
c) AA
a) Aa
What is population genetics?
a) The study of natural selection and adaptation
b) The study of genetic variation within individuals
c) The study of variation in allele frequencies over time and space within populations
d) The study of the effects of mutations on phenotypes
c) The study of variation in allele frequencies over time and space within populations
Why are most mutations neutral or weakly deleterious?
a) Because they have large effects on phenotypes
b) Because mutations of large phenotypic effect are usually positive and favored by natural selection
c) Because they have positive effects on fitness
d) Because mutations with large phenotypic effects are usually strongly deleterious and are removed by natural selection
d) Because mutations with large phenotypic effects are usually strongly deleterious and are removed by natural selection
What is an allele?
a) A gene
b) A locus
c) A phenotype
d) Any part of the genome that varies among individuals
d) Any part of the genome that varies among individuals
In a population under Hardy-Weinberg equilibrium, you measure the frequency of the aa genotype (the blue line in the figure above) to be 0.4. What is the approximate frequency of the Aa heterozygote? you may eyeball on this figure.
a) 0.3
b) 0.5
c) 0.8
d) 0.2
b) 0.5
