A phylogenetic tree that is "rooted" is one A) that extends back to the origin of life on Earth. B) at whose base is located the common ancestor of all taxa depicted on that tree. C) that illustrates the rampant gene swapping that occurred early in life's history. D) that indicates our uncertainty about the evolutionary relationships of the taxa depicted on the tree. E) with very few branch points.

B

The correct sequence, from the most to the least comprehensive, of the taxonomic levels listed here is A) family, phylum, class, kingdom, order, species, and genus. B) kingdom, phylum, class, order, family, genus, and species. C) kingdom, phylum, order, class, family, genus, and species. D) phylum, kingdom, order, class, species, family, and genus. E) phylum, family, class, order, kingdom, genus, and species.

B

The common housefly belongs to all of the following taxa. Assuming you had access to textbooks or other scientific literature, knowing which of the following should provide you with the most specific information about the common housefly? A) order Diptera B) family Muscidae C) genus Musca D) class Hexapoda E) phylum Arthropoda

C

If organisms A, B, and C belong to the same class but to different orders and if organisms D, E, and F belong to the same order but to different families, which of the following pairs of organisms would be expected to show the greatest degree of structural homology? A) A and B B) A and C C) B and D D) C and F 3 E) D and F

E

Darwin analogized the effects of evolution as the above-ground portion of a many-branched tree, with extant species being the tips of the twigs. The common ancestor of two species is most analogous to which anatomical tree part? A) a single twig that gets longer with time B) a node where two twigs diverge C) a twig that branches with time D) the trunk E) neighboring twigs attached to the same stem

B

Dozens of potato varieties exist, differing from each other in potato-tuber size, skin color, flesh color, and shape. One might construct a classification of potatoes based on these morphological traits. Which of these criticisms of such a classification scheme is most likely to come from an adherent of the phylocode method of classification? A) Flesh color, rather than skin color, is a valid trait to use for classification because it is less susceptible to change with the age of the tuber. B) Flower color is a better classification criterion, because below-ground tubers can be influenced by minerals in the soil as much as by their genes. C) A more useful classification would codify potatoes based on the texture and flavor of their flesh, because this is what humans are concerned with. D) The most accurate phylogenetic code is that of Linnaeus. Classify potatoes based on Linnaean principles; not according to their color. E) The only biologically valid classification of potato varieties is one that accurately reflects their genetic and evolutionary relatedness.

E

The term "homoplasy" is most applicable to which of these features? A) the legless condition found in various types of extant lizards B) the 5-digit condition of human hands and bat wings C) the beta-hemoglobin genes of mice and of humans D) the fur that covers Australian moles and North American moles E) the basic skeletal features of dog forelimbs and cat forelimbs

A

If, someday, an archaean cell is discovered whose SSU-rRNA sequence is more similar to that of humans than the sequence of mouse SSU-rRNA is to that of humans, the best explanation for this apparent discrepancy would be A) homology. B) homoplasy. C) common ancestry. D) retro-evolution by humans. E) co-evolution of humans and that archaean.

B

The best classification system is that which most closely A) unites organisms that possess similar morphologies. B) conforms to traditional, Linnaean taxonomic practices. C) reflects evolutionary history. D) corroborates the classification scheme in use at the time of Charles Darwin. E) reflects the basic separation of prokaryotes from eukaryotes.

C

Which of the following pairs are the best examples of homologous structures? A) bat wing and human hand B) owl wing and hornet wing C) porcupine quill and cactus spine D) bat forelimb and bird wing E) Australian mole and North American mole

A

Some molecular data place the giant panda in the bear family (Ursidae) but place the lesser panda in the raccoon family (Procyonidae). Consequently, the morphological similarities of these two species are probably due to A) inheritance of acquired characteristics. B) sexual selection. C) inheritance of shared derived characters. D) possession of analogous structures. E) possession of shared primitive characters.

D

In angiosperm plants, flower morphology can be very intricate. If a tree, such as a New Mexico locust, has flowers that share many morphological intricacies with flowers of the sweet pea vine, then the most likely explanation for these floral similarities is the same general explanation for the similarities between the A) dorsal fins of sharks and of dolphins. B) reduced eyes of Australian moles and North American moles. C) scales on moth wings and the scales of fish skin. D) cranial bones of humans and those of chimpanzees. E) adaptations for flight in birds and adaptations for flight in bats.

D

The importance of computers and of computer software to modern cladistics is most closely linked to advances in A) light microscopy. B) radiometric dating. C) fossil discovery techniques. D) Linnaean classification. E) molecular genetics.

E

Which mutation should least require realignment of homologous regions of a gene that is common to several related species? A) 3-base insertion B) 1-base substitution C) 4-base insertion D) 1-base deletion E) 3-base deletion

B

The common ancestors of birds and mammals were very early (stem) reptiles, which almost certainly possessed 3-chambered hearts (2 atria, 1 ventricle). Birds and mammals, however, are alike in having 4-chambered hearts (2 atria, 2 ventricles). The 4-chambered hearts of birds and mammals are best described as A) structural homologies. B) vestiges. C) homoplasies. D) the result of shared ancestry. E) molecular homologies.

C

Generally, within a lineage, the largest number of shared derived characters should be found among two organisms that are members of the same A) kingdom. B) class. C) domain. D) family. E) order.

D

Which of the following is not true of all horizontally oriented phylogenetic trees, where time advances to the right? A) Each branch point represents a point in absolute time. B) Organisms represented at the base of such trees are ancestral to those represented at higher levels. C) The more branch points that occur between two taxa, the more divergent their DNA sequences should be. 9 D) The common ancestor represented by the rightmost branch point existed more recently in time than the common ancestors represented at branch points located to the left. E) The more branch points there are, the more taxa are likely to be represented.

A

Ultimately, which of these serves as the basis for both the principle of maximum parsimony and the principle that shared complexity indicates homology rather than analogy? A) the laws of thermodynamics B) Boyle's law C) the laws of probability D) chaos theory E) Hutchinson's law

C

Shared derived characters are most likely to be found in taxa that are A) paraphyletic. B) polyphyletic. C) monophyletic.

C

A taxon, all of whose members have the same common ancestor, is A) paraphyletic. B) polyphyletic. C) monophyletic.

C

The term that is most appropriately associated with clade is A) paraphyletic. B) polyphyletic. C) monophyletic.

C

If birds are excluded from the class Reptilia, the term that consequently describes the class Reptilia is A) paraphyletic. B) polyphyletic. C) monophyletic.

A

If the eukaryotic condition arose, independently, several different times during evolutionary history, and if ancestors of these different lineages are extant and are classified in the domain Eukarya, then the domain Eukarya would be A) paraphyletic. B) polyphyletic. C) monophyletic.

B

When using a cladistic approach to systematics, which of the following is considered most important for classification? A) shared primitive characters B) analogous primitive characters C) shared derived characters D) the number of homoplasies E) overall phenotypic similarity

C

The four-chambered hearts of birds and the four-chambered hearts of mammals evolved independently of each other. If one were unaware of this independence, then one might logically conclude that A) the birds were the first to evolve a 4-chambered heart. B) birds and mammals are more distantly related than is actually the case. C) early mammals possessed feathers. D) the common ancestor of birds and mammals had a four-chambered heart. E) birds and mammals should be placed in the same family.

D

Phylogenetic hypotheses (such as those represented by phylogenetic trees) are strongest when 11 A) they are based on amino acid sequences from homologous proteins, as long as the genes that code for such proteins contain no introns. B) each clade is defined by a single derived character. C) they are supported by more than one kind of evidence, such as when fossil evidence corroborates molecular evidence. D) they are accepted by the foremost authorities in the field, especially if they have won Nobel Prizes. E) they are based on a single DNA sequence that seems to be a shared derived sequence.

C

Cladograms (a type of phylogenetic tree) constructed from evidence from molecular systematics are based on similarities in A) morphology. B) the pattern of embryological development. C) biochemical pathways. D) habitat and lifestyle choices. E) mutations to homologous genes.

E

A researcher wants to determine the genetic relatedness of several breeds of dog (Canis familiaris). The researcher should compare homologous sequences of __________ that are known to be __________. A) carbohydrates; poorly conserved B) fatty acids; highly conserved C) lipids; poorly conserved D) proteins or nucleic acids; poorly conserved E) amino acids; highly conserved

D

Concerning growth in genome size over evolutionary time, which of these does not belong with the others? A) orthologous genes 13 B) gene duplications C) paralogous genes D) gene families

A

Nucleic acid sequences that undergo few changes over the course of evolutionary time are said to be conserved. Conserved sequences of nucleic acids A) are found in the most crucial portions of proteins. B) include all mitochondrial DNA. C) are abundant in ribosomes. D) are proportionately more common in eukaryotic introns than in eukaryotic exons. E) comprise a larger proportion of pre-mRNA (immature mRNA) than of mature mRNA.

C

Species that are not closely related and that do not share many anatomical similarities can still be placed together on the same phylogenetic tree by comparing their A) plasmids. B) chloroplast genomes. C) mitochondrial genomes. D) homologous genes that are poorly conserved. E) homologous genes that are highly conserved.

E

Which kind of DNA should provide the best molecular clock for gauging the evolutionary relatedness of several species whose common ancestor became extinct billions of years ago? A) that coding for ribosomal RNA B) intronic DNA belonging to a gene whose product performs a crucial function C) paralogous DNA that has lost its function (i.e., no longer codes for functional gene product) D) mitochondrial DNA E) exonic DNA that codes for a non-crucial part of a polypeptide

A

A phylogenetic tree constructed using sequence differences in mitochondrial DNA would be most valid for discerning the evolutionary relatedness of A) archaeans and bacteria. B) fungi and animals. C) Hawaiian silverswords. D) sharks and dolphins E) mosses and ferns.

C

The lakes of northern Minnesota are home to many similar species of damselflies of the genus Enallagma that have apparently undergone speciation from ancestral stock since the last glacial retreat about 10,000 years ago. Sequencing which of the following would probably be most useful in sorting out evolutionary relationships among these closely related species? A) nuclear DNA B) mitochondrial DNA C) small nuclear RNA D) ribosomal RNA E) amino acids in proteins

B

Which statement represents the best explanation for the observation that the nuclear DNA of wolves and domestic dogs has a very high degree of homology? A) Dogs and wolves have very similar morphologies. B) Dogs and wolves belong to the same order. C) Dogs and wolves are both members of the order Carnivora. D) Dogs and wolves shared a common ancestor very recently. E) Convergent evolution has occurred.

D

The reason that paralogous genes can diverge from each other within the same gene pool, whereas orthologous genes diverge only after gene pools are isolated from each other, is that A) having multiple copies of genes is essential for the occurrence of sympatric speciation in the wild. B) paralogous genes can occur only in diploid species; thus, they are absent from most prokaryotes. C) polyploidy is a necessary precondition for the occurrence of sympatric speciation in the wild. D) having an extra copy of a gene permits modifications to the copy without loss of the original gene product.

D

If the genes of yeast are 50% orthologous to those of humans, and if the genes of mice are 99% orthologous to those of humans, then what percentage of the genes of fish might one validly predict to be orthologous to the genes of humans? A) 10% B) 30% C) 40% D) 50% E) 80%

E

What is true of gene duplication (NOTE: gene duplication is a process that is distinct from DNA replication)? 17 A) It is a type of point mutation. B) Its occurrence is limited to diploid species. C) Its occurrence is limited to organisms without functional DNA-repair enzymes. D) It is most similar in its effects to a deletion mutation. E) It can increase the size of a genome over evolutionary time.

E

Paralogous genes that have lost the function of coding for a functional gene product are known as "pseudogenes." Which of these is a valid prediction regarding the fate of pseudogenes over evolutionary time? A) They will be preserved by natural selection. B) They will be highly conserved. C) They will ultimately regain their original function. D) They will be transformed into orthologous genes. E) They will have relatively high mutation rates.

E

Theoretically, molecular clocks are to molecular phylogenies as radiometric dating is to phylogenies that are based on the A) fossil record. B) geographic distribution of extant species. C) morphological similarities among extant species. D) amino acid sequences of homologous polypeptides.

A

The most important feature that permits a gene to act as a molecular clock is A) having a large number of base pairs. B) having a larger proportion of exonic DNA than of intronic DNA. C) having a reliable average rate of mutation. D) its recent origin by a gene-duplication event. E) its being acted upon by natural selection

C

Neutral theory proposes that A) molecular clocks are more reliable when the surrounding pH is close to 7.0. B) most mutations of highly conserved DNA sequences should have no functional effect. 18 C) DNA is less susceptible to mutation when it codes for amino acid sequences whose side groups (or R groups) have a neutral pH. D) DNA is less susceptible to mutation when it codes for amino acid sequences whose side groups (or R groups) have a neutral electrical charge. E) a significant proportion of mutations is not acted upon by natural selection.

E

When it acts upon a gene, which of these processes consequently makes that gene an accurate molecular clock? A) transcription B) directional natural selection C) mutation D) proofreading E) reverse transcription

B

Which of these would, if it had acted upon a gene, prevent this gene from acting as a reliable molecular clock? A) neutral mutations B) genetic drift C) mutations within introns D) natural selection E) most substitution mutations involving an exonic codon's 3rd position

D

The HIV genome's reliably high rate of change permits it t o serve as a molecular clock. Which of these features is most responsible for this genome's high rate of change? A) the relatively low number of nucleotides in the genome B) the relatively small number of genes in the genome C) the genome's ability to insert itself into the genome of the host D) the lack of proofreading by the enzyme that converts HIV's RNA genome into a DNA genome

D

Which process hinders clarification of the deepest branchings in a phylogenetic tree that depicts the origins of the three domains? A) binary fission B) mitosis C) meiosis D) horizontal gene transfer E) gene duplication

D

What kind of evidence has recently made it necessary to assign the prokaryotes to either of two different domains, rather than assigning all prokaryotes to the same kingdom? A) molecular B) behavioral C) nutritional D) anatomical E) ecological

A

What important criterion was used in the late 1960s to distinguish between the three multicellular eukaryotic kingdoms of the five-kingdom classification system? A) the number of cells present in individual organisms B) the geological stratum in which fossils first appear C) the nutritional modes they employ D) the biogeographic province where each first appears E) the features of their embryos

C

Which is an obsolete kingdom that includes prokaryotic organisms? A) Plantae B) Fungi C) Animalia D) Protista E) Monera

E

Members of which kingdom have cell walls and are all heterotrophic? A) Plantae B) Fungi C) Animalia D) Protista E) Monera

B

Which kingdom has been replaced with two domains? A) Plantae B) Fungi C) Animalia D) Protista E) Monera

E

Which eukaryotic kingdom is polyphyletic and therefore not acceptable, based on cladistics? A) Plantae B) Fungi C) Animalia D) Protista E) Monera

D

Which eukaryotic kingdom includes members that are the result of endosymbioses that included an ancient proteobacterium and an ancient cyanobacterium? A) Plantae B) Fungi C) Animalia D) Protista E) Monera

A

The human nuclear genome includes hundreds of genes that are orthologs of bacterial genes, and hundreds of other genes that are orthologs of archaean genes. This finding can be explained by proposing that A) neither archaea nor bacteria contain paralogous genes. B) the eukaryotic lineage leading to humans involved at least one fusion of an ancient bacterium with an ancient archaean. C) the infection of humans by bacteriophage introduced prokaryotic genes into the human genome. D) horizontal gene transfer did not occur to any significant extent among the prokaryotic ancestors of humans.

B

Which process is observed in prokaryotes and is responsible for the vertical components of the various bacterial and archaean lineages? A) mitosis B) meiosis C) sexual reproduction D) binary fission

D

Which of these processes can be included among those responsible for the horizontal components of this phylogeny? A) endosymbiosis B) mitosis C) binary fission D) point mutations E) S phase of the cell cycle

A

Which portion of this tree may ultimately be better depicted as a "ring"? A) the bacterial lineage B) the archaean lineage C) the eukaryotic lineage D) the weblike part near the base of the tree E) the part corresponding to the first living cell on Earth

D

A large proportion of archaeans are "extremophiles," so called because they inhabit extreme environments with high acidity and/or high temperature. Such environments are thought to have been much more common on the primitive Earth. Thus, modern extremophiles survive only in places that their ancestors became adapted to long ago. Which of these is, consequently, a valid statement about modern extremophiles, assuming that their habitats have remained relatively unchanged? A) Among themselves, they should share relatively few ancestral traits, especially those that enabled ancestral forms to adapt to extreme conditions. B) On a phylogenetic tree whose branch lengths are proportional to amount of genetic change, the branches of the extremophiles should be shorter, relative to branches of the nonextremophilic archaeans. C) They should contain genes that originated in eukaryotes that are the hosts for numerous species of bacteria. D) They should currently be undergoing a high level of horizontal gene transfer with nonextremophilic archaeans.

B

In Figure 26.4 from your textbook, which similarly inclusive taxon descended from the same common ancestor as Canidae? A) Felidae B) Mustelidae C) Carnivora D) Canis E) Lutra

B

Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V. A grouping that includes species T, X, Y, and Z makes up A) a valid taxon. B) a monophyletic clade. C) an ingroup, with species U as the outgroup. 26 D) a paraphyletic grouping. E) a polyphyletic grouping.

D

In a comparison of birds with mammals, having four appendages 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. E) a character useful for sorting bird species.

A

If you were using cladistics to build a phylogenetic tree of cats, which of the following would be the best outgroup? A) lion B) domestic cat C) wolf D) leopard E) tiger

C

The relative lengths of the amphibian and mouse branches in the phylogeny in Figure 26.12 in your textbook indicate that A) amphibians evolved before mice. B) mice evolved before amphibians. C) the genes of amphibians and mice have only coincidental homoplasies. D) the homologous gene has evolved more slowly in mice. E) the homologous gene has evolved more rapidly in mice.

D

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) base phylogenetic trees only on the fossil record, as this provides the simplest explanation for evolution. D) choose the tree that represents the fewest evolutionary changes, either in DNA sequences or morphology. E) choose the tree with the fewest branch points.

D

Linnaeus was a "fixist" who believed that species remained fixed in the form in which they had been created. Linnaeus would have been uncomfortable with A) classifying organisms using the morphospecies concept. B) the scientific discipline known as taxonomy. C) phylogenies. D) nested, ever-more inclusive categories of organisms. E) a hierarchical classification scheme.

C

Which of the following is (are) problematic when the goal is to construct phylogenies that accurately reflect evolutionary history? A) polyphyletic taxa B) paraphyletic taxa C) monophyletic taxa D) Two of the responses are correct.

D

Which individual would make the worst systematist? One who is uncomfortable with the A) Linnaean system of classification. B) notion of hypothetical phylogenies. C) PhyloCode method of classification. D) notion of permanent polytomies

B

Which of the following is true of all horizontally oriented phylogenetic trees, where time advances to the right? A) Each branch point represents a point in absolute time. B) Organisms represented at the base of such trees are descendants of those represented at higher levels. C) The fewer branch points that occur between two taxa, the more divergent their DNA sequences should be. D) The common ancestor represented by the rightmost branch point existed more recently in time than the common ancestors represented at branch points located to the left. E) The more branch points there are, the fewer taxa are likely to be represented.

D

There is some evidence that reptiles called cynodonts may have had whisker-like hairs around their mouths. If true, then what can be properly said of hair? A) It is a shared derived character of mammals, even if cynodonts continue to be classified as reptiles. B) It is a shared derived character of the amniote clade, and not of the mammal clade. C) It is a shared ancestral character of the amniote clade, but only if cynodonts are reclassified as mammals. D) It is a shared derived character of the mammals, but only if cynodonts are reclassified as mammals

D

A phylogenetic tree constructed using sequence differences in mitochondrial DNA would be most valid for discerning the evolutionary relatedness of A) archaeans and bacteria. B) fungi and animals. C) chimpanzees and humans. D) sharks and dolphins. E) mosses and ferns. A phylogenetic tree constructed using sequence differences in mitochondrial DNA would be most valid for discerning the evolutionary relatedness of A) archaeans and bacteria. B) fungi and animals. C) chimpanzees and humans. D) sharks and dolphins. E) mosses and ferns.

C

Which statement represents the best explanation for the observation that the nuclear DNA of wolves and domestic dogs has a very high degree of sequence homology? A) Dogs and wolves have very similar morphologies. B) Dogs and wolves belong to the same order. C) Dogs and wolves are both members of the order Carnivora. D) Dogs and wolves shared a common ancestor very recently.

D

What kind of evidence has recently made it necessary to assign the prokaryotes to either of two different domains, rather than assigning all prokaryotes to the same kingdom? A) molecular B) behavioral C) nutritional D) anatomical E) ecological

A

What important criterion was used in the late 1960s to distinguish between the three multicellular eukaryotic kingdoms of the five-kingdom classification system? A) the number of cells present in individual organisms B) the geological stratum in which fossils first appear C) the nutritional modes they employ D) the biogeographic province where each first appears E) the features of their embryos

C

Traditionally, zoologists have placed birds in their own class, Aves. More recently, molecular evidence has shown that birds are more closely related to reptiles than their anatomy reveals. Genetically, birds are more closely related to crocodiles than crocodiles are to turtles. Thus, bird anatomy has become highly modified as they have adapted to flight, without their genes having undergone nearly as much change. 62) Taxonomically, what should be done with the birds? A) The traditional stance is correct. Such dramatic morphological change as undergone by birds merits that the birds be placed in their own order, separate from the reptiles. B) The birds should be reclassified, and their new taxon should be the subclass Aves. Genetic similarity trumps morphological dissimilarity. C) The rest of the reptiles should be reclassified as a subclass within the class Aves. D) Science is consensual. Taxonomy is a science. Variant classification schemes involving the birds should be tolerated until consensus is reached.

D

Traditional zoologists have long agreed that birds evolved from dinosaurs. What keeps such zoologists from agreeing that birds, like dinosaurs, should be considered reptiles? A) There is not yet enough evidence to be sure. B) Stubbornness, insofar as they are unwilling to change their thinking when new data warrants it. C) They deny the validity of genetic molecular data. D) They differ in what they consider to be important traits for assigning organisms to the class Reptilia.

D

For a proponent of PhyloCode classification, what is true of the reptile clade if birds are not included in it? A) It becomes paraphyletic and, thus, an invalid reflection of evolutionary history. B) It becomes a subclass, instead of a class. C) It becomes a superclass, whereas the birds remain a class. D) PhyloCode does not concern itself with what is, or is not, a clade.

A

Which of the following is the best explanation for the high degree of sequence homology observed in Exon I among these five species? A) It is the most-upstream exon of this gene. B) Due to alternative gene splicing, this exon is often treated as an intron. C) It codes for a polypeptide domain that has a crucial function. D) These five species must actually constitute a single species. E) This exon is rich in G-C base pairs; thus, it is more stable.

C

Regarding these sequence homology data, the principle of maximum parsimony would be applicable in A) distinguishing introns from exons. B) determining degree of sequence homology. C) selecting appropriate genes for comparison among species. D) inferring evolutionary relatedness from the number of sequence differences.

D

Which of these four gene parts should allow the construction of the most accurate phylogenetic tree, assuming that this is the only part of the gene that has acted as a reliable molecular clock? A) Intron I B) Exon I C) Intron VI D) Exon V

C