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Question 01

What are the three major branches in the Tree of Life?

a) Plants, Animals, and Fungi

b) Bacteria, Algae, and Protozoa

c) Archaea, Bacteria, and Eukaryotes

d) Mitochondria, Chloroplasts, and Nuclei

Question 02

How long ago did land plants, animals, and fungi last share a common ancestor?

a) 50 millions years ago

b) 2 billion years ago

c) 1 billion years ago

d) 540 million years ago

Question 03

Phylogenetic relatives are species that:

a) look like each other.

b) have similar developmental control genes.

c) share more recent ancestors than they share with less related species.

d) live on the same continent.

Question 04

What is the name for a group that does not contain all of the extant species that descended from a common ancestor?

a) monophyletic

b) polyphyletic

c) paraphyletic

d) quasiphyletic

Question 05

What is the name for a group that contains species descended from several ancestors that are also the ancestors of species placed in other named groups?

a) monophyletic

b) polyphyletic

c) paraphyletic

d) quasiphyletic

Question 06

Convergence is an example of:

a) homology.

b) homoplasy.

c) orthology.

d) monophyly.

Question 07

Why do we think that the wing of the bat and the leg of the horse are both descended from a similar structure in a common ancestor?

a) They have most of the same multiple elements in the same complex relationships produced at similar times in development under the control of the same developmental genes.

b) They develop using different mechanisms.

c) They are made of the same tissues.

d) They share precisely the same elements.

Question 08

Modern systematists:

a) always choose the simplest phylogenetic tree, the one that implies the least change.

b) always choose the most likely phylogenetic tree, the one that makes it most likely that the data gathered would be observed.

c) use a combination of methods.

d) always choose the tree that would be most likely given their prior expectation of what it should look like.

Question 09

Shared derived traits:

a) are not phylogenetically informative.

b) are called symplesiomorphies.

c) are called synapomorphies.

d) are used to define outgroups.

Question 10

Why is it important to have a pretty good hypothesis of what the outgroup might be?

a) So that you can root the tree at a place that is probably appropriate.

b) Not so that you can define what is the primitive and what is the derived state of characters

c) So that you can avoid constructing a paraphyletic group.

d) So that you can establish homology.

Question 11

Why do the DNA sequences of two species have to be aligned properly before we can compare them to find out at how many nucleotide positions they differ?

a) Because mutations destroy genetic information.

b) Because insertions and deletions cause the original DNA sequence to expand and contract in different ways in separate lineages.

c) Because translation is imperfect.

d) Because the molecular clock ticks at a different pace in every lineage.

Question 12

Why do we think that molecular clocks exist and are accurate enough to be informative?

a) Because theory tells us that the rate of fixation of neutral alleles should be different in small and in large populations.

b) Because data on protein evolution shows that protein molecules change at similar rates in different lineages.

c) Because we can measure the rate of fixation of neutral alleles in modern populations and extrapolate to the distant past.

d) Because the ages of lineages inferred from molecular clocks are often quite different from the ages inferred from fossils.

Question 13

What is the microevolutionary processes that forms the basis of the molecular clock?

a) The Hardy-Weinberg equilibrium.

b) Genetic variation and natural selection.

c) Mutation and drift.

d) Differential reproductive success of single genes.

Question 14

Why is the genealogy of genes not always the same as the phylogeny of species and not always the same as the genealogy of other genes in the same organism?

a) Because genes and species occur at different levels of biological organization.

b) Because two copies of one gene can originate within a population before speciation occurs, and this can happen independently in different genes.

c) Because in the history of species it has not necessarily always reproduced sexually.

d) Because genes disappear from lineages much more rapidly than species speciate.

Question 15

In what direction is the coalescent process conceived as working?

a) Forward in time to a diverse array of descendant sequences.

b) In the direction of increasing disorder.

c) Backward in time to a common ancestral sequence.

d) Towards a liquid drop.

Question 16

Is giving organisms names that reflect natural relationships a problem?

a) No. It was solved by Linneus with a simple hierarchy of six levels: phylum, class, order, family, genus, species.

b) Yes, because if we want the name to indicate the position of the species in the Tree of Life, then every name needs to reflect all the branches in the Tree leading to that species. There are a huge number of such branches.

c) No. We do not need to worry about what we call things because everyone will understand what we mean anyway.

d) No, we have international commissions to take care of that kind of thing. Whatever they decide is ok so long as it works.

Question 17

What kind of gene should we sequence to describe the relationships among clades that diverged more than a billion years ago?

a) A gene that has been under strong selection to diverge among the clades in question.

b) A gene that has been under strong stabilizing selection over the entire period in question.

c) A gene that mutates so rapidly that every organism has a different version of it.

d) A gene that has only been inherited asexually.

Question 18

The reason that we can use phylogenetic methods to identify who transmitted HIV to a victim is that:

a) HIV is an RNA virus that mutates rapidly enough that every person has a different population of variants.

b) HIV acquires from its host a characteristic sequence that serves as a marker.

c) HIV does not experience genetic drift and therefore expresses a constant signal of its identity.

d) HIV reproduces asexually.

Question 19

Which of the following is not a reason to think that all life on the planet is descended from one common ancestor and that therefore there is only one Tree of Life?

a) The genetic code is nearly universal and quite similar when it does vary, as among various mitochondrial lineages.

b) All biological membranes have the same lipid bilayer structure.

c) Viruses do not have lipid cell membranes or carbohydrate cell walls. They have protein coats.

d) Complex pathways of intermediate metabolism are shared among Bacteria, Archaea, and Eukaryota.

Question 20

Molecular systematics tells us that the closest free-living relatives of mitochondria are:

a) archaeans living in hot, deep-sea vents.

b) cyanobacteria.

c) oxymonads.

d) that all tetrapods always have five digits.

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