Quiz 1 Flashcards
(130 cards)
1
Q
Define population genetics
A
The fate of individual mutations can be predicted based on their “fitness” and a few properties of the species (population size, spatial distribution, etc.)
2
Q
Define quantitative genetics
A
Change in the trait value (quantifiable measure of a specific characteristic of an organism) can be predicted based on its relationship to fitness and the variation present in a population.
3
Q
How did muslim scholars before Darwin/Wallace contribute to evolutionary thought? What did their ideas include? (4)
A
Anticipated many of the ideas of Darwin and Wallace:
- Hierarchies of complexity among (mineral, plant, animal)
- Temporal transitions between levels of hierarchy (life forms are not static but evolve/develop progressively into more complex forms)
- Species were not fixed, could evolve
- Humans came from an ape/monkey ancestor
*But still religious (invoke God explicitly) and differing from Darwin/Wallace in many ways
4
Q
Pre-Darwin/Wallace beliefs regarding the origin of species
A
Elizabethan “great chain of being”
The prevailing dogma: species “fixed” through time (came from Christian thought)
5
Q
Carl Linnaeus (4)
A
- Father of modern taxonomy
- Naturalist
- Classified life’s diversity (taxonomy)
- Found similarities between species but that that God had just created some species to look more similar
6
Q
Georges Cuvier (2)
A
- Said that fossils resemble but are not exactly the same as modern species, many past species are extinct
- Lead to the thought that species are immutable (fixed) but the absence of necessary conditions results in extinction - thus number of species delcining
7
Q
Jean-Baptise Lamarck (3)
A
- Life driven from simple to complex (complex species descended from microbes, and microbes were continually generated spontaneously)
- Adaptation occurs through inheritance of acquired changes
- Philosophie Zoologique: advocated mutability of species, over generations organisms could proceed from one step to the next, i.e. evolve
8
Q
True or false: It was Lamarck that was the first to introduce that species aren’t fixed
A
True
9
Q
Lamarkian transformation (2)
A
- “Internal force” (something) that changes the offspring during the lifetime of the organism
- Inheritance of “acquired” characters
10
Q
Lamarkian transformation vs. Darwinian evolution
A
Lamarkian transformation: didn’t think that species all shared a common ancestor. Recognized that species change over time, but that they each had different origins
Darwinian evolution: life evolving from a common ancestor (branches)
11
Q
Charles Lyell (2)
A
Published Principles of Geology, introducing the ideas that:
1. Extinction is permanent, species could not re-evolve as Lamarck proposed (Lamarck proposed that species could be replaced if they went extinct)
2. Uniformitarianism: the processes (e.g. erosion, volcanic activity) responsible for the past (unobserved) events are still active and therefore observable
12
Q
Uniformitarianism
A
- Gradual changes
- The processes now are the same processes occurring in the past
- Earth must be way older than previously thought
- Still recognize catastrophic events (just not as the primary force)
13
Q
Which of the following statements is central to the idea of uniformitarianism?
a) natural laws that are observable today also operated in the past
b) catastrophic events such as floods and volcanoes have played the primary role in shaping the earth’s existing features
c) geological change happens gradually for the most part
d) a and c are correct
e) all are correct
A
D
14
Q
Thomas Malthus
A
Responsible for the principles of population growth and limited resources -> under exponential population growth not everyone can survive
- if not everyone can survive, once you get to carrying capacity, there’s a struggle for existence
15
Q
Charles Darwin and uniformitarianism (4)
A
- Invited to serve as unofficial naturalist for HMS Beagle in 1831
- Was a naturalist (getting as many natural specimens as possible)
- In the Andes, Darwin found marine fossil deposits 7000 ft above ground indicating that Lyell’s principles of uniformitarianism are clear
- Fossils that had once been marine in origin were now 7000 ft above, which as to do with tectonic forces over a LONG PERIOD OF TIME. Findings supported the idea that Earth’s landscape changes slowly and progressively through natural processes as the seafloor must have been gradually uplifted over millions of years
16
Q
True or false: Darwin’s finches all diversified to fit different niches from a common ancestor
A
True
17
Q
What had Darwin written regarding the origin of the finches?
A
“One species had been taken and modified for different ends”
- Evolution by natural selection
18
Q
Alfred Russel Wallace
A
- Born 14 years after Darwin
- A backpacking naturalist who made voyages to Brazil and the Malay Archipelago
- While suffering from a malarial fever, he had a “eureka moment”, realizing the importance of competition and limited resources. He then independently developed the theory of evolution by natural selection.
19
Q
What 2 similar ideas were presented in Wallace’s letter to Darwin?
A
- Common ancestry
- Natural selection
20
Q
What was the first official release of the theory of evolution by natural selection?
A
Letters from Darwin and Wallace which were presented at the Linnean Society in 1858 by Darwin and Wallace
21
Q
What are the preliminary facts for Darwin’s theory of evolution by natural selection? (3)
A
- Species have high fertility
- But population size remained fairly constant
- Thus there must be limited resources
22
Q
What are the preliminary inferences for Darwin’s theory of evolution by natural selection? (2)
A
- Limited resources result in a struggle for existence
- Fittest is most likely to survive
23
Q
What are the further facts and final inference for Darwin’s theory of evolution by natural selection? (2)
A
- Variation is ubiquitous (found everywhere)
- Variation is heritable (Darwin didn’t know how though)
Final inference: natural selection leads to evolution
24
Q
What are the three “main ingredients” for evolution?
A
Phenotypic variation -> differential survival/mating success -> reproduction and inheritance -> phenotypic variation
25
What was the reaction to Darwin's theory? (3)
- After he presented it, people did not realize that Darwin/Wallace's ideas were important (no striking discoveries, people thought that the ideas were obvious)
- Publication of the book caused considerable more debate
- Most people accepted evolution, i.e. that species were not fixed in time. The idea of natural selection was rejected by most because it lacked a satisfactory theory of inheritance
26
What 2 ideas that Darwin published were the focus of considerable debate?
1. Blending mechanism of inheritance
2. Gradualism
27
Describe Darwin's "blending mechanism of inheritance"
"particles" of inheritance explain transmission of traits from parents to offspring
- Parental body parts produce "gemmules". Gemmules move to sex organs and are passed on during reproduction
- The strength and number of gemmules determined the characteristic of the offspring. Consequently, the trait of an offspring are a blend of the parents (ex: red and white parents would lead to pink offspring)
28
Describe Darwin's theory of gradualism
Darwin theorized small changes from one generation to the next.
- Changes large enough to result in the formation of new species must occur during long periods of time.
29
What 2 laws are associated with Gregor Mendel?
Law of segregation and law of independent assortment (i.e. no blending)
30
True or false: Darwin knew about Mendel, and Mendel's publication eventually led to a revival of Darwin's theory
False; Darwin did not know about Mendel
- However, his publication (that went unnoticed for many years) eventually led to a revival of Darwin's theory, but initially dismissed Darwin's theory as blending was not the primary mechanism of inheritance.
31
Describe Hugo de Vries reaction to Darwin and his significant implications (2)
Rediscovered Mendel's work when finding evidence that genetic differences cause discrete differences in phenotype
Significant implications:
1. Hereditary mechanism produces large changes between generations, so evolution must be saltatory (occurs through sudden significant leaps rather than gradual changes)
2. Continuous variation that biometricians had been reporting must be a consequence of the environment (rather than being inherited genetically)
Overall: Evolution is not gradual, natural selection is not an important mechanism, therefore Darwin must be wrong.
32
On what point(s) would Darwin/Wallace and Jean-Baptiste Lamarck have agreed?
a) Adaptation occurs when individuals change to adapt to their environment
b) life is spontaneously generated all the time
c) species give rise to a new species
d) simple organisms have existed for a shorter period of time than complex organisms
e) they would have disagreed on all of these points
C
All the other points are Lamarck only
33
The modern synthesis
Debate of relevance for discrete vs. continuous variation in the early 1900's led to the development of quantitative genetics and the resolution that individual genes differ
- did mathematical approaches to predicting how mutations will spread
34
Importance of the Hardy Weinberg Equilibrium (2)
- The Hardy Weinberg Equilibrium led to the field of population genetics because it demonstrated the consequences of Mendelian Genetics in a population
- Until this time, evolutionary biologists had been interested in changes in phenotypes over generations, but population genetics portrayed evolution as changes in allele frequencies over generations.
35
Who was the rift between geneticists and proponents of natural selection resolved by?
Theoretical research of three biologists: Fisher, Haldane and Wright
36
What is an example of how people misread Darwinian thought?
Eugenics
37
T. Dobzhansky, E. Mayr and G. Simpson were responsible for what?
Interpreted the theory and provided evidence from nature - brought population genetics to the majority of evolutionary biologists (they showed that Darwinian evolution is consistent with genetics)
38
Dr. Peter and Rosemary Grant
Have been working on the evolution of Darwin's Finches in the Galapagos for more than 30 years
- showed that evolution can happen quite quickly
39
What do genome sequencing technologies allow for in evolutionary studies?
Allow us to pinpoint the exact changes that result in these trends, which helps us understand signatures of natural selection.
40
Intergenic regions
Opposite of genic regions, not used for protein production directly but can harbour regulatory regions that determine whether a gene gets turned on.
41
True or false: there are lots of transposable elements in the genome
- Explain what a transposon is in general
True
- Repetitive elements that act as "parasites" in the genome
42
True or false: there is lots of variation in genome size between species but not a lot of variation within a clade
False; there is lots of variation between species but still also a lot of variation within a clade
- e.g. some flowering plants have different genome sizes
43
True or false: in general, a larger genome correlate with a greater number of genes
True
44
Bigger genomes correspond with (smaller/larger) cells
Larger
45
What is the ultimate source of variation?
Mutation
46
True or false: An unbroken chain of mutations separates us from our distant ancestors
True
47
In terms of mutations, we need a balance between which two things in order to get evolution?
A balance between variability and fidelity.
48
What are three examples of bigger scale mutations?
Inversion, chromosome fusion, genome duplication (an entire genome duplication that changes us from diploid to polyploid)
49
What 3 things do mutations result from?
1. Errors in DNA replication, crossing over, or segregation of chromosomes during meiosis
2. Effects of chemical or physical influences that react with and change the structure of DNA
3. The activity of selfish genetic elements (i.e. transposons, like viruses in the genome, little pieces of DNA that includes genes that affects its copying. Can sometimes proliferate and jump around the genome so these can change phenotype)
50
Point mutation
Can occur during actual DNA replication causing a change in a single base pair and yields a Single Nucleotide Polymorphism (SNP) in the population if it persists.
51
What are the 3 types of point mutations?
1. Missense mutation
2. Nonsense mutation
3. Silent (synonymous) mutation
52
Describe the role of the environment on mutation rate and explain the mice study
Pollution can increase the rate of mutation
Study: Kept mice near major highway and two steel mills, in conditions with vs. without HEPA air filtration
- Mutation rate was 2X higher near unfiltered industrial sites (20 pedigrees in each group)
- Paternal, but not maternal groups differed: because paternal has more cell divisions, since testes are constantly dividing (While ovaries divide fully in the embryo)
53
Describe transposon-induced mutations in corn kernels
The insertion of a transposable element in the gene for colour in corn kernels can cause the loss of the ability to form pigment
- This occurs in many different cells, which results in the variegated pattern
54
Somatic vs. germ-line mutations
Somatic mutations occur in the cells in the rest of the body (e.g. most forms of cancer-causing mutations), while germ-line mutations occur in the cells that divide to form gametes (the "stuff" of evolution)
55
Why are more mutations found at the top of a tree than at the bottom?
The top of the tree has undergone more cell divisions than the branches lower down. More opportunity for mutation.
56
Genomic mutation rate formula and unit
Genome size * mutation rate per base pair
- unit: Mutations/cell division
57
Observation vs. prediction
Observation: piece of data collected which you can compare to your predictions
Prediction: expected data
58
Population mutation rate formula and meaning
Nµ (population size * nucleotide mutation rate) represents the average number of mutations introduced into the entire population per generation at a specific nucleotide position (the probability that in one generation of mating (a parent producing one new offpsring) there will be a change from the nucleotide present to a new one.)
59
Explain why dog face morphology is so variable
The ratio of the number of Glutamine (polyQ) to Alanine (polyA) repeats is highly correlated with changes in dog facial morphology
- This is particularly interesting, because the mutation rate for repeats (10^-5-10^-4) is much higher than point mutations (10^-8), making this trait much more evolvable
60
True or false: tiny changes in regulatory alleles have a large effect on phenotype
- give an example
True
- Evolved tooth gain in sticklebacks is associated with cis-regulatory allele of Bmp6
61
How has genomics started giving us new ways to study cancer?
The genomic revolution has given us an unprecedented way to study mutations. Scientists are now sequencing many different samples from different types of cancer and finding large differences in mutation profile.
62
How is population defined in the context of evolution?
A group of individuals that have approximately equal probabilities of mating with each other.
63
Null model in population genetics
If we want to understand something as complicated as evolution, first we must represent what happens in the absence of evolution
- This gives us a null model. We can compare observations to this null model to learn more about evolution.
64
What question does Hardy-Weinberg answer?
What will happen to the frequency of a mutation (an allele) in the absence of natural selection?
65
What will happen to the frequency of a mutation (an allele) in the absence of natural selection?
No change in allele frequency (evolution occurs when allele frequency changes)
66
Formula for allele frequency
Frequency of A = [# copies of A]/(ploidyN)
67
Formula for genotype frequency
Frequency of AA = [# individuals AA]/N
68
What are the 5 assumptions of the Hardy-Weinberg model?
1. A single locus with two alleles does not mutate between generations
2. No immigration or emigration to/from the population
3. The population is very big (infinite, in theory) so we can assume that there's no genetic drift
4. There is no natural selection (the fitness of each genotype is equal, so survival ability is the same, number of offspring is the same and there's equal number of males and females of each genotype)
5. Mating is random with respect to the trait of interest (under random mating, individual gametes have equal probabilities of combining with each other, regardless of the alleles they carry at the locus of interest
69
What is the sum of the frequency of a dominant allele, A (p) and a recessive allele, a (q) under the HWE assumptions?
p+q=1
- Because of the assumptions of large population size, no mutation, no natural selection and no gene flow, the frequency of these alleles does not change from one generation to the next.
70
Haplotype definition and how the haplotypes of eggs and sperm are related
The haplotype of egg will be independent of the haplotype of sperm as it fertilizes that egg to form a zygote
71
Hardy-Weinberg equation
p^2 + 2pq +q^2 =1
- In the absence of changes in allele frequencies, this combination of genotypes will persist forever
72
Why do we care about Hardy-Weinberg genotype frequencies?
We can measure genotype frequencies for any locus and see if they match expectations for HWE
So: if we see a big deviation from HWE then we can conclude pronounced evolutionary change might be happening at the locus
- We can make inferences about what might be happening based on whether the model fits the observations
- The Hardy-Weinberg equation can be used to identify when the basic assumptions are violated
73
A population that is perturbed by a violation of the Hardy-Weinberg assumptions will return to HWE in __ generation(s) of random mating, once the assumptions are met
One
74
What does it mean if you find a population where the number of both homozygous genotypes exceeds the number of heterozygotes?
You know it's not in HWE
75
When there is no association between loci above randomness, this is called ________, and deviations from this are called ______/______
Linkage equilibrium (LE), linkage disequilibrium (LD)/Gametic Phase Disequilibrium
76
What is D?
A measure of disequilibrium
77
Formula for D using haplotype proportions
D = p[AB]*p[ab] - p[Ab]*p[aB]
78
Define x1, x2, x3 and x4 in terms of D
x1 = p[A]p[B] + D
x2 = p[A]p[b] - D
x3 = p[a]p[B] - D
x4 = p[a]p[b] +D
79
What is the most important genetic factor affecting association between locus A and B?
Recombination
80
When two loci are located on two chromosomes, four types of gametes will be produced in _____ proportions.
Equal
81
If two genes are on different loci, what is the probability of recombinant genotype (i.e. gametes that differ from the parents)
1/2
82
Meiosis with no crossover between genes on the same chromosome will result in...
All parental gametes
83
Meiosis with a crossover between genes on the same chromosome will result in...
1/2 parental gametes and 1/2 recombinants
84
What does the probability of recombination depend on?
The proximity of two loci on a chromosome and their proximity to the centromere
- Two loci can be so close together that recombination almost never occurs
85
What does a higher rate of recombination mean in terms of LD?
LD decreases more rapidly
86
If D>0, the association between alleles (increases/decreases) the frequency of the x1, so after one generation of random mating, the frequency of x1 becomes...
Increases
x1'=p[A]*p[B]+D-rD
87
If the recombination rate is higher, then the [ab] frequency in subsequent generations will be...
Higher
88
Define x1', x2', x3' and x4' in terms of rD
x1'=x1-rD
x2'=x2+rD
x3'=x3+rD
x4'=x4-rD
89
The amount of disequilibrium decreases by a factor of ___ each generation
1-r
90
Formula for Dt and what it applies to
D = D (1-r)^t
- Applies both when loci are on the same or on different chromosomes. Even with different chromosomes and r=0.5, LD still decays over several generations (going back to what would happen under randomness). This is different from HWE, because HWE goes back after one generation of random mating
91
Given no change in allele/gamete frequencies, a single generation of random mating for a single locus with two alleles results in...
HWE
92
Reaching linkage equilibrium requires (4)
1. Several generations
2. Random mating
3. No changes in allele frequency
4. Recombination between loci (r>0)
93
Explain how LE and HWE are related
Both LE and HWE are illustrating what happens when the probability of different combinations of alleles is determined completely at random.
- They give us a null hypothesis of what is happening when there are factors forcing the system in one direction.
94
LD decays in proportion to how much (2)
LD there is already (D) and the rate of recombination (r)
95
Define genetic drift and its short-term/long-term effects
A change in allele frequencies resulting from random sampling involved in the individuals that contribute to the next generation
- produces unpredictable outcomes during a particular episode, although the average (expected) outcome during many episodes can be predicted
96
What is a random process in evolution? Are the consequences of random processes more significant for small populations or large populations?
Events that occur if their probability of occurrence is not affected by an individual's phenotype
- More significant for small populations
97
When does sampling error occur?
Occurs when you calculate a statistic on only a subset of the population
98
The probability of drawing exactly Y copies of the A allele can be described by a _____ distribution
- Describe this distribution
Binomial
- The binomial distribution describes the probability of getting y (A allele) successes from k trials (N= population size), if the probability of success is x (p = allele frequency)
99
Random variation between generations in allele frequencies and the traits they control should be particularly evident in (small/large) populations
Small
100
Formula for variance in allele frequency after one generation?
pq/2N
101
The fluctuation in allele frequencies should be much bigger in (small/large) populations
Small
102
The time to allele fixation is faster in (small/large) populations
Small
103
prob[fixation of neutral allele] =
(neutral allele has no effect on fitness)
p=1/2N
(proportion of an allele)
104
If both alleles have equal fitness, then they are...
"Neutral" and they each have the same chance of fixing in any given mating
105
How many generations does it take for a new mutation to fix in a new population?
4N generations (for diploids)
106
Fixation takes (shorter/longer) with larger populations
Longer
107
Fixation is fastest when the allele is at a (lower/higher) frequency
Higher
108
True or false: time to fixation of an allele is greatly dependent on the allele frequency
False; it is weakly dependent on the allele frequency
109
True or false: the assumptions for LE and HWE are the same
True
110
Formula for number of new mutations that occur in each generation in each population
2Nµn
µ = mutation rate per base pair
n = number of base pairs
(for diploids)
111
Formula for the number of mutations that fix each generation (rate of fixed mutations/generation)
nµ
n= number of base pairs
µ = mutation rate per base pair
112
Formula for calculating the # of accumulated mutations per branch
Tnµ
(2Tnµ for both branches if number of generations are the same for both species since divergence)
113
Genetic distance definition
The "genetic distance" is the number of pairwise differences in nucleotides between two sequences
114
Using the molecular clock requires calculating the genetic distance at what type of loci, and how is this ensured (2)?
Requires calculating genetic distance at neutral loci by using:
- Non-coding DNA (more likely to be neutral)
- Synonymous mutations in coding regions (no change in the protein so no selection on the sequences)
115
True or false: every population with a fixed size has genetic drift
True
116
True or false: the molecular clock works best between closely related species (e.g. mammals) but works less well between bacteria and humans
True
117
What 3 reasons explain why the molecular clock works better for closely related species?
1. Differences in mutation rate
2. Differences in generation time
3. Saturation of all possible synonymous mutation sites (can't tell if the differences you observe are due to one or many mutation events)
118
What are the 4 assumptions of an ideal population?
1. Has a constant (non-fluctuating) size
2. Experiences no selection
3. All mating is completely random
4. Random chance of each offspring having a particular parent
119
How is the frequency of the number of offspring individuals distributed?
Using a Poisson distribution
120
In the p[fix neutral mutation] formula 1/2N, is N actual population size or effective population size?
Actual (N)
121
In the time to fixation formula 4N, is N the actual population size or the effective population size?
Effective (Ne)
122
The molecular clock 'ticks' at approximately the rate of mutation (with random noise), and is (independent/dependent) of popoulation size
Independent
123
Nucleotide diversity increases with....
Effective population size and mutation rate
124
Effective population size definition
The size of an ideal population that would act the same as the real population in question in the action of genetic drift
125
Nucleotide diversity?
The average genetic distance per base pair between two randomly chosen individuals from a population
126
If you are comparing two (almost) identical sequences that are 18 bp long, and there's 4 nucleotide differences between the two sequences, what would the nucleotide diversity be?
4/18
127
Formula for determining genetic diversity within a population?
- What assumption does this depend on?
π=4Neµ
- depends on the assumption that all mutations are neutral
128
Define a bottleneck
Temporary reductions in population size causing drift, thereby reducing genetic variation
129
(Common/rare) alleles are likely to be lost during a bottleneck
Rare
130
What two things does the loss of an allele depend on?
Loss depends on the severity of the bottleneck and the frequency of the allele
