Phylogeny and Tree of Life
On a phylogenetic tree, what do the tips represent?
Taxa, such as species or groups of organisms.
Learning Objective: Given a phylogenetic tree, accurately label its major components and identify the kind of taxon represented at the tips.
What are the four postulates of natural selection?
Variation
Heritability
Struggle for existence
Differential survival and reproduction
Learning Objective: Describe the four postulates of natural selection.
What is the ultimate source of new genetic variation?
Mutation.
Explanation: Mutation creates new DNA sequence variants. Other processes such as crossing over and independent assortment rearrange existing genetic variation.
Learning Objective: Defend the statement that mutation is the ultimate source of genetic variation.
What is the process by which prokaryotes increase genetic diversity by taking up foreign DNA directly from their surroundings?
Transformation.
Explanation: Transformation occurs when a prokaryote takes up DNA from its environment and incorporates it into its own genetic material. This is one form of genetic recombination, which increases genetic diversity.
Learning Objective: Describe structural and functional adaptations of prokaryotes, including their genetic adaptations.
What is the major difference between oxygenic and anoxygenic photosynthesis?
Oxygenic photosynthesis produces oxygen; anoxygenic photosynthesis does not.
Explanation: Oxygenic photosynthesis uses water as an electron donor and releases O₂. Anoxygenic photosynthesis uses other electron donors and does not produce oxygen.
Learning Objective: Describe key differences between oxygenic and anoxygenic photosynthesis.
A group contains an ancestor and all of its descendants. What type of group is this?
A monophyletic group, or clade.
Learning Objective: Recognize and label monophyletic groups.
A student says, “A giraffe stretched its neck because it needed to reach higher leaves, and its offspring inherited the longer neck.” What is wrong with this explanation?
It incorrectly describes evolution as individuals changing because they need to.
Explanation: Natural selection acts on heritable variation already present in a population. Individuals do not evolve traits because they need them. Individuals with advantageous heritable traits may survive and reproduce more successfully.
Learning Objective: Explain and debunk misconceptions about natural selection.
Why is mutation described as random with respect to fitness?
Mutations do not occur because an organism “needs” a particular beneficial trait.
Explanation: A mutation can be beneficial, harmful, or neutral depending on the environment. Natural selection determines its consequences for fitness after the mutation occurs.
Learning Objective: Explain why mutation is random with respect to its impact on fitness.
A bacterium lives in an environment with no organic carbon available but has abundant inorganic chemicals. Is it most likely a phototroph, heterotroph, chemotroph, and/or autotroph?
Chemotroph and autotroph
Explanation: A chemotroph obtains energy from chemicals rather than light, while an autotroph obtains carbon by fixing inorganic carbon (such as CO₂). A bacterium using inorganic chemicals for energy and inorganic carbon for carbon would therefore be a chemoautotroph.
Learning Objective: Describe nutritional and metabolic adaptations of prokaryotes.
Why could oxygenic photosynthesis dramatically change Earth’s atmosphere?
It continuously produced O₂ as a byproduct, allowing oxygen to accumulate after major oxygen sinks became saturated.
Explanation: Before oxygenic photosynthesis, free oxygen was scarce. Microbial oxygen production eventually transformed atmospheric chemistry.
Learning Objective: Discuss how microorganisms determined Earth’s atmospheric composition.
You are given these relationships: A and B are sister taxa; C is sister to A+B; D is sister to A+B+C. Which taxon is the outgroup?
D.
Explanation: D branches off before the A+B+C group and is therefore the most distantly related taxon in this particular comparison.
Learning Objective: Create a phylogenetic tree from a set of relationships and explain the reasoning used to build it.
Why is natural selection considered the process underlying adaptive evolution?
Because heritable traits that increase survival or reproduction become more common over generations.
Explanation: Selection changes the frequency of heritable traits in populations. Over many generations, populations can become better suited to their environments.
Learning Objective: Recognize natural selection as the process underlying adaptive evolution.
Two siblings inherit different combinations of their parents’ chromosomes. Name two mechanisms that contribute to this variation.
Independent assortment and crossing over.
Explanation: Independent assortment produces different combinations of parental chromosomes, while crossing over produces chromosomes containing new combinations of alleles.
Learning Objective: Recognize how independent assortment and crossing over generate genetic variation.
Is all bacteria in the human body harmful? Explain.
No. Many bacteria are beneficial or neutral.
Explanation: Microbiome members can aid digestion, produce useful compounds, interact with the immune system, and prevent pathogen colonization.
Learning Objective: Describe beneficial and harmful effects of prokaryotes on humans.
Why does the existence of oxygen-rich environments today provide evidence that microorganisms profoundly altered Earth’s atmosphere?
Oxygen was not abundant in Earth’s early atmosphere, so the presence of large amounts of O₂ requires a biological source capable of producing it over geological time.
Explanation: Oxygenic photosynthesis provides a mechanism for producing atmospheric oxygen, with cyanobacteria playing a major historical role.
Learning Objective: Discuss, using evidence, how microorganisms determined Earth’s atmospheric composition.
A student says, “Species A is more evolved than species B because A is farther to the right on the tree.” Evaluate the accuracy of this claim.
The claim is incorrect.
Explanation: Phylogenetic trees do not represent organisms as more or less evolved based on their position on the page. All living taxa have been evolving for the same amount of time since their common ancestors. The tree represents relationships, not a ladder of progress.
Learning Objective: Interpret phylogenetic trees and explain evolutionary relationships.
Explain how simple nonliving molecules could potentially give rise to increasingly complex biological systems without assuming that a fully formed cell appeared instantly.
A possible sequence is: abiotic molecules → organic molecules → polymers → compartmentalization/protocells → self-replicating molecules → increasingly complex cells.
Explanation: Origin-of-life hypotheses propose a gradual transition from chemistry to increasingly organized systems.
Learning Objective: Describe steps by which simple cells may have originated from nonliving materials.
You compare four genome sequences and obtain the following similarities:
A–B: 97%
A–C: 82%
A–D: 60%
C–D: 61%
Create the most likely simplified phylogenetic relationship.
A and B should form a sister group, while C and D are more distantly related.
Explanation: Greater sequence similarity provides evidence for more recent common ancestry, assuming the sequences are homologous and appropriate for comparison.
Learning Objective: Compare genome sequences and create phylogenetic trees.
A hospital notices that MRSA cases increased after frequent antibiotic use. Explain the evolutionary mechanism responsible for this pattern.
Antibiotic exposure creates selection favoring bacteria with heritable resistance. Resistant bacteria survive and reproduce at higher rates, increasing the frequency of resistance.
Explanation: The antibiotics do not make individual bacteria intentionally adapt. Instead, they change the relative reproductive success of existing variants.
Learning Objective: Identify causes and consequences of antibiotic resistance and apply the concept to MRSA.
Imagine cyanobacteria suddenly disappeared before atmospheric oxygen accumulated. Predict how Earth’s biosphere might differ.
Atmospheric oxygen would likely be much lower, aerobic metabolism would be more limited, and many later organisms dependent on oxygen-rich environments might never have evolved in the same way.
Explanation: Cyanobacteria’s oxygen production helped create environmental conditions that permitted the expansion of aerobic metabolism and contributed to later evolutionary changes.
Learning Objective: Explain why cyanobacteria and oxygenic photosynthesis were a key event in life’s history.
Two scientists propose different evolutionary histories for four species. Tree A requires two independent gains of a trait, while Tree B requires one gain and one loss. If the goal is to minimize evolutionary changes, which tree is preferred and why?
Tree B, because it requires fewer evolutionary changes.
Explanation: This is an application of parsimony. When multiple explanations are possible, the hypothesis requiring fewer evolutionary changes is generally preferred, assuming other evidence does not contradict it.
Learning Objective: Using a phylogenetic tree and trait data, determine where evolutionary changes most likely occurred.
A student argues: “Because organisms adapt to their environments, evolution must have a goal.” Do you defend or reject this reasoning?
Reject it. Adaptation is the result of natural selection acting on existing heritable variation. Selection can produce populations that are better suited to their current environments, but there is no predetermined endpoint or goal.
Learning Objective: Recognize natural selection as adaptive evolution and debunk goal-directed evolution.
Defend this statement: “Mutation is the ultimate source of genetic variation, but mutation alone does not explain why a particular variant becomes common.”
Mutation creates new genetic variants, but mechanisms such as natural selection, genetic drift, and reproduction determine how their frequencies change.
Explanation: Mutation introduces novelty; evolution then acts on the resulting variation.
Learning Objective: Defend the statement that mutation is the ultimate source of genetic variation.
Design a strategy that could reduce the evolution and spread of antibiotic-resistant bacteria without eliminating antibiotic use entirely.
Strategies could include appropriate antibiotic prescribing, avoiding unnecessary antibiotics, infection-control measures, hygiene, surveillance, and completing appropriate treatment regimens as directed.
Explanation: Reducing unnecessary selection pressure and transmission can slow the spread of resistance while preserving antibiotics for situations where they are needed.
Learning Objective: Identify and evaluate causes and consequences of antibiotic resistance.
A student says, “Oxygen has always been abundant because animals need it.” Evaluate the accuracy of this statement.
It is incorrect. Animals evolved much later than the earliest life and did not create Earth’s oxygen-rich atmosphere. Microorganisms, particularly cyanobacteria, produced oxygen through oxygenic photosynthesis long before animals evolved.
Learning Objective: Discuss how microorganisms determined Earth’s atmospheric composition and explain the importance of cyanobacteria.