Evo Bio Midterm 1 Flashcards
(102 cards)
1
Q
What does mutation do?
A
Creates new alleles
2
Q
What does natural selection, gene flow, and genetic drift do?
A
Determines the fate of new alleles
3
Q
Freq. of a new mutation
A
1/2N (2 for diploid -> 2 sets of genes, one from each parent)
4
Q
What is the relationship between natural selection and adaptation?
A
Natural selection is the only evolutionary force that consistently leads to adaptation
5
Q
What does natural selection require?
A
Needs variation amongst individuals that is inherited
Differences in fitness among individuals with different phenotypes
6
Q
What is evolution?
A
Change in the inherited traits (allele frequencies) of a population over time
7
Q
Conditions for no change in allele frequency from one generation to the other
A
No fitness effect, no mutation, large population, proper mixing
8
Q
What happens before gene flow?
A
Migration -> then the alleles spread
9
Q
Genetic drift among populations
A
Increases genetic differences among populations (fixes and removes different alleles)
10
Q
Genetic drift within population
A
Decreases genetic variation within population (reduces heterozygosity)
11
Q
Gene flow on a global scale
A
Gene flow is a homogenizing force
12
Q
Gene flow on a local scale
A
Gene flow is not a homogenizing force
13
Q
What do mutation and migration (GF) do together?
A
Introduce new alleles into a population
14
Q
What does selection do?
A
Deleterious alleles appear and are eliminated by selection
15
Q
What does Lamarck’s theory say about the Breeder’s Equation?
A
If S is very strong, there will be a response to selection (even if h^2 is 0)
16
Q
What does Darwin’s theory say about the Breeder’s Equation?
A
S can be really weak, but as long as that trait is heritable (H^2), it will appear in the next generation
17
Q
What is true of the Breeder’s Equation if h^2 is 0?
A
No matter how big S is, if h^2 is 0, R is 0
18
Q
True or False: If a variation in a trait is influenced by genes, it will run in families
A
True!
19
Q
True or False: If a variation in a trait runs in families, it is influenced by genes
A
False! Gene-environment correlations lead to overestimates of heritability
20
Q
What is heritability?
A
The proportion of phenotypic variation that is due to genetic differences among individuals
21
Q
How can you ensure high heritability?
A
Increase Vg and decrease Vp, or increase both
22
Q
Broad-sense heritability
A
H^2 = Vg/Vp
Definition:
23
Q
Narrow-sense heritability
A
H^2 = Va/Vp
Definition
Va -> the effects of multiple genes add up to determine a trait
24
Q
What do Quantitative trait loci (QTL) and Genome-wide association study (GWAS) have in common?
A
Both find genes that contribute to quantitative traits
Looking for a statistical association between a marker locus and phenotype
25
Differences between QTL and GWAS?
QTL:
- Using genomic markers (genomic code that we are really sure present there), not using mutations
- Breeding populations so you can see where the markers are (crossbreeds)
Genome-wide association study (GWAS)
- Using the genomic code itself (SNPs) to find the differences there --> therefore a much higher marker density
- Differences in the mutations between 2 individuals
- Narrows in on a smaller region of the genome than QTL analysis
26
Why was there an extreme population decline in African elephants?
Going from 2000 to 100 elephants because of the Civil War in Mozambique -> After war, tuskless females were much more common
27
What were Darwin's 2 major insights?
1) All species descended from a single common ancestor
2) Natural selection is a major agent of evolutionary change -> variation of changes for reproductive success
28
Shared ancestry -> descent with modification
More closely related species tend to be closer to each other than distantly related species
29
What is homology?
Similarity between species that results from inheritance of traits from a common ancestor
Ex: Universal molecular homology; codon-based genetic code (shared amongst all organisms)
30
What is artificial selection?
The identification by humans of desirable traits in plants and animals, and the steps taken to enhance and perpetuate those traits in future generations (Basically natural selection except selection isn't imposed by nature)
31
Does evolution operate for the "good of the species"?
NO, it operates at the level of the individual
32
Video of bacteria and antibiotic: Which forces of evolution work best?
Appearance of mutations but also selection selecting which mutations work best
33
Which evolutionary force is the ultimate source of genetic variation?
Mutation -> variation among individuals is the substrate for NATURAL SELECTION
34
Which mutations are visible/invisible to natural selection?
Synonymous mutations invisible to natural selection -> non-synonymous mutations captured by natural selection
35
Plants and whole-genome duplications
Whole-genome duplications are especially common in plants (thanks to common ancestor) -> a little more rare in animals
36
Germline mutations
Contribute to evolution (passed between generations) -> present in reproductive cells (eggs and sperm)
36
What is fitness?
An individual's genetic contribution to the next generation -> often measured as survival or reproductive success
37
C. Elegan experiment
All mutations occurring are sticking around in the population -> these mutations are harmful in the absence of natural selection; therefore, the mutations that are present in the C. elegans are deleterious
*eliminated natural selection as a factor in this experiment
38
First experiment: Selection of coat color in mice
- Individuals differ in survival and reproductive success based on their given phenotype
- Dark colored mice on dark soil and light colored mice on light backgrounds
- Used clay models of mice, collected them afterward, and found which ones had been attacked
- Crypsis -> The degree to which a mouse matches its background
- Used molecular genetics to figure out which gene determines fur color -> melaonocortin 1 receptor (MC1R mutated = light colored fur ; MCIR not mutated -> dark colored fur)
39
What is adaptation?
(Noun) A trait that increases the fitness of an individual relative to that of individuals lacking the trait
(Verb) The process by which the trait with the highest fitness increases in frequency in the population
40
Function of adaptation
Matches an organism with its environment
41
What does selection act on the level of?
Individuals, not the alleles
42
What is the selection coefficient (S) ?
The difference in fitness between the most fit and least fit genotype
43
Selection coefficient: When A is dominant..
Heterozygous individuals will have the same fitness as AA and the same fur color
44
Selection coefficient: When A is recessive..
Heterozygous individuals will have the same fitness as aa and the same fur color
45
Rare beneficial alleles: Dominance and recessiveness
A rare beneficial allele will increase more quickly when its dominant than when it's recessive
- When allele is dominant, it is visible to selection in the heterozygotes
- When allele is recessive, it is hiding in the heterozygotes
46
Population mean fitness
Average of all the fitnesses in a population
- Evolution by natural selection increases the population mean fitness
47
What is gene flow?
The movement of alleles between populations that then leads to evolutionary change
- When migrants move between populations, they make the allele frequencies in those populations more similar to each other (homogenizing evolutionary force)
48
What is migration?
The movement of individuals between populations, but not always alleles
- Maybe migrants have not contributed alleles to the next generation
49
What is a metapopulation?
A population of populations; discrete populations linked by migration
50
"Isolation by distance"
The further away you are, the more isolated two populations are
- The idea of geographic distance between populations: Humans that lived closer together were more genetically similar (and tend to exchange more migrants) than humans that lived further apart
51
What is genetic drift?
Random change (or sampling) in allele frequencies from one generation to the next
- Results from chance events — any random process that affects who survives or reproduces, or which alleles get transmitted to the next generation (ex: Mendelian assortment)
52
Effective population size (Ne)
The number of individuals that contribute to the next generation's gene pool
-Almost always smaller than the census size (N) -> due to unequal sex ratios, variance in reproductive success, etc.
53
In what kind of population is genetic drift the most important?
Small populations
- Ex: In a population of 4, the allele A was lost at 20 generations, while in a population size of 400, the allele A was not lost
54
Correlation between population size and drift + selection
Population size determines the relative strength of drift and selection
55
Negative values (selection + drift)
Can only get negative values if selection disfavors an allele
56
What can blending inheritance could/could not explain?
COULD explain why the offspring of tall and short parents are intermediate, but COULDN'T explain why some flowers are shorter or taller than their parents
57
What does polygenic inheritance account for?
Accounts for why the F1s are all very similar and why the parental phenotypes are recoverable
Polygenic inheritance: when multiple genes work together to influence a trait
58
What are quantitative/continuous traits?
Characteristics that are influenced by multiple genes as well as environmental factors
Experiment: 3 plants are siblings and have the same genotype, but were grown in different environments
59
Breeder's Equation
R = h^2S
This equation measures EVOLUTION
R = response to selection (change in the trait mean)
h^2 = heritability
S = selection
60
Heritability Equation
Heritability = Genetic variation/phenotypic variation
Vg/Vg +VE
61
Heritability being close to 0 or 1
Heritability close to 0 is due to the environment, heritability close to 1 is due to the genes
62
"Correlation between relatives"
Relatives should be more similar to each other than non relatives because they share the same genes
63
Parent-offspring resemblance
Measured through parent-offspring regression
Average trait value of the parents on the x-axis
Average trait value of the offspring on the y-axis
Data point represents a family of __ -> cannot measure heritability from a single data point
Slope of the line = heritability (narrow-sense heritability)
Ex: If parent-offspring regression is 0.79, thet means that 79% of distribution of ___ is attributed to genetics
64
How do you measure heritability?
Quantitative genetics uses resemblance among relatives to infer heritability
Using either parent-offspring resemblance or siblings resemblance (<-- measured in a single generation for SR)
65
Narrow-sense vs broad-sense heritability
Broad-sense: H^2 = Vg/Vp (Vg+Ve)
Narrow-sense: H^2 = Va/Vp
--> We use narrow-sense heritability because heritability is due to the additive effects of alleles
Variation among individuals is due to additive effects among individuals
66
Siblings Resemblance: Monozygotic Twins and Heritability
If monozygotic twins tend to resemble each other, we infer high heritability
67
Siblings Resemblance: Full Siblings and Half Siblings and Heritability
If full siblings and half siblings are equally similar and dissimilar, than heritability is not affected by genes
However, if full siblings and half siblings differ, than it is affected by genes and we can infer that the full siblings share more alleles to each other
68
If you take organisms and grow them in a similar environment and differences arise...
Then it is most probable that it is affected by genes
69
Why should we use caution when interpreting estimates of heritability from wild populations?
Heritability is going to be an overestimate because it measured similarity based on the environment AND genes, not just genes
70
Key Point about Gene-Environment Correlation
Within the same environment, differences between families is due to genetic differences
Within different environments, differences between families is due to environmental differences
71
What is selection differential (S) ?
Difference in the average trait of a population and the average trait of the surviving individuals
Alternative definition: Difference between the mean of the selected group and the mean of the population
How to calculate: Mean of population - mean of selected group
72
QTL (Quantitative trait loci)
Markers (genes we know the location of) close to the QTL will be genetically similar
Genomic position / linkage group (x-axis)
LOD (on y-axis): Measures the strength of the relationship between genotype and phenotype
--> A peak tells you that the gene is somewhere there
@ each locus, asking whether individuals with diff phenotypes have diff genotypes
finding a candidate gene and seeing if there's a phenotypic difference
-> if there is, then its due to that gene
Highlight anything that crosses threshold of significance
73
Why is recombination with QTL important?
More recombination will shorten the length of the chromosome, which requires many crosses -> will be easier to find the gene of interest
-> dependent on crosses (with individuals who differ of the trait of interest) so we know that a variation occurred
-> recombination does not break up linked genes, therefore the QTL and marker loci are linked together
74
Genome-wide association study (GWAS)
Genome position (x-axis), -log10P [(y-axis) measures the significance between genotype and phenotype]
Finding every region of genome with SNP (single nucleotide polymorphism)
--> Sequencing whole genome instead of spots
Each point is a SNP
Use of Manhattan Plot
75
Selection in Breeder's Equation
Some variants survive and reproduce at higher rates than others
76
Selection differential (Breeder's Equation)
X-Axis (Trait), Y-axis (Number of individuals)
The larger the difference between means (selection differential), the stronger selection acts on a population
Only works for binary fitness outcomes (survived/ did not survive)
77
Selection gradient (Breeder's Equation)
Trait on x-axis, relative fitness on y-axis
Measures relationship between trait and fitness
SLOPE = SELECTION GRADIENT
Works for any measure of fitness (survival, number of offspring etc.)
78
Selection Gradient -> Absolute Fitness vs. Relative Fitness
Absolute fitness (W) -> Measured fitness values (# offspring, survival, etc.)
Relative fitness (w) -> captures whether fitness is higher or lower on avg. in population
Absolute fitness divided by population mean fitness (W/Wbar)
79
If selection were weaker, what would a graph look like?
The slope would be flatter -> no relationship between trait and fitness
ex: individuals with longer tails wouldn't make more offspring than individuals with shorter tails
80
If a selection gradient is negative, would there be strong or weak selection?
Strong selection -> there is still a relationship between trait and fitness
ex: Favors mice with shorter tails
81
Because both selection gradient and heritability are both measured as the slope of the line, what should we pay attention to?
AXES.
Heritability -> Midparent trait on x-axis, midoffpsring trait on y-axis
Selection gradient -> Trait on x-axis, number of offspring on y-axis
82
What is the agent of selection?
Imposes natural selection on a trait that belongs to the target of selection
82
Directional Selection
Favors larger (or smaller) trait values
--> moves the trait mean
83
Stabilizing selection
Favors intermediate trait values
--> Individuals who are close to the population mean have the highest fitness
--> lost individuals with very small/large trait values
84
Disruptive selectioon
Favors extreme trait values
-> Proportionately there are more extreme values relative to intermediate decreasing
85
Breeder's Equation -> Response to selection (R) (change in the trait mean)
Change in the trait mean across generations
86
Genetic correlation
Shared heritable variation between traits
Caused by pleiotropy (one gene affecting multiple traits) or linkage disequilibrium (genes being inherited together)
if two traits share the same genetic basis, selection on one trait will also cause evolution in the other
87
The Siberian fox domestication experiment
Tameness was the target of selection
When tameness increased, floppy ears also increased
When tameness decreased, foxes do not have floppy ears
88
How do we test if a trait is an adaptation?
TEST FOR SELECTION
- Measure selection on the trait
- Establish that the trait is the target of selection (not a correlated trait)
- Identify the agent of selection
- Demonstrate functional link between the trait and fitness
DETERMINE THAT THE TRAIT IS HERITABLE
- Demonstrate that variation in the trait is genetic, not environmental
- Optional: find the gene(s) through QTL or GWAS
89
Similarities of Blending inheritance/ particulate (Mendelian) inheritance
Both are mechanisms of heredity
90
Differences between Blending inheritance/ particulate (Mendelian) inheritance
Blending inheritance is incorrect and was the major reason natural selection was not accepted as a primary mechanism of evolutionary change
91
Blending Inheritance / Particulate (Mendelian) inheritance
Particulate inheritance: Variation does not get blended away
BI was the most widely accepted model prior to the "rediscovery" of Mendel's work and laws ~1900. Through the BI model, Darwinian natural selection was thought to be unlikely to drive evolutionary change. Therefore, natural selection had to rely on either a high rate of inherited novelty or some alternative model of inheritance (e.g. Darwin's increased reliance on use/disuse, pan genesis, etc.). With Mendelian inheritance, there is no incompatibility between natural selection and evolutionary change.
92
Gould and Lewontin: Spandrel Example
Spandrel: Triangular spaces formed between arches in architecture
Authors argued that spandrels, while appearing to be intentionally designed, are actually byproducts of architectural necessity rather than planned features
Argued against the adaptationist programme -> not all traits in organisms are necessarily adaptations shaped by natural selection, but may instead be byproducts of other evolutionary processes or constraints
Challenges the adaptationist view by suggesting that not all beneficial traits are necessarily the result of direction selection for their current function
93
Why is convergent / parallel evolution in a trait evidence for adaptive evolution, as opposed to evolution driven by gene flow, mutation, or drift?
Natural selection is the relationship between the trait and fitness --> It favors individuals (or genotypes/ alleles) with trait values that are a better functional match to their environment.
By contrast, genetic drift and gene flow are random with respect to phenotype, so they don't predictably increase (population mean) fitness. Mutations can either increase or decrease fitness.
93
Evolutionary Constraint / Correlated responses to selection
A factor that limits the direction or range of evolution
-explains why some things have not evolved/ have evolved in certain ways
93
Reading a QTL Graph where the genes are not linked/not near QTL
Shouldn't see difference with the markers (all will look the same) because it is not near the QTL
94
Migration: Mainland and island
Migration matters more if the allele frequencies are different between the mainland and island
95
Frequency: Fixation and Loss (Genetic Drift)
Fixation has a frequency of 1, loss has a frequency of 0
Allele either permanently fixed/lost in population (occurs over many periods of time)
96
Adaptationist Programme
Dominant approach in evolutionary biology that state that natural selection is the primary force shaping organic form, function, and behavior
Views organisms as collections of adaptations (instead of integrated beings), each optimally designed by natural selection for its specific function
Suboptimality in traits is explained as a compromise between selective demands
96
Critique of Adaptationist Programme (Gould and Lewontin)
Argue that adaptationist programme often ignore important factors like developmental constraints, phyletic heritage, and random genetic drift
97
How did Darwin use domesticated animals to illustrate (1) Descent with modification from a common ancestor, and (2) Natural (or artificial) selection as a driver of evolutionary change
- pigeon-breeding in HIGH demand around the time -> used the well documented pedigrees established to trace how breeders mated pigeons to get certain traits
2 Key Findings from Breeding Experiments
- All the different breeds could reproduce together AND produce viable (offspring that can survive and reproduce) offspring that indicated that they were the same species
- Certain crosses would yield traits that were present in the common ancestor (rock dove)
Artificial selection: Humans were able to drive the evolution of many pigeon breeds by acting on desirable traits that were advantageous to breeders
Natural selection: Nature selects for traits that are best suited to an organism's environment over a longer period of time than humans could
