Chapter 16 Quiz

. Refer to the figure. The organisms shown here are all "archosaurs." The first six are "dinosaurs," but Crocodiles are not.

The node that represents the most recent common ancestor of all archosaurs is _______, and the node that represents the most recent common ancestor of all dinosaurs is _______.

E; A

E; B

C; B

D; C

E; D

. Refer to the graph.

The data in the graph suggest that

nucleotides in the third-base position evolve more slowly than those in the first-base position.

nucleotides in the third-base position evolve more slowly than those in the second-base position.

different types of data are most informative at different timescales.

mitochondrial genes evolve too slowly to be useful in molecular phylogenies.

divergence rates of third-base position nucleotides are constant over a 500 million year timescale.

. The figure shows relationships among major groups of vertebrates.

According to the data in the figure,

mammals are monophyletic for both phylogenies.

the morphological phylogeny does not largely resemble the DNA sequence phylogeny.

amphibians are more closely related to mammals (monotremes, marsupials, and placental mammals) than they are to reptiles (tuatara, lizards, snakes, turtles, crocodiles, and birds).

the position of turtles is consistent, regardless of data used to build the phylogeny.

amphibians are an outgroup for both phylogenies.

. You examine long sequences from four genes in three closely related species, species A, B, and C. Genes 1–3 all suggest A and B are each other's closest relative, but gene 4 suggests that A and C are. Assuming that the "true" phylogeny is that A and B are sister species, which explanation is least likely to account for the different relationship shown by the fourth sequence?

The sequence similarity of the fourth gene between A and C is a result of homoplasy.

The fourth gene may have been polymorphic in the common ancestor of the species group, and incomplete lineage sorting during diversification has rendered the gene trees different than the species tree.

Relatively recent hybridization has allowed introgression of the gene between species A and C.

The rate of evolution of the fourth gene differs greatly among these species B.

The gene has experienced strong directional selection in species B and strong purifying selection in species A and C.

. Which complication to phylogenetic inference is most likely to be widespread in a group of species that have undergone an evolutionary radiation?

Introgression of genes between species

High rates of similarity because of homoplasy

Incomplete lineage sorting

Great variability of the rates of molecular evolution

None of these are consistently an issue in evolutionary radiations.

. Likelihood is preferable to parsimony to infer a phylogeny when

there is a great deal of homoplasy.

a researcher wishes to incorporate different models of molecular evolution into phylogenetic estimates.

evolutionary rates vary greatly among the taxa of interest.

a researcher wishes to include a measure of confidence in the nodes of the phylogeny.

All of the above

. Which observation does not provide evidence that birds are theropod dinosaurs?

There are many fossil therapods that have been found with feathers.

Birds and theropods are both missing the fifth toe, and the first toe is rotated backward.

Both fossil theropods and modern birds have a wishbone.

Birds and theropods have three-digits on their forelimbs.

Both pterosaurs and birds evolved flight.

. Which of these would be an advantage of using Bayesian inference instead of maximum likelihood to construct a phylogeny based on DNA sequence data?

Bayesian methods allow one to estimate branch lengths.

Bayesian methods allow one to incorporate prior information to weight probabilities.

Bayesian methods are less prone to errors based on incorrect assumptions.

Both b and c

All of the above

. Which data would not affect maximum likelihood estimates of phylogenies when comparing different tree hypotheses?

The tree topology

The lengths of the branches

The branching order of the tree

Nucleotide substitution rate

All of these are important for finding the most likely tree.

. If we use molecular clocks to estimate that the most recent common ancestor of a species pair existed 5 million years ago in a specific region, what strata of fossil-bearing rock would be the best choice for finding a fossil most similar to that ancestor?

Strata exactly 5 million years old

Strata slightly younger than 5 million years old

Strata much younger than 5 million years old

Strata slightly older than 5 million years old

Strata much older than 5 million years old

. Refer to the figure. Imagine you have a phylogeny that you are sure is correct that includes five species. You examine a gene sequence and discover that species A and E differ by 100 base pairs, species B and E differ by 101 base pairs, species C and E differ by 180 base pairs, and species D and E differ by 183 base pairs.

What would you say is the most likely pattern of evolutionary rates among these species?

Rates of evolution have been equal in all lineages.

Species D has increased rate of change much more than the other species.

Rates of evolution increased for species C and D after they diverged from their common ancestor with species B.

Rates of evolution decreased for species B after it diverged from its common ancestor with species C and D.

Species C and D both drastically increased rate of evolutionary change after they diverged from their common ancestor.

. Stickleback fish found in lakes rapidly evolve a low armor plate morphology when compared to marine populations. Analysis of the gene responsible shows that populations with low plating form one clade and marine populations form another. However, gene trees formed with other genes show that the low plating phenotype probably evolved independently multiple times. How have scientists resolved these contradictory gene trees?

A single origin of the low plating gene in the oceanic population that remained at a low frequency until lakes were colonized. Then the gene independently became fixed in each.

The mutation first appeared in a single lake, but gene flow between lakes connected by rivers has spread the mutation to new populations where it increased in frequency.

High armor evolved independently from a low armor state in the oceanic population, where it increased in frequency to near fixation.

All of the populations in lakes are very closely related. The other genes suggesting different topologies of relatedness are biased by geographic covariation.

Mating between individuals of different populations has allowed introgression of the gene into many lake populations.

. Mammals, like humans and apes, have five digits on their fore and hind limbs. Modern horses have one. How might you reconstruct the ancestral state of mammal toe number?

Investigate the number of toes on all extant horses and apes.

Investigate the number of toes for other mammals and use parsimony to deduce the ancestral state.

Investigate the number of toes for an outgroup that is closely related to mammals, for example reptiles or amphibians.

Either b or c

All of the above

. The major utility of the comparative method is that it ensures _______ in studies of adaptation in groups of species.

large enough sample size

independence of data points

homogeneity of variances

that data have a linear relationship

All of the above

. Historically, humans were placed into the taxonomic family Hominidae, and the great apes (orangutan, gorilla, bonobo, and chimpanzee) were placed into Pongidae. Modern taxonomists now place humans, along with the other great apes, into a single family, Hominidae. Use the phylogeny in the figure to identify the fact that led to this revision.

Chimpanzees and bonobos are sister taxa and form a monophyletic group.

Gibbons are an outgroup to the great apes and can be used as part of ancestral character analysis.

Chimps and bonobos are more closely related to humans than they are to the other great apes.

Great apes were identified as a polyphyletic taxon and had to be reorganized.

Humans are a crown group; all of the extinct ancestors of humans are a stem group.

. Refer to the figure showing a phylogenetic tree of some snakes and lizards.

According to the figure, which statement is true?

Lacertilia (lizards) is a monophyletic taxon.

Squamata is a paraphyletic taxon.

The closest relative of Micrurus (coral snake) is Tamnophis (garter snake).

If we created a new taxon consisting of the venomous snakes (shown in figure as group V), it would be paraphyletic.

Serpentes is a crown group and Squamata is a stem group.

Chapter 16 Quiz

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