BIO 345 FINAL EXAM
Exam 1:
1.1 Origin and Aims of Evolutionary Theory
How does geography affect the distribution of species? Convergent evolution, some places the species
have evolved to fit the environment.
Necessary and sufficient conditions for natural selection Variance in the population • Causes differences
in fitness • Is heritable across generations
Descent with modification all species, living and extinct, have descended, without interruption, from one
or a few original forms of life
1.2 Life on Earth
Uniformitarianism- same natural laws and processes that operate in the universe now, have always
operated in the universe in the past and apply everywhere in the universe
Tree of life
Common ancestry of living things
Interpreting phylogenetic trees
Determine common ancestry
Infer traits in tips based on mutation events
Identify equivalent tree
1.3 Adaptation
Fitness: A simple way to define fitness is to call it the number of offspring an individual leaves into the
next generation (viable offspring)
Both reproduction and survival components - which component is more important? The individual must
reach reproductive age, but reproduction is more important to an organism's fitness. Survival is
necessary to reach a sexually viable age, so survival assists reproduction, but reproduction overall is still
the end goal
How fitness depends on environmental context Environment is a crucial factor in determining fitness,
because it shapes what alleles would hypothetically be adaptive/maladaptive at a given time. A trait
that is adaptive in the desert is maladaptive in the tundra.
Determine if an example is an adaptation- Evolution is not always indicative of an adaptation.
Hemoglobin, for example, is red because of the protein structure, not any adaptive value. Also, many
persistent traits that are apparently naturally selected may just be attributed to random genetic drift
and hitchhiking genes/pleiotropy. So for these reasons, we cannot ASSUME a feature to be an
adaptation unless sufficient evidence suggests so. The following measures can be utilized to determine
if a trait is an adaptation:
, - Complexity: Even if we cannot immediately guess the function of a structure, we know that
complexity cannot evolve via the other aforementioned mechanisms, and that natural selection
must have been utilized. Example: Retina eye
- Functional morphology/physiology can be used to determine the usage of a certain
characteristic, and determine if it is adaptive
- Experiment
- Utilize a comparative method (hypothetico-deductive method)
Analyze evidence for adaptive hypotheses Four bullet points mentioned above (I think)
Artificial selection and hitchhiking- peep recitation 1 activity
Tradeoffs and constraints we must recognize that there is a FIXED amount of available energy/nutrition
that can be utilized in functions. In other words, not all of the best conceivable alleles can be fixed due
to this constraint (often called a phylogenetic constraint). An example of this is humans having a high
number of cervical vertebrae, which is maladaptive and often causes cancer.
Plasticity- Plasticity can be defined as the trait of being flexible. This trait can be expressed in different
ways, and is capable of change. An example of a lack of plasticity is an anteater, if all bugs in its
environment died off, it wouldn’t have the dietary plasticity necessary to adapt and eat other things.
Genetic linkage of traits Many genes can be pleiotropic, where an allele controls multiple traits. So,
selection acting upon one of those traits may indirectly select for the other, resulting in selection of an
allele that isn’t necessarily advantageous. These are called correlated traits. Breeder’s equation can be
utilized here (G→ genetic covariance)
Where the creativity of evolution comes from this is derived from the improbability of an advantageous
allele going into fixation. Population genetics shows us that the likelihood of a single advantageous
mutated allele going into fixation is low. If this mutation is common, it will obviously fix over time, but it
can (and often has) prevent the rarer mutations from fixing over time. This same concept also must be
considered for deleterious alleles
2.1 Mutation
Synonymous and Non-synonymous mutations - Nonsynonymous alters the amino acid sequence of a
protein and hence can change the biological structure of an organism, Synonymous do not alter AA
sequence
In what ways are mutations random and in what ways are they non-random? Random most of the time.
Mutations can be considered to be “non-random” when they are initiated by an environmental external
factor that was NOT random. To clarify, an example of this would be a carcinogen (like tobacco) inducing
a mutation in the tumor-suppressor gene (as there is a proven linkage between these two) causing
mutation. Or, when skin is exposed to UV, that portion of the skin is more susceptible to mutation. So,
although mutations are random, the environmental factors that induce these mutations are not
The evolutionary importance of (genetic) variation in the population heritable genetic variability within a
population encompasses two of the three necessities defined by Darwin for natural selection. 1)
heritability 2) genetic variance within a population 3) differential survival and reproduction (which is
dictated by environmental factors). EVOLUTION CANNOT OCCUR WITHOUT GENETIC
VARIATION IN A GIVEN POPULATION
Mutation-selection balance I think this is the last part of the answer below, about how natural selection
balances the mutation rate over time. It selects against deleterious mutations (by lowering the mutation
, rate) since deleterious mutations are most common (due to structure/function of enzymes and
proteins), but the potential for adaptive/beneficial mutation prevents natural selection from moving the
mutation rate to zero.
The typical frequency of beneficial, neutral and deleterious mutations- Deleterious mutations tend to be
by far the most common of any mutation (in an individual). For example, structure and function is
fundamental to molecular biology, and a deleterious mutation could be a simple mutation that changes
that protein structure, disabling its behavior. This, in turn, LOWERS the rate of mutation over time (in
eukaryotes, at least), because deleterious mutations must be selected against. Neutral mutations are
common as well, and occasionally, a mutation will be beneficial. Adaptive mutations prevent natural
selection from selecting mutation rates to arrive at 0.
-I think the question is referring to the frequency of the mutations in a population, so deleterious would
be rare because those organisms often die and they are selected against, and neutral is most common
because they are not affecting us and they happen all the time, and beneficial is intermediate. Neutral
and beneficial are prevalent. (this is what she said in the review session)
Explain how mutation rates themselves will evolve (depending on where a population is on its adaptive
landscape)
The types (mechanisms) of mutation Mutation is the ultimate source of variation. This can include a
point mutation (nonsense, missense, silent) or a frameshift (deletion, insertion). Structural mutations
can occur as well, which are errors that occur when chromosomes are replicated. This includes,
deletion, duplication, invasion, fission( splitting chromosome into 2) , fusion(fusion of 2 chromosomes
into one). ALSO: nucleoside analogs (induces mutation by replacing base pairs, and have different
pairing rules causing mutations), intercalating agents (which induce frameshift mutations by making
base pairs more far apart, and DNA Polymerase becomes more prone to skipping), and radiation1.
Nonsense- results in a stop codon. Missense-single nucleotide change results in a codon that codes for a
different amino acid.
2.2 Migration
2.3 Genetic Drift
What is genetic drift? Change in allele frequencies over time due to random sampling of organisms Null
models in science the simplest, default model to explain what is going on (this is the definition from
lecture)
Why Hardy-Weinberg is the null model for population genetics If HWE is not met, this means that the
allele frequencies are changing, thus evolution is taking place.
The allele and genotype frequencies do not change.
Assumptions of Hardy-Weinberg equilibrium No mutation, no genetic drift, no natural selection, random
mating, closed population.
The frequencies of diploid genotypes given the allele frequencies of the two alleles under HW
equilibrium-25%, 50%, 25%
Number of generations necessary to go from a highly skewed population to HW equilibrium it only takes
one generation of random mating to reach HW equilibrium
Exam 1:
1.1 Origin and Aims of Evolutionary Theory
How does geography affect the distribution of species? Convergent evolution, some places the species
have evolved to fit the environment.
Necessary and sufficient conditions for natural selection Variance in the population • Causes differences
in fitness • Is heritable across generations
Descent with modification all species, living and extinct, have descended, without interruption, from one
or a few original forms of life
1.2 Life on Earth
Uniformitarianism- same natural laws and processes that operate in the universe now, have always
operated in the universe in the past and apply everywhere in the universe
Tree of life
Common ancestry of living things
Interpreting phylogenetic trees
Determine common ancestry
Infer traits in tips based on mutation events
Identify equivalent tree
1.3 Adaptation
Fitness: A simple way to define fitness is to call it the number of offspring an individual leaves into the
next generation (viable offspring)
Both reproduction and survival components - which component is more important? The individual must
reach reproductive age, but reproduction is more important to an organism's fitness. Survival is
necessary to reach a sexually viable age, so survival assists reproduction, but reproduction overall is still
the end goal
How fitness depends on environmental context Environment is a crucial factor in determining fitness,
because it shapes what alleles would hypothetically be adaptive/maladaptive at a given time. A trait
that is adaptive in the desert is maladaptive in the tundra.
Determine if an example is an adaptation- Evolution is not always indicative of an adaptation.
Hemoglobin, for example, is red because of the protein structure, not any adaptive value. Also, many
persistent traits that are apparently naturally selected may just be attributed to random genetic drift
and hitchhiking genes/pleiotropy. So for these reasons, we cannot ASSUME a feature to be an
adaptation unless sufficient evidence suggests so. The following measures can be utilized to determine
if a trait is an adaptation:
, - Complexity: Even if we cannot immediately guess the function of a structure, we know that
complexity cannot evolve via the other aforementioned mechanisms, and that natural selection
must have been utilized. Example: Retina eye
- Functional morphology/physiology can be used to determine the usage of a certain
characteristic, and determine if it is adaptive
- Experiment
- Utilize a comparative method (hypothetico-deductive method)
Analyze evidence for adaptive hypotheses Four bullet points mentioned above (I think)
Artificial selection and hitchhiking- peep recitation 1 activity
Tradeoffs and constraints we must recognize that there is a FIXED amount of available energy/nutrition
that can be utilized in functions. In other words, not all of the best conceivable alleles can be fixed due
to this constraint (often called a phylogenetic constraint). An example of this is humans having a high
number of cervical vertebrae, which is maladaptive and often causes cancer.
Plasticity- Plasticity can be defined as the trait of being flexible. This trait can be expressed in different
ways, and is capable of change. An example of a lack of plasticity is an anteater, if all bugs in its
environment died off, it wouldn’t have the dietary plasticity necessary to adapt and eat other things.
Genetic linkage of traits Many genes can be pleiotropic, where an allele controls multiple traits. So,
selection acting upon one of those traits may indirectly select for the other, resulting in selection of an
allele that isn’t necessarily advantageous. These are called correlated traits. Breeder’s equation can be
utilized here (G→ genetic covariance)
Where the creativity of evolution comes from this is derived from the improbability of an advantageous
allele going into fixation. Population genetics shows us that the likelihood of a single advantageous
mutated allele going into fixation is low. If this mutation is common, it will obviously fix over time, but it
can (and often has) prevent the rarer mutations from fixing over time. This same concept also must be
considered for deleterious alleles
2.1 Mutation
Synonymous and Non-synonymous mutations - Nonsynonymous alters the amino acid sequence of a
protein and hence can change the biological structure of an organism, Synonymous do not alter AA
sequence
In what ways are mutations random and in what ways are they non-random? Random most of the time.
Mutations can be considered to be “non-random” when they are initiated by an environmental external
factor that was NOT random. To clarify, an example of this would be a carcinogen (like tobacco) inducing
a mutation in the tumor-suppressor gene (as there is a proven linkage between these two) causing
mutation. Or, when skin is exposed to UV, that portion of the skin is more susceptible to mutation. So,
although mutations are random, the environmental factors that induce these mutations are not
The evolutionary importance of (genetic) variation in the population heritable genetic variability within a
population encompasses two of the three necessities defined by Darwin for natural selection. 1)
heritability 2) genetic variance within a population 3) differential survival and reproduction (which is
dictated by environmental factors). EVOLUTION CANNOT OCCUR WITHOUT GENETIC
VARIATION IN A GIVEN POPULATION
Mutation-selection balance I think this is the last part of the answer below, about how natural selection
balances the mutation rate over time. It selects against deleterious mutations (by lowering the mutation
, rate) since deleterious mutations are most common (due to structure/function of enzymes and
proteins), but the potential for adaptive/beneficial mutation prevents natural selection from moving the
mutation rate to zero.
The typical frequency of beneficial, neutral and deleterious mutations- Deleterious mutations tend to be
by far the most common of any mutation (in an individual). For example, structure and function is
fundamental to molecular biology, and a deleterious mutation could be a simple mutation that changes
that protein structure, disabling its behavior. This, in turn, LOWERS the rate of mutation over time (in
eukaryotes, at least), because deleterious mutations must be selected against. Neutral mutations are
common as well, and occasionally, a mutation will be beneficial. Adaptive mutations prevent natural
selection from selecting mutation rates to arrive at 0.
-I think the question is referring to the frequency of the mutations in a population, so deleterious would
be rare because those organisms often die and they are selected against, and neutral is most common
because they are not affecting us and they happen all the time, and beneficial is intermediate. Neutral
and beneficial are prevalent. (this is what she said in the review session)
Explain how mutation rates themselves will evolve (depending on where a population is on its adaptive
landscape)
The types (mechanisms) of mutation Mutation is the ultimate source of variation. This can include a
point mutation (nonsense, missense, silent) or a frameshift (deletion, insertion). Structural mutations
can occur as well, which are errors that occur when chromosomes are replicated. This includes,
deletion, duplication, invasion, fission( splitting chromosome into 2) , fusion(fusion of 2 chromosomes
into one). ALSO: nucleoside analogs (induces mutation by replacing base pairs, and have different
pairing rules causing mutations), intercalating agents (which induce frameshift mutations by making
base pairs more far apart, and DNA Polymerase becomes more prone to skipping), and radiation1.
Nonsense- results in a stop codon. Missense-single nucleotide change results in a codon that codes for a
different amino acid.
2.2 Migration
2.3 Genetic Drift
What is genetic drift? Change in allele frequencies over time due to random sampling of organisms Null
models in science the simplest, default model to explain what is going on (this is the definition from
lecture)
Why Hardy-Weinberg is the null model for population genetics If HWE is not met, this means that the
allele frequencies are changing, thus evolution is taking place.
The allele and genotype frequencies do not change.
Assumptions of Hardy-Weinberg equilibrium No mutation, no genetic drift, no natural selection, random
mating, closed population.
The frequencies of diploid genotypes given the allele frequencies of the two alleles under HW
equilibrium-25%, 50%, 25%
Number of generations necessary to go from a highly skewed population to HW equilibrium it only takes
one generation of random mating to reach HW equilibrium
