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Evolution > Lec 4 > Flashcards

Lec 4 Flashcards

1
Q

Population genetics

A

How and why allele frequencies change over time

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2
Q

Types of Variation: Phenotypic variation

A

To be heritable, this has to be genetically based

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3
Q

Types of variation: Non-genotypic variation

A

NOT heritable and plays NO role in evolution

I.e. derived from environmental factors

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4
Q

The DNA molecule: The source of genetic variation

A

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

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5
Q

The DNA molecule

A

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

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6
Q

Structure of a genome

A

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

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7
Q

Information flow

A

DNA -> (transcription) pre-mRNA -> (splicing) mRNA -> (translation) protein -> phenotype

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8
Q

From DNA to proteins

A

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

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9
Q

Transcription

A

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

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10
Q

Translation

A

mRNA -> protein sequence

Each strand of RNA codes for amino acid

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11
Q

Relationship between codon triplets and amino acids

A

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

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12
Q

Proteins are the main functional elements in living organisms and are responsible for most biological processes including:

A

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

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13
Q

Making the wrong protein or altering protein structure can have __________ effects on phenotype

A

Major

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14
Q

Epigenetics

A

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

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15
Q

Allele

A

Variant of a gene or particular sequence of DNA

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16
Q

Genotype

A

Combination of alleles at a particular locus

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17
Q

Locus

A

Any particular location on a chromosome, can be big or small

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18
Q

Outcome of genotype is _________

A

phenotype

Phenotype is what you see

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19
Q

There are 23 chromosome pairs:

A

1 each from maternal and paternal side

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20
Q

Form of DNA determines trait of tasting PIC or not tasting it

A

Alleles are represented by letters: Capital - dominant, lower = recessive

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21
Q

In order to get a recessive phenotype from two parents with dominant phenotype, the parents must be ______

A

Heterozygotes

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22
Q

The dominant trait (is, is not) always the most common trait

A

is NOT

Dominant allele may not be common in the population (i.e. polydactyly)

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23
Q

An allele (does, does not) have to be a gene

A

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

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24
Q

Uppercase vs. lowercase letters referring to alleles

A

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

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25
Q

A locus is:

a) A location in the genome
b) A particular genotype
c) Different genetic variants
d) A particular phenotype

A

a) A location in the genome

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26
Q

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

A

b) Any part of the DNA sequence that varies between individuals

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27
Q

Mendelian Genetics and Modes of Transmission

A

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

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28
Q

Mendel’s Laws derived from experiments: Law of Segregation

A

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
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29
Q

Mendel’s Laws derived from experiments: The Law of Independent Assortment

A

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)

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30
Q

Blending vs. Particulate Inheritance

A

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

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31
Q

Phenotypes CAN be blended, but ____________ remains particulate with ______________

A

Inheritance; co-dominant alleles

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32
Q

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

A

b) F2 generations have parental and intermediate phenotypes

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33
Q

Punnett square

A

Predicting phenotypes

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34
Q

What are the eye colors of the two black boxes?

a) Brown, brown
b) Blue, blue
c) Blue, brown
d) Brown, blue

A

d) Brown, blue

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35
Q

Darwinian + Mendelian Genetics

A

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

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36
Q

The Modern Synthesis: Mendel + Darwin

A

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

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37
Q

The Modern Synthesis: Individuals Vary

A

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

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38
Q

The Modern Synthesis: Offspring Resemble their Parents

A

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

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39
Q

The Modern Synthesis: The individuals with alleles best suited to their environment survive

A

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

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40
Q

The Modern Synthesis + Darwinian Evolution

A

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

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41
Q

The sources of variation

A

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

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42
Q

How are new variations produced? There are FOUR ways to introduce new genetic variants into a population

A

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

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43
Q

Mutation

A

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

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44
Q

What is a mutant?

A

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

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45
Q

Types of mutations with evolutionary significance

A

Point mutations

  • Synonymous
  • Non-synonymous

Frameshift mutations

Inversions

Duplications

Chromosome re-arrangements

Polyploidy

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46
Q

Point mutations/single nucleotide polymorphisms (SNPs)

A

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

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47
Q

Synonymous changes

A

Changes at degenerate bases are “synonymous” or “silent” - they don’t change the amino acid

Usually very SMALL to NO phenotypic effect

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48
Q

Non-synonymous changes

A

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

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49
Q

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

A

c) AAU -> AAG

Aspargine -> Lysine

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50
Q

Indels and Frameshifts

A

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

51
Q

Inversions

A

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

52
Q

Duplications and Translocations have _______ phenotypic effects

A

LARGE

53
Q

Duplication

A

A segment of the chromosome is duplicated

54
Q

Translocation

A

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)

55
Q

Gene Duplications

A

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

56
Q

Chromosome inversions and translocations

A

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

57
Q

Polyploidy

A

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

58
Q

Genetic Recombination

A

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

59
Q

Which type of mutation is LEAST likely to have an effect on phenotype?

a) Inversion
b) Deletion
c) Synonymous mutation
d) Non-synonymous mutation

A

c) Synonymous mutation

60
Q

What effects do most mutations have on fitness?

A

Slightly negative and neutral - most mutations are neutral or slightly deleterious

61
Q

From an evolutionary standpoint, we classify mutations based on their

A

Fitness effect

62
Q

Fitness effects

A

Typically neutral, beneficial, or deleterious

63
Q

Mutations with _______ phenotypic effects are more likely to accumulate

A

Small

Mutations are mostly neutral or weakly deleterious

64
Q

Mutations with _____ phenotypic effects are normally negative and rapidly eliminated by natural selection

A

large

65
Q

In rare cases, mutations with large effects are ______ and those are strongly selected by natural selection

A

Beneficial

66
Q

Fitness effects of mutations: Random generation

A

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

67
Q

The randomness of mutations was not always known

A

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

68
Q

How to distinguish the hypotheses?

A

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

69
Q

Evidence for random mutation

A

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

70
Q

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

A

d) Mutations randomly generate genetic variants, and natural selection acts on those variants

71
Q

Mutation rates

A

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

72
Q

Mutation rates vary ______-

A

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

73
Q

Mutation rates very in different parts of the _______, across different tissue types, among sexes, and among families

A

Genome

74
Q

Fitness consequences of mutations

A

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

75
Q

Fitness consequences of mutations to heat shock proteins in yeast

A

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

76
Q

At 25C (low temperatures), what effect did most mutations in the heat shock protein have on fitness?

a) Positive
b) Negative
c) Neutral

A

c) Neutral

77
Q

At HIGH temperatures, what effect did most mutations in the heat shock protein have on fitness?

a) Positive
b) Negative
c) Neutral

A

b) Negative

78
Q

Do beneficial mutations arise to help organisms adapt to new environments? Why or why not?

A

NO, mutations occur randomly. Those that are beneficial for the environment will be SELECTED FOR, but the environment does not stimulate a mutation

79
Q

Why do most mutations have neutral or deleterious fitness consequences?

A

Because they are changing things at a genetic level, and many times this is detrimental rather than helpful because genetic processes are very specific

80
Q

Rediscovering Mendel

A

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
81
Q

Discrete vs. Continuous traits

A

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

82
Q

Reginald Punnett

A

Punnett in 1908 showed several examples of traits that were subjected to Mendelian inheritance, including brachydactyly

83
Q

G. Udny Yule’s criticism

A

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

84
Q

G. H. Hardy’s answer

A

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
85
Q

Population genetics

A

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

86
Q

Individual-Level Thinking

A

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

87
Q

Population-level thinking

A

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

88
Q

Central questions we will ask with population genetics

A

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?

89
Q

Quantitative vs. Qualitative Predictions

A

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

90
Q

Models (in science)

A

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

91
Q

Everything we do in population genetics is based on models: The Modern Synthesis

A

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

92
Q

Annotation of alleles and genotypes in this course

A

A and a will be used to indicate different alleles, NOT adenine or denoting which is dominant/recessive

93
Q

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

A

Di-allelic

Any particular locus can ONLY have 2 alleles

94
Q

Allele frequency (f)

A

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

95
Q

The Hardy-Weinberg Model

A

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?
96
Q

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

A

c) 14/20

Count each red allele and divide by total number of alleles

97
Q

We’re interested in the frequencies of genotypes and alleles so we can measure how and why they vary

A

What if we only know the frequency of alleles?

We can PREDICT genotype frequencies from allele frequencies, but we have to make some ASSUMPTIONS

98
Q

Random Mating

A

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)

99
Q

Chance that OFFSPRING has A1A1 genotype =

A

fA1 x fA1 = (fA1)^2

100
Q

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

A

C) fA2 x fA2

101
Q

Chance that OFFSPRING has A2A2 genotype =

A

fA2 x fA2 = (fA2)^2

102
Q

Chance that OFFSPRING has A1A2 genotype =

A

fA1fA2 + fA2fA1 = 2fA1fA2

103
Q

Expected genotype frequencies under random mating; the probabilities must sum to 1

A

(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

104
Q

Random mating (does, does not) change the allele frequencies in a population

A

Does NOT

We are just reshuffling alleles into homozygotes and heterozygotes each generation

105
Q

hardy-weindberg Equilibrium

A

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

106
Q

The Hardy-Weinberg Equilibrium: Conclusions

A

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

107
Q

Population genetics is the study of _____ in allele frequencies in populations

A

Changes

108
Q

What does it mean that the expectation is that allele frequencies in populations DO NOT CHANGE over time?

A

We study agents that cause deviations from HWE and change allele frequencies between generations

109
Q

What are assumptions of Hardy-Weinberg Equilibrium?

A

1) No selection
2) No mutation
3) No migration
4) Large population
5) Random mating

110
Q

What are assumptions?

A

Assumptions are the conditions under which a model is valid

111
Q

The Hardy-Weinberg Model

A

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

112
Q

5 Agents of Evolutionary Change

A

1) Mutation
2) Gene flow
3) Non-random mating
4) Genetic drift
5) Selection

Cause allele frequencies to change over time

113
Q

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

a) The allele frequencies in a population will not change only if the original allele frequencies are 60% and 40%

114
Q

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

A

b) Because they are unlikely to affect the phenotype

115
Q

What is the frequency of the blue allele in this population?

a) 7/10
b) 12/20
c) 8/20
d) 5/20

A

c) 8/20

116
Q

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

A

c) Mutations randomly generate genetic variants, and natural selection acts on those variants

117
Q

Based on the information provided, what is the phenotype of the individual in the black box?

a) Small
b) yellow
c) Big
d) Green

A

d) Green

118
Q

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

a) 0.7

119
Q

What is the genotype in the black box?

a) Aa
b) aa
c) AA

A

a) Aa

120
Q

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

A

c) The study of variation in allele frequencies over time and space within populations

121
Q

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

A

d) Because mutations with large phenotypic effects are usually strongly deleterious and are removed by natural selection

122
Q

What is an allele?

a) A gene
b) A locus
c) A phenotype
d) Any part of the genome that varies among individuals

A

d) Any part of the genome that varies among individuals

123
Q

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

A

b) 0.5

Evolution (15 decks)

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