Mid-Term 1 Flashcards
(154 cards)
1
Q
Did Lamarck become best known for disproving heritability of anatomical features depends primarily on use and disuse of those structures?
A
No
2
Q
Did Charles Darwin cite patterns from the fossil record and the efficacy of selective breeding as support for his theory of evolution by natural selection?
A
Yes
3
Q
Did George Cuvier become the first paleontologist to conclude that the fossil record provided evidence for evolution?
A
No
4
Q
Did Aristotle become the first philosopher to propose that species evolved?
A
No
5
Q
If the two species share characteristics from convergent evolution…
A
Convergent evolution indicates that unrelated species shared similar environmental conditions; so, they have similar characteristics to better adapt.
6
Q
If an individual’s unique characteristic increases its fitness, then
A
Individuals in the population with the advantageous trait have an increased fitness in comparison to the rest of the population.
7
Q
Criteria for natural selection
A
- Variation
- Inheritance of favorable traits
- High rate of survival/reproduction in better suited variants
- Correlation between phenotype and fitness
8
Q
Artificial selection
A
Fitness is not associated with lifetime reproductive success
9
Q
Vestigal
A
Features that are remnants but serve no adaptive function
10
Q
LAW OF SUCCESSION
A
Bio-geographic evidence- reflects the observation that living species in the area are often close relatives of the fossil forms found in the same area
11
Q
Environmental effects on evolutionary changes in anatomy
A
Natural selection will result in significant changes to anatomy in order to better adapt
12
Q
Allele
A
One of the variants at a genetic locus that is segregating in a population
13
Q
Evolutionary fitness
A
The extent to which a particular genotype or phenotype is passed on to the next generation
14
Q
Weakest evidence in favor of an evolutionary explanation
A
Perfected designs in nature
15
Q
Endemic group
A
The ecological state of a species being unique to a defined geographic location; one group colonizes and adapt to their individual environment
16
Q
Heterozygous advantage
A
-leads to the persistence of recessive traits
17
Q
Transitional forms
A
- do not necessarily have to be from the direct ancestor of the modern species
18
Q
TRUE Statement
A
Darwin’s gradualist ideas of evolution derived in part from theories that explained geologic features as the consequence of slow, continuous mechanisms that operated in the past as they do now.
19
Q
ASK YOUR TA ABOUT: Quiz 1, Q# 17 Quiz 2, Q# 2 Quiz 3, Q# 9 Quiz 3, Q# 11 Quiz 3, Q# 17 How to determine whether an amino acid s more likely to have a certain type of mutation? Week 4, second lecture quiz questions. Quiz 4
A
JUST ASK THE DAMN QUESTIONS
20
Q
Why does Darwin get more credit than Wallace for the theory of natural selection?
A
Darwin backed up his theory with massive amounts of evidence in On the Origin of Species, whereas Wallace’s initial treatment of the topic, though logically correct, was less thoroughly substantiated.
21
Q
The “modern synthesis” of evolutionary biology combines…
A
Darwinian natural selection with Mendelian genetics.
22
Q
How did the work of Thomas Malthus influence Darwin’s development of the theory of natural selection? Malthus …
A
argued that many problems of humanity result from population growth rates that outpace growth in resource availability, which inspired Darwin to consider the importance of overproduction of offspring in the “struggle for existence.”
23
Q
Darwin considered all EXCEPT which of the following to be a “difficulty” of his theory of natural selection?
A
the lack of evidence that offspring tend to resemble their parents in phenotypic traits
24
Q
Why does the panda’s “thumb” provide good evidence for evolution?
A
because it is a reasonably good solution to the foraging habits of pandas, but it appears to have evolved within constraints imposed by common ancestry with other bears
25
Given the facts that organisms have a huge capacity to reproduce, yet resources are limited so they seldom overpopulate, what inference can be made?
not all offspring will survive and reproduce
26
We saw that allele frequencies change due to migration according to: pI(t+1) = (1-m) pI + (m) pC. If the starting allele frequency on the island is p = 0.8 and on the continent p = 0.3, what will pI be in the next generation if the migration rate to the island is 0.4?
0.6
27
What do you conclude from this example with the butterfly Heliconius cydno alithea? With a larger population size alleles will:
not change in frequency as much due to drift as in small populations
28
Which of the following is an example of drift?
A volcano explodes on an island and only a few tortoises survive. They do not have the same diversity of alleles as before.
29
If the two plants in the white boxes are the ones that reproduce, what will p be in the next generation?
1.0 _they were both RR in the figure that was shown
30
Darwin's four postulates state the conditions under which natural selection will occur. Which of the following is NOT one of these necessary conditions?
Variation among individuals is based on environmental rather than genetic variation
31
If environmental conditions were to change such that only individuals within the black rectangle could survive to reproduce, which of the following statements would be TRUE?
We expect the mean body weight of individuals that survive to reproduce to be higher than the mean body weight of the whole population.
32
Which of these was NOT a finding of the genome study of Darwin's finches?
the age of each species corresponds to the age of the islands
33
Disruptive selection:
Favours the extreme phenotypes
34
Disruptive selection:
Favours the extreme phenotype
35
The allele has no effect on the fitness of the individual carrying the mutation.
It could eventually reach a frequency of 0.5 or be fixed or lost from the population, but that will be a random effect based on the population and its size.
36
Source of Genetic Variation
Recombination
37
Genetic variation
Multiple alleles within a gene pool
38
Mutation in somatic cells equals
The mutation may be expressed in the individual, but will not be passed along to its offspring.
39
Allele "fixed"
It is an indication of no genetic variation that locus in the population
40
In a hypothetical population of 1000 frogs there exists a gene with two alleles. 280 of the frogs are homozygous dominant (DD), and 220 are homozygous recessive (dd).
What is the frequency of heterozygotes in the population?
0.50
41
Human ABO blood groups are determined by a single gene with 3 alleles: A, B, and O. In a sample of 300 individuals, 100 are blood type A and genotype AA, 100 are blood type B and genotype BO, and 100 are blood type O and genotype OO. What are the allele frequencies?
33.3% A, 16.6% B, 50% O
42
What is the long-term fate of either allele of a gene with two alleles in which the fitness of the heterozygote is superior to that of both homozygotes?
Both alleles will remain in the population because heterozygote gametes will form with each allele in a separate gamete.
43
You are given the following information about a population:
• There are two alleles: C and c.
• C codes for green hair and c codes for white hair.
• C is dominant over c.
• The frequency of the c allele is 0.3.
• The population is comprised of 100 individuals.
Assuming the population is in Hardy-Weinberg equilibrium, how many individuals have green hair
91% of the population will have green hair.
44
Evidence of better fitness:
More offspring in a given time
45
Why is inbreeding depression a concern for such populations?
Related individuals are more likely to mate with one another and this increases the probability that two deleterious alleles will be present in the offspring.
46
Why does genetic drift have more of an impact on the evolution of small populations than large ones?
Sampling from generation to generation is more variable in small populations than large.
47
Isolation
causes greater difference between their genetic sequences
48
Functionally constrained sections of genes
Do not have much genetic variability
49
Why are synonymous mutations more frequently found as genetic variants in lab populations than nonsynonymous mutations?
synonymous mutations do not harm the organism, while many nonsynonymous mutations could be lethal before birth
50
How would you detect a synonymous mutation in a lab population?
from the sequence of the DNA
51
Why do these solutions imply that "gene flow homogenizes population allele frequencies?
when there is migration, the allele frequencies will not stop changing until they are the same on the island and the continent
52
Fixation due to drift will happen most rapidly in a:
smaller population with unequal sex ratio
53
Darwin's four postulates state the conditions under which natural selection will occur. Which of the following is NOT one of these necessary conditions?
Variation among individuals is based on environmental rather than genetic variation.
54
If environmental conditions were to change such that only individuals within the black rectangle could survive to reproduce, which of the following statements would be TRUE?
We expect the mean body weight of individuals that survive to reproduce to be higher than the mean body weight of the whole population.
55
Which of these was NOT a finding of the genome study of Darwin's finches?
the age of each species corresponds to the age of the islands
56
Disruptive selection:
Favours the extreme phenotypes
57
What do you conclude from this example with the butterfly Heliconius cydno alithea? With a larger population size alleles will:
not change in frequency as much due to drift as in small populations
58
Examine the array of absolute fitnesses below. Assume that the average number of offspring produced by adults does not vary with genotype.
Genotype: B1B1
Probability of survival from birth to adulthood: 0.80
Genotype: B1B2
Probability of survival from birth to adulthood: 0.60
Genotype: B2B2
Probability of survival from birth to adulthood: 0.60
Given this information, the relative fitness of the B2B2 genotype is: 0.75
59
Examine the array of absolute fitnesses below. Assume that the average number of offspring produced by adults does not vary with genotype.
Genotype: B1B1
Probability of survival from birth to adulthood: 0.80
Genotype: B1B2
Probability of survival from birth to adulthood: 0.60
Genotype: B2B2
Probability of survival from birth to adulthood: 0.60
Given this information, which of the following statements is TRUE? Assume that we are considering dominance, recessivity, and codominance with respect of the mapping of genotype to fitness.
The B1 allele is recessive and advantageous.
60
Examine the array of absolute fitnesses below. Assume that the average number of offspring produced by adults does not vary with genotype.
Genotype: B1B1
Probability of survival from birth to adulthood: 0.80
Genotype: B1B2
Probability of survival from birth to adulthood: 0.60
Genotype: B2B2
Probability of survival from birth to adulthood: 0.60
If the B2 allele occurs at a frequency of 0.2 among newborns, and if we can assume that newborn genotypes occur at Hardy-Weinberg expected frequencies, which of the following is the frequency of the B2B2 genotype among adults after selection?
(0.75)(0.22)/mean fitness
61
Examine the figure below. If we defined a taxon to include only the extant coelacanths and lungfish but not their most recent common ancestor, it would be a _____ group.
polyphyletic
62
In phylogenetics, what do we mean by the term "character polarity"?
the direction of evolutionary change in a character from the ancestral state to the derived state
63
To conduct a phylogenetic analysis, we need an outgroup to
determine dervied v. ancestral character states
64
When a new neutral mutation arises in a diploid population,
the probability of fixation due to genetic drift = 1/2N.
65
Which of the following is the BEST definition of inbreeding in the context of population genetics?
breeding among individuals that are genetically similar because of reduced variation due to drift in small populations
66
Why does our estimate of the current effective population size in humans (around 10,000) deviate so dramatically from the census size of about 7.5 billion people?
because the human population size was much less than its current value during most of our evolutionary history
67
Polyphyletic
three or more groups did not evolve from a common ancestor
68
Proof of Evolution
- Change over time (i.e. fossil record)
- Descent w/ modification (i.e. homology (genetic/ morphological); analogy- convergent evol. (morph); embryology; vestigial traits; Transitional form)
- Biogeography (Law of succession, Endemic Biotas, )
69
Homology
a trait possessed by two or more
species that is derived, with or without
modification from their common ancestor.
A state of similarity in structure and anatomical
position but not necessarily in function between
different organisms indicating a common ancestry
or evolutionary origin.
70
Analogy
traits that are similar in function but
| differ in basic structure (although often “look” alike).
71
Vestigial traits
Rudimentary traits that are homologous to fully
| functional traits in closely related species.
72
Transitional form
A species that exhibits traits common to ancestral and
derived groups, especially when the groups are
sharply differentiated
73
Law of Succession
living species in an area are
frequently closely related to fossils in that area
providing evidence that the species evolved there
74
Endemic Biotas
organisms found in limited regions
| along with close relatives
75
Natural Selection?
One of four mechanisms that cause evolution.
Differential survival and reproduction causes
change in trait over time.
76
Adaptation?
Properties of organisms that enable them to
| survive and reproduce in their environment.
77
‘transformism
Lineage persist and change from one form to the other (individuals evolve)
78
Fact #1
All species have such great potential fertility that their
population size would increase exponentially if all individuals
that are born reproduced successfully
79
Fact #2
Populations tend to remain stable in size, except for
| seasonal fluctuations
80
Fact #3
Environmental resources are limited
81
Inference #1
Struggle for existence caused environmental limitation on survival
82
Facts #4 and #5
```
Individuals of a
population vary
extensively in their
characteristics.
• Much of this variation is
heritable (passed on
from parents to
offspring).
```
83
Inference #2
Survival in the struggle for existence is not
random, but is correlated with the traits of
individuals.
84
Inference #3
differential reproductive success will lead to gradual change in a
population, with favorable characteristics
accumulating over generations
85
Darwin’s “One long argument”
All species, living and extinct, have descended from a
single common ancestor
• Species are mutable (changeable)
• Variation exists in nature
• There is a struggle for existence
• Some variants survive and reproduce better than
others
• Natural and Sexual selection determine which
variants survive and reproduce
• Over the immeasurable span of geologic time, species
change, new species arise, and some species go
extinct.
86
Darwin’s “Difficulties on Theory”
Absence of transitional forms
• Organs of extreme perfection
• Evolution of Instinct (behavior)
• Hybrid sterility and interfertility of “varieties”
• Blending Inheritance (Mendel’s work was
published in 1865 but Darwin was unaware of
Mendel’s work, as was the rest of the world, until
1900)
• Nature of variation
87
The modern synthesis
Mendel & Darwin: Natural selection works with variation
observed in populations AND according to Mendelian
inheritance
88
imperfect solutions in evolution
Evolutionary processes work with existing constraints and
variation to produce new arrangements that can be juryrigged
to solve new problems.
89
Mutation effects
Neutral – most mutations have no phenotypic
effect and do not influence fitness (95%??).
• Deleterious – of those that have an effect,
most are deleterious (4.99%??)
• Beneficial – exceedingly rare but exceptionally
important for adaptation.
90
Mutation Rate
estimated from rate that
detectable new genetic variants arise in lab pops
```
Rules::
Transitions > transversions
• Repetitive sequence > unique
• Nonfunctional sequences > functional
– Introns > Exons
• Within Exons:
– Synonymous > Non-synonymous
– 3rd codon position > 1st & 2nd
S
```
91
Mechanisms of Evolution
Natural selection, migration (gene flow), genetic drift,
92
Migration
Movement of alleles between populations
• Interpretation: Gene flow
• Mechanisms: Dispersal of animals
– Transport by wind, water, animals
93
Gene flow
the movement of alleles from one population to another
| population by movement of individuals or gametes (homogenizes population allele frequencies)
94
Hardy Weinberg
Null Model: the formal
expression of a process not affected by
determined forces.
```
Provides expected: 1. Allele frequencies
2. Genotype frequencies
Assuming: 1. diploid, sexual organisms
2. random mating
AND
3. No mutation
4. No gene flow
5. No genetic drift
6. No selection
```
Populations go to HWE after 1 generation of
random mating.
• HWE is very simple but is used frequently in
empirical population genetics
95
Genotype Frequencies
```
p-squared= Dominant homo
q-squared= Recessive homo
```
96
Types of Point Mutation
Silent (Synonymous)
Missense (Non-synonymous)
Nonsense (convert AA to stop)
Readthrough (convert stop to AA)
97
Transitions or Transversions
Transitions more common than transversions,
| and less likely to be missense mutations.
98
Frameshift mutations
Mutation that causes addition or deletion of nucleotide(s), causing a shift in the reading
frame of the codons in the mRNA
99
Chromosome level: Types of Mutation
Deletion, duplication, inversion, translocation
100
Survival Rate
the after selection population/ the before selection
101
Relative Fitness
the individual genotypes divided by highest fitness
102
Selection coefficient
1-relative fitness
103
Mean fitness
the summantion of each allele frquency times its relative fitness
104
Frequency-dependent selection
Fitness depends of freq. of alleles not on fixed
attributes
• Rare type has advantage (first selection favors one
allele, then it favors the other)
• Direction of selection fluctuates
105
Systematics
the study of the diversification of living forms,
both past and present, and the relationships among living
things through time.
The ordering of the diversity of nature through construction
of a classification system.
Contains both taxonomy and
phylogenetics.
106
Taxonomy
the discovery, recognition, definition, and
| naming of groups of organisms
107
Phylogenetics
is the study of evolutionary relationships
among groups of organisms (e.g. species, populations),
resulting in a hypothesis about the evolutionary history of
taxonomic groups. This hypothesis is represented by an
evolutionary tree (phylogeny, phylogram, cladogram).
Also referred to as phylogenetic systematics, cladistics
108
Cladogenesis
s is evolution that results in the
| splitting of a lineage
109
Anagenesis
is evolution within a lineage.
110
Character fixation in a lineage
A mutant allele can go to fixation either by natural
| selection or by genetic drift. Otherwise it is lost.
111
phylogeny
a hypothesis of evolutionary relationships among taxa
112
sister groups
two lineages branching from a node
| each other’s closest relatives in the tree
113
monophyletic group = clade
an ancestor and all of its descendant lineages
| grouped by shared, derived characters
114
paraphyletic group
an ancestor and only some of its descendant lineages
| grouped by shared, ancestral characters = symplesiomorphies
115
polyphyletic group
does not include te common ancestor
116
Characters and character-states
A
character is a general category for which species manifest
different states
117
Homologous characters
A homology is a character shared between two or
more species that was present in their common
ancestor
118
homoplasy
```
a character shared between two
or more species that was not present in their
common ancestor (wings in birds & bats)
```
119
Plesiomorphy
Primitive or ancestral character state
120
Shared ancestral states
Symplesiomorphy = Ancestral homology
| homologous trait retained from the ancestor of the group
121
Derived character state
Apomorphy
122
Unique derived character state:
Autapomorphy
| A derived trait unique to one species in the group of study
123
Shared, derived character state
Synapomorphy
124
Factors affecting (reducing) Ne
```
– Disease & old age
– Small breeding groups
– Population fluctuation
– Variable fertility
– Sex ratio
– Social structure
• Dominance
• Territoriality
• Harems
– Overlapping generations
```
125
Inbreeding
mating among kin;
In small populations:
• drift reduces heterozygosity
• individuals become genetically more similar
• inbreeding increases (even if mating is random)
126
Points to Remember (Microevolution)
Allele frequencies fluctuate randomly:chance = the only
factor
2. Allele diversity declines, therefore heterozygosity declines
a) Rate of decline = a measure of rate of genetic drift
b) Therefore, rate of decline = a measure of population size
3. Isolated groups (demes) diverge from one another;
eventually each becomes fixed for one allele or another at
the locus of interest
4. Evolution by genetic drift is faster in small populations—
time to fixation or loss is faster
Probability of eventual fixation of an allele = frequency of the
allele at present (p)
6. Probability of eventual loss = 1 – p.
7. If a large number (infinitely large number) of isolated groups
(demes) initially have identical frequencies, they will diverge in
frequencies, but the global frequency does not change.
8. Final point: All of the above happens independently in all
polymorphic loci in the genome—assuming no other
evolutionary forces
127
The Neutralist-Selectionist debate (agreements)
Agree:
– Most "functional” mutations are deleterious and are
removed.
– Some mutations are favourable and are fixed.
128
Neutral theory
Advantageous (adaptive) mutations are very rare
– Most of the amino acid changes and polymorphisms are
neutral, and created by genetic drift.
– The concept of Molecular clock
129
Selectionist theory
Advantageous mutations are more common
– Molecular evolution will are dominated by selection
– No Molecular clock
130
Evidence in support of the Neutral theory
Pseudogenes (dead genes that have no function and no fitness
effect) evolve very fast.
• Synonymous codon positions (3-fold, 4-fold degenerate sites)
evolve faster than non-synonymous sites, and should evolve
with a constant rate. (not always true)
• Genes that have important functions should evolve slower
131
Methods to detect positive selection
Ka / Ks test: suitable for between species
• McDonald-Kreitman (MK) test
– Compare between species and within species
• Fixation index (Fst)
– Testing difference in allele frequency between population
• Linkage disequilibrium (LD)
– Look for nonrandom association of alleles at linked loc
132
Negative selection
(purifying selection)
– Selective removal of deleterious mutations (alleles)
– Result in conservation of functionally important amino acids
– Examples: ribosomal proteins, RNA polymerase, histones
Ka / Ks
= Non-synonymous / Synonymous substitutions
= 0
133
Positive selection
(adaptive selection, Darwinian selection)
– Increase the frequency of beneficial mutations (alleles) that
increase fitness (success in reproduction)
– Examples: male seminal proteins
involved in sperm
competition, membrane receptors on the surface of innate
immune system
Ka / Ks
= Non-synonymous/Synonymous substitutions
= 5
134
Nearly Neutral Theory
Theory suggests most mutation events at the molecular
level are slightly deleterious rather than strictly neutral.
The nearly neutral theory predicts a relationship
between population size and the rate of molecular
evolution:
In small populations, drift dominates and slightly
deleterious mutations behave as neutral – slightly
deleterious mutations can fix relatively quickly.
In large populations, little drift, more pronounced
selection, so slightly deleterious mutations less likely to
fix and do so slowly.
135
McDonald-Kreitman (MK) Test
McDonald-Kreitman (MK) Test compares divergence
between two species with polymorphism within each
species.
• If a gene evolves neutrally, i.e. the DNA substitutions
follow random drift, then the polymorphism within each
species should follow the same pattern as divergence
between species.
• This predicts similar ratio of synonymous and nonsynonymous
substitutions between and within species
136
Factors that influence reproductive
| output
```
Individual’s current condition (health)
• Ability to avoid predation
• Access to mates
• Amount of investment into offspring
• Ability to identify a mate who will produce as
many high quality offspring as possible
```
137
Good Mate
```
High condition
• Good at avoiding predation
• Likelihood to produce attractive offspring
(offspring that will mate)
• High investment in offspring
```
138
Altruism
```
Individuals
sacrifice their own
evolutionary fitness for
others
• Cannot evolve by
individual selection
– Cheaters would be
favored
– Eventually the trait would
disappear
```
139
Direct fitness
personal reproduction
140
Indirect fitness
reproduction by relatives, made possible
| by an individual’s actions
141
Inclusive fitness
the sum of an individual’s reproduction
through relatives made possible by its action (indirect
fitness) and its own reproduction (direct fitness)
142
Kin Selection
mechanism of increasing inclusive fitness
| through apparent altruism
143
Altruism is more likely to spread when:
Benefits to recipient are great
• Cost to altruist is low
• Participants are closely related
144
Coefficient of relatedness
How to calculate:
1) Draw all paths
2) Multiply probabilities within path
3) Add probabilities across paths
145
Speciation
```
Occurs through “normal” evolutionary processes
-mutation
• gene flow
• genetic drift
• natural selection
• sexual selection
```
146
Ways to identify a species
*Species are groups of individuals that evolve
independently from other such groups, i.e., they
are independent evolutionary lineages.
*Individuals of the same species are able to
contribute to the same gene pool.
*Species (may) consist of several interbreeding
populations.
*The taxonomic distinction “species” is the smallest
independent evolutionary unit. It defines the
boundary for the spread of an allele
147
Biological Species Concept
Groups of actually or potentially interbreeding
organisms that are reproductively isolated (absence of gene flow
between groups of individuals due to intrinsic
features of organisms) from
other such groups
148
Pros of BSC
```
Advantages of BSC
• Focuses on gene flow
• Grouping principle clear
–Capable of interbreeding: same species
–Incapable of interbreeding: different species
```
149
Problems of BSC
```
Hybridization between “good” species
• Ring Species
• Asexual organisms don’t interbreed
• Populations are often geographically separate
• Fossils
```
150
Barries to Gene flow
Extrinsic: geographical features like
mountains, rivers, oceans, forest
(geographic isolation)
2. Intrinsic: genetically based properties of
organisms that limit gene flow
(reproductive isolation)
\\Prezygotic barriers: Features that prevent
individuals from different groups from creating a
zygote.
Postzygotic barriers: Features that prevent zygote
from developing into a healthy and/or fertile
adult.
151
Intrinsic barriers to gene flow:
```
Prezygotic barriers
1. Ecological differences
2. Temporal differences
3. Sexual (behavioral) differences
4. Gametic incompatibility
Postzygotic barriers
1. Zygote mortality
2. Hybrid inviability
3. Hybrid sterility
4. Other hybrid problems...
```
152
Peripatric Speciation
```
An isolated group is severed
from the original population
• Rare genes move to
fixation, with potential role
for genetic drift
• If these genes are associated
with reproduction, speciation may
result
```
153
Parapatric
```
In parapatric speciation
there is no specific extrinsic
barrier to gene flow.
• The population is
continuous but does not
mate randomly.
• Mating with geographic
neighbors more often.
• In this mode, divergence
may happen because of
reduced gene flow within
the population and varying
selection pressures across
the population’s range
```
154
Sympatric
```
Does not require geographic
isolation to reduce gene flow
between parts of a
population.
• Exploiting a new niche may
automatically reduce gene
flow with individuals
exploiting the other niche.
• This may occasionally
happen when, for example,
herbivorous insects shift to
new host plant species.
```
