Bio 212 Exam 2
Week 5: Chapter 6; Genetic Drift & Natural Selection
1. How is the field of population genetics linked to our understanding of evolution?
Population genetics provides the math and theory that describe how allele frequencies change over time. In this framework, evolution is literally defined as a change in allele frequency across generations.
2. Be able to describe Hardy-Weinberg equilibrium
Know what it does. Hardy-Weinberg denotes expected frequencies of the next generation and predicts genotype frequencies in the absence of evolution.
Know the HW assumptions. HW predictions are only accurate if the population is infinitely large, there is no selection, no migration in or out of the population (no gene flow), no mutation, and mating is random with respect to genotype.
Know how it is used to detect genetic drift, natural selection. If actual genotype frequencies differ from H-W predictions, one or more assumptions have been violated, meaning evolution (like drift, selection, etc.) is happening.
3. Can you describe some mechanisms for evolution without the presence of selection?
Mutation: Change in a DNA sequence
Migration: Movement of individuals in or out of populations which allows gene flow
Assortative mating: Non-random mating with respect to genotype
Inbreeding: Mates are more closely related than two individuals selected at random from the population (mating between relatives)
Genetic drift: Random changes in the gene frequencies of a population from generation to generation
Bottlenecks: An event where the number of individuals in a population is drastically reduced.
Founder Effect: when a small number of individuals leave a larger population to start a new population.
4. Understand what is meant by genetic drift.
What is it? Evolution arising from random changes in allele frequencies of a population from one generation to the next due to random mating.
What are its effects on gene frequencies? By chance, some genes may drift out of a population and become lost or some genes may become fixed.
How did Buri’s fruit fly experiment demonstrate genetic drift? This experiment had very small population sizes and genetic drift is stronger in small populations.
What are factors that affect genetic drift (e.g., population size, migration)?
Drift is stronger in small populations and weaker in large ones. Immigration/gene flow can offset drift by reintroducing alleles. A single immigrant has a bigger effect on the gene pool of a small population.
5. Understand what is meant by a genetic bottleneck.
For the example of northern elephant seals, how is it that their population size has increased but the genetic diversity of the population has not? Population was placed under government protection and rate of population increases is faster than rates of mutation, thus larger population size still has very low genetic diversity.
6. Understand what is meant by a founder effect.
For the example of Pitcairn and Norfolk islanders, how might migration (or lack thereof) affect genetic diversity and genetic-based diseases? Lived in isolation and genetic diversity remains low. Some mutineers went to Norfolk Island and 255 of the descendants have a hereditary form of migraines.
7. Understand what is meant by natural selection.
The process by which individuals better adapted for their way of life in their environment preferentially survive and reproduce to leave more offspring.
8. What conditions are needed for natural selection to operate (variation, differential reproduction, heredity)?
Variation in traits, differential reproduction, hereditary = the more advantageous traits allows individuals to have more offspring, that trait becomes more common in the population.
9. What is the evidence that population size can affect the strength of natural selection to act in a population?
Natural selection becomes more selective at higher population sizes. As the population becomes smaller, drift has a greater effect than natural selection.
10. How can an understanding of artificial selection help inform scientists about evolution?
Scientists can select particular phenotypic trait and observe how this selection affects allele frequencies of populations over time. Scientists (or breeders) intentionally choose traits (e.g., corn size, dog breeds, E. coli experiments). Watching allele frequencies change under controlled selection helps us understand natural selection in the wild.
11. Drift vs. selection – know how population size affects each one, and thus which is relatively more important in small or large populations.
Genetic drift is weaker in large populations and stronger in small populations. Natural selection becomes more effective at higher population sizes. As population size becomes smaller, drift has a greater effect than natural selection.
12. Can you describe the different types of fitness?
Physical fitness vs. evolutionary fitness: Strength, speed, flexibility, stamina vs. survival and reproduction
Evolutionary fitness: Survival and reproduction
Relative fitness: Fitness of a phenotype compared with other phenotypes in the population
Absolute fitness: Absolute reproductive success (i.e., the total number of offspring produced)
Which type of evolutionary fitness (absolute or relative) determines the outcome of selection? Why? To answer this question, think about the definition of evolution.
Relative fitness determines the outcome of selection, because evolution depends on which genotypes leave more offspring relative to others — not just how many overall.
14. Can you describe and understand the different types of natural selection?
Positive selection: when an allele increases the relative fitness of a genotype
Negative selection: when an allele lowers the relative fitness of a genotype
Mutation-selection balance: when the rate at which deleterious alleles created by mutation equals the rate at which deleterious alleles are eliminated by selection
Balancing selection: maintains multiple alleles (e.g., heterozygote advantage).
Explain how heterozygote advantage works? What type of selection is this? What is the evidence of malaria in humans that this is an example of heterozygote advantage. Why does it prevent selection from purging deleterious alleles? Do we expect it in all cases, or primarily for recessive alleles (why)?
Heterozygote advantage (aka overdominance) is when heterozygotes have higher fitness than either homozygote.
Type of selection: Balancing selection.
Example: The sickle-cell allele (HbS) in humans — AS heterozygotes are resistant to malaria but don’t suffer full sickle-cell disease.
This maintains both A and S alleles in the population.
It mainly occurs when deleterious alleles are recessive — selection can’t fully remove them because they’re “hidden” in heterozygotes.
16. Be able to describe the different patterns of natural selection.
Directional: favors individuals at one end of the distribution of a traits
Stabilizing: favors individuals with a trait near the mean of the population
Disruptive: selects against the population mean
Understand the three selection models and know how to interpret the graphs of allele frequencies and genotypes.
Strength of natural selection. depends on selection coefficient and heritable variation.
17. We can observe evolution during our lifetime. Be able to explain the examples, noting how each example links to different types of selection and/or evolutionary processes.
Oldfield mice: coat color evolved via convergent evolution (different mutations in Mc1r and Agouti) to match sandy or dark environments — directional selection.
Galapagos finches (before/after drought): drought selected for larger beaks that could crack hard seeds — directional selection; later shifts showed balancing selection as environment fluctuated.
Human lactase gene: mutation in LCT gene allowed digestion of milk into adulthood — positive selection; evolved independently in African and European populations (convergent evolution).
18. Can you explain what is meant by a selective sweep?
The process through which a new beneficial mutation that increases its frequency in the population reduces or eliminates genetic variation among nucleotide sequences that are near the mutation
19. Can you explain how humans can affect evolution of other taxa? Think about natural experiments, intentional artificial selection, unintentional artificial selection.
Natural experiments: studying natural selective pressures (e.g., finches, Oldfield mice).
Intentional: artificial selection (breeding crops, pets, bacteria).
Unintentional: human activities (overfishing → smaller fish, trophy hunting → smaller horns, climate change → color morphs in snowshoe hares).
Population Genetics: the study of the distribution of alleles in populations and causes of change in allele frequency over time.
Genetic Drift: evolution arising from random changes in allele frequencies of a population from one generation to the next due to random mating.
Genetic Bottleneck: An event where the number of individuals in a population is drastically reduced.
Founder Effect: when a small number of individuals leave a larger population to start a new population.
Natural Selection: the process by which individuals better adapted for their way of life in their environment preferentially survive and reproduce to leave more offspring with their traits to future generations.
Adaptation: a trait produced by natural selection that helps an organism survive and/or reproduce in its current environment.
Artificial Selection: an evolutionary process in which humans consciously select for or against particular traits of an organism.
Positive selection: when an allele increases the relative fitness of a genotype
Negative selection: when an allele lowers the relative fitness of a genotype
Mutation-selection balance: when the rate at which deleterious alleles created by mutation equals the rate at which deleterious alleles are eliminated by selection
Balancing selection: when natural selection maintains more than one allele
Week 6: Chapter 7; Molecular Evolution
Similar to how we can construct trees of species of taxa, can you explain how genes (or genetic loci) can have their own genealogy?
Each gene (or genetic locus) has its own evolutionary history — called a gene tree. Mutations create new alleles that are passed to descendants. Over time, these alleles can become fixed, revealing patterns of ancestry. So, just like we build species trees, we can build gene trees that trace how versions of a gene have evolved and spread through generations.
What is the basis of these molecular phylogenies?
Molecular phylogenies can be based on comparison of DNA sequences for homologous genetic loci between species. Can be genes, pseudogenes, introns, endogenous retroviral sequences. Because DNA directly encodes inheritance, comparing base sequences (A, T, G, C) gives a clear record of evolutionary relationships.
Understand and interpret the use of molecular data to construct phylogenetic trees.
To construct a molecular phylogenetic tree, scientists compare the number of nucleotide or amino acid differences between homologous genes. One species can be used as a reference (baseline), and each difference is tallied. The branch lengths in the tree reflect the number of accumulated mutations — more mutations = more evolutionary time since divergence.
What is coalescence and how can this concept help us to find a common ancestor?
Coalescence is when you trace all copies of a gene (alleles) in a population backward in time until they converge at a single common ancestral copy. That coalescent point represents the most recent common ancestor for that gene. This helps researchers estimate when alleles or species shared a common ancestor.
Can you explain the difference between complete lineage sorting and incomplete lineage sorting?
Complete lineage sorting is if the alleles assort into the species as the species evolve then gene tree matches the species tree. Incomplete lineage sorting is if alleles do NOT assort into the species as the species evolve, then the gene tree and species tree do not match.
In the case study for HIV in humans that we discussed in class, what was the role of host switching? How did the use of molecular phylogenies help us understand where HIV evolved from?
Host switching occurs when a virus evolves mutations that allow it to infect a new host species. In HIV, this happened when SIV (Simian Immunodeficiency Virus) from chimpanzees and sooty mangabeys mutated so it could infect humans.
Molecular phylogenies showed that:
HIV-1 evolved independently from chimp SIV several times (lineages M, N, O, P).
A specific mutation in the viral shell protein made infection of humans possible.
Using genetic data, scientists traced the origin to chimpanzee SIV in Central Africa around the early 1900s.
Can you explain the difference between natural selection and neutral evolution?
Natural selection: favors mutations that improve fitness — adaptive evolution.
Neutral evolution: most molecular changes are neutral (don’t affect fitness) and spread by genetic drift, not selection.
Motoo Kimura’s Neutral Theory (1968): most evolution at the molecular level is neutral.
Do neutral mutations affect the phenotype? Explain.
Neutral mutations do not affect phenotype because they don’t change protein function or expression. Examples: synonymous substitutions or mutations in noncoding regions (introns, pseudogenes).
Types of neutral mutations
Synonymous substitutions (remember how to read the codon table): DNA changes that don’t alter amino acids → no change in protein or phenotype.
Mutations in introns, pseudogenes. occur in noncoding DNA → don’t affect function, so they accumulate freely.
Understand how molecular clocks use mutation rates in neutral loci to estimate divergence times among taxa. What is the role of fossils that have known dates of geologic time?
The molecular clock uses the rate of neutral mutations to estimate how long ago species diverged. Because neutral mutations accumulate at a steady rate, the number of differences between species’ DNA sequences reflects time since divergence.
Fossils with known ages are used to calibrate the clock, giving absolute dates for evolutionary events.
Example: Cytochrome C mutation rates line up with fossil divergence times.
Week 6/7: Chapter 8; Adaptation
What is the definition of an adaptation?
A trait produced by natural selection that helps an organism survive and/or reproduce in its current environment.
What criteria are required to determine that a trait is an adaptation (heritable, functional, increases fitness)?
Heritable: a genetic basis that can be passed to offspring
Functional: if it has been shaped by natural selection for a particular task, then the trait must be capable to perform that task
Increase fitness: it must benefit the organism
In addition to the criteria, what is one example of a further consideration that is often considered to determine if a trait is an adaptation?
How did the trait first evolve? Did the traits arise when the current function arose?
What evolutionary process is known to produce adaptations?
Natural selection is the only evolutionary process known to produce adaptations.
Do adaptations often involve many genes or one gene? Why does this make sense?
Adaptations often involve many genes because complex traits have multiple structures controlled by multiple genes.
What general categories of forms of adaptations have been described (anatomical, molecular, behavior)?
Anatomical: physical structures (e.g., wings, fangs, mimicry in insects)
Molecular: proteins, biochemical pathways (e.g., snake venom proteins, opsins)
Behavior: learned or instinctive actions (e.g., echolocation in bats, mating displays)
Understand the definition of complex adaptations and how they can evolve.
Complex adaptations: Traits that require multiple interacting components (genes, structures, or processes).
Evolve gradually, not all at once.
How they evolve:
Each change (mutation, duplication, or expression tweak) must be neutral or beneficial.
Evolution works step-by-step, building complexity over time.
Key mechanisms:
Gene duplication:
Copies a gene → one keeps old function, the other can evolve a new one.
Example: olfactory receptor genes in humans and elephants.
Gene recruitment:
An existing gene gets expressed in a new tissue or at a new time.
Example: certain keratin genes recruited for feather development — keratins originally used for scales were expressed in new patterns to form feathers.
Can you describe the models to evolve complex adaptations? Be able to provide examples foreach.
Incremental additions: Small, optional changes become obligate over time (Bolus Spider)
Scaffolding: Traits that are needed while an adaptation is evolving are lost once the adaptation is in place (development of lungs)
Co-option: Traits already involved for one function evolve a new function (feathers)
In class, we discussed three examples of complex adaptations: snake venom, animal body plans, eyes. For each example, be able to explain the evidence for the evolution of each of the complex adaptations.
Snake venom: gene recruitment, gene duplication
Crotamines - duplication of defensin genes, which were recruited as venom.
Venom evolved before snakes evolved.
Animal body plans: changes in expression of regulatory genes during development
Hox genes = highly conserved between bilaterians, regulate body layout
Gene duplication allows fine-tuning of expression in different parts of the body
Dorsal-ventral patterning
Location of nerve cord, gut in protostomes and deuterostomes
Some homologous genes have different names because they were discovered independently
Changes in gene expression in these regulatory genes accounts for big differences in body layout
Image-forming or “camera” eye.
Opsins - gene duplication
Crystallins - recruitment of heat shock proteins
Steps in evolution from light-sensitive eye spots to vertebrate camera eye.
Can you describe some constraints that have been documented regarding the evolution of complex adaptations? Be sure to address the laws of physics, phylogenetic inertia, and antagonistic pleiotropy.
Laws of Physics: size of insects is limited by their reliance on passive diffusion of gases, if they are too big cannot get sufficient oxygen.
Phylogenetic inertia: evolution is constrained by the previous state.
Antagonistic pleiotropy: Possible when a single gene affects two or more traits
How does convergence also demonstrate that there may be some constraints on the evolution of complex adaptations?
Address the role(s) of similar selective pressures experienced by taxa that are evolutionarily unrelated.
Convergence:
Unrelated species evolve similar traits because they face similar selective pressures.
Example: Dolphins (mammals) and ichthyosaurs (reptiles) both evolved streamlined bodies.
Shows there are limited “solutions” nature can build under certain constraints.
How might modification of gene networks encourage convergent solutions to shared problems?
Role of Gene Networks:
Shared genetic toolkits (like Hox or opsin genes) mean different organisms can tweak the same networks → similar outcomes (even if unrelated).
Evolution reuses what’s available instead of inventing from scratch.
Adaptation: a trait produced by natural selection that helps an organism survive and/or reproduce in its current environment
Vestigial structures: a trait was adaptive for an organism's ancestor, but that evolved to be non-functional because of a change in the organism's environment.
Protostomes: mostly invertebrates; the first opening in the embryo becomes the mouth
Deuterostomes: vertebrates and invertebrates; the first opening in the embryo becomes the anus and the second opening becomes the mouth