25. Phylogeny

The analytical approach to understanding the diversity and relatedness of both extant and extinct organisms is called __________.

What is the focus of the branch of biology called taxonomy?

The binomial system assigns to each organism a unique name that describes its __________.

The two-part format of the scientific name, referred to as binomial, ensures that __________.

Which of the following is the correct taxonomic name for the African forest elephant?

A taxon __________.

Rabbits and guinea pigs both belong to class Mammalia. This means they must also both belong to __________.

Species A and species B are in the same phylum. Species A and species C, but not species B, are in the same order. From this information you can conclude that __________.

Universal phylogenetic trees built from different genes sometimes give inconsistent results. What basic assumption on which phylogenetic trees are based has probably been violated during the history of life?

By applying a molecular clock, researchers have proposed that the first HIV-1 M invasion into humans occurred in the __________.

What does a branch point in a phylogenetic tree represent?

Which of the following methods to establish phylogenetic relationships among organisms has been developed most recently?

Researchers can use molecular homologies to __________.

Which of the following would be the least useful in determining the relationships among various species?

The idea of using molecules as clocks to time evolutionary events is very attractive, but there are many problems in actually applying the technique. What seems to be the best way to get reliable results?

A phylogenetic tree of bird families constructed by cladistic analysis would be a hypothesis about which of the following?

What is the evolutionary significance of orthologous genes?

What is the evolutionary significance of paralogous genes?

Many researchers who study the kingdom Protista argue that all of these organisms should not be placed in the same kingdom because these organisms could not have evolved from a common ancestor. In other words, they argue that the kingdom Protista is __________.

Using cladistic analysis, a taxonomist wishes to construct a phylogenetic tree showing the relationships among various species of mammals. Which of the following would be the least useful for this purpose?

Which statement below is true about an outgroup?

Unlike a regular phylogenetic tree, phylogenetic trees with branch lengths proportional to time can be used to __________.

Paralogous genes __________.

Which statement below is true of parsimonious trees?

Birds and mammals have a four-chambered heart, but most reptiles have a three-chambered heart. How does this fact affect the construction of phylogenetic trees for these groups?

If you wanted to determine the lineage of plants that have evolved on a relatively young archipelago—approximately 15,000 years old—what type of nucleic acid should you compare?

In a comparison of birds and mammals, the condition of having four limbs is a. a shared ancestral character. b. a shared derived character. c. a character useful for distinguishing birds from mammals. d. an example of analogy rather than homology.

To apply parsimony to constructing a phylogenetic tree, a. choose the tree that assumes all evolutionary changes are equally probable. b. choose the tree in which the branch points are based on as many shared derived characters as possible. c. choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology. d. choose the tree with the fewest branch points.

Fill in the blanks on the phylogenetic tree (on the facing page) to show current hypotheses for the origin of multicellular organisms. a. b. c. d. e. f.

Fill in this concept map about systematics a. b. c. d. e. f. g

Critique the following statement: The absence of a trait cannot be used as a synapomorphy in phylogenetic analysis; only shared derived traits that are present in the clade can be used.

Where are protein components of the extracellular matrix synthesized? a. in the rough ER b. in the Golgi apparatus c. in the plasma membrane d. in the extracellular layer itself

How are hypotheses about the evolutionary relationships among living organisms tested?

VISUAL SKILLS In Figure 26.4, which similarly inclusive taxon is represented as descending from the same common ancestor as Canidae? a. Felidae b. Mustelidae c. Carnivora d. Lutra

Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V. A grouping that consists of species T, X, Y, and Z (but not U or V) makes up a. a monophyletic taxon. b. an ingroup, with species U as the outgroup. c. a paraphyletic group. d. a polyphyletic group.

Which of the following correctly describe an active site? Select True or False for each statement. T/F It is the location in an enzyme where substrates bind. T/F It is the place where a molecule or ion binds to an inactive enzyme to induce a shape change to make it active. T/F It is the portion of an enzyme where chaperones bind to help enzymes fold. T/F It is the site on an enzyme where catalysis occurs.

Which of the following is an example of homoplasy? a. hair in humans and fur in mice b. astragalus ankle bones in hippos and deer c. Hox genes in humans and flies d. streamlined bodies in dolphins and ichthyosaurs

Which of the following kingdoms or domains is a hodgepodge of different evolutionary lineages? a. Bacteria; b. Protista; c. Archaea; d. Plantae; e. Animalia

.VISUAL SKILLS Based on the tree below, which statement is correct? (A)Lizards and goats form a sister group. (B)Salamanders are a sister group to the group containing liz-ards, goats, and humans. (C)Salamanders are more closely related to lizards than to humans. (D)Goats and humans are the only sister group shown in this tree.

In Figure 33.2, which two main clades branch from the most recent common ancestor of the eumetazoans? a. Porifera and Cnidaria b. Lophotrochozoa and Ecdysozoa c. Cnidaria and Bilateria d. Deuterostomia and Bilateria

Explain the lock-and-key model of enzyme activity. What is incorrect about this model?

How do the extracellular filaments in plants differ from those in animals? a. Plant filaments resist compression forces; animal filaments resist pulling forces. b. Animal filaments consist of proteins; plant filaments consist of polysaccharides. c. Plant extracellular filaments never move; animal filaments can slide past one another. d. Plant filaments run parallel to one another; animal filaments crisscross.

What important assumption does parsimony make when assessing which phylogenetic tree is most accurate? Why was parsimony misleading in the case of the astragalus during the evolution of artiodactyls?

VISUAL SKILLS Based on the tree below, which statement is not correct?

a.Goats and humans form a sister group. b. Salamanders are a sister group to the group containing lizards, goats, and humans. c. Salamanders are as closely related to goats as to humans. d. Lizards are more closely related to salamanders than to humans.

If you were using cladistics to build a phylogenetic tree of cats, which of the following would be the best outgroup? a. wolf b. domestic cat c. lion d. leopard

You can use a 'one-snip test' to identify monophyletic groups—meaning that if you 'cut' any branch on a tree, everything that 'falls off' is a monophyletic group. Why is this valid?

In terms of structure, how do channel proteins differ from carrier proteins?

VISUAL SKILLS The relative lengths of the frog and mouse branches in the phylogenetic tree in Figure 26.13 indicate that a. frogs evolved before mice. b. mice evolved before frogs. c. the homolog has evolved more rapidly in mice. d. the homolog has evolved more slowly in mice.

If you were using cladistics to build a phylogenetic tree of cats, which would be the best choice for an outgroup? a. kangaroo b. leopard c. domestic cat d. iguana

Use the fossil evidence shown in Figure 25.6 to determine whether flight evolved earlier in insects or in birds. Is flight an example of homology or convergent evolution? Explain.

Which of the following could provide the best data for determining the phylogeny of very closely related species? a. the fossil record b. their morphological differences and similarities c. a comparison of nucleotide sequences in homologous genes and mitochondrial DNA d. a comparison of their ribosomal DNA sequences

You have discovered an enzyme that appears to function only when a particular sugar accumulates. Which of the following scenarios would you predict to be responsible for activating this enzyme? a. The sugar cleaves the enzyme to form the active conformation. b. The sugar is an allosteric regulatory molecule for the enzyme. c. The sugar is a competitive inhibitor for the enzyme. d. The sugar phosphorylates the enzyme to form the active conformation

Phylogenies are created based on the principle that all species descending from a recent common ancestor                   . a. should be identical; b. should share characteristics that evolved in that ancestor; c. should be found as fossils; d. should have identical DNA sequences; e. should be no more similar than species that are less closely related

The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells. Why are Archaea considered a monophyletic group according to the three-domain hypothesis? a. Because this group includes all organisms except eukaryotes. b. Because this group includes an ancestral population and all of its descendants. c. Because all members of this group lack membrane-bound organelles. d. Because this group evolved after the origin of bacteria.

Which are more likely to be closely related: two species with similar appearance but divergent gene sequences or two species with different appearances but nearly identical genes? Explain.

Explain why changes in the regulation of developmental genes may have played such a large role in the evolution of new forms.

What types of molecular comparisons are used to determine the very early branching of the tree of life? Explain.

A paleontologist compares fossils from three dinosaurs and Archaeopteryx, the earliest-known bird. The following table shows the distribution of characters for each species, where 1 means that the character is present and 0 means it is not. The outgroup (not shown in the table) had none of the characters. Arrange these species on the phylogenetic tree below and indicate the derived character that defines each branch point.