Phylogeny and the Tree of Life Part 2

36) Use the figure to answer the following question. If the figure is an accurate depiction of relatedness, then which of the following should be an accurate statement? A) If all species depicted here make up a taxon, this taxon is monophyletic. B) The species present at position 4 is ancestral to species E, but not species D. C) Species C is more closely related to species B than D is to B D) The species present at position 3 is ancestral to C, D, and E. Answer: A 37) Use the following figure and description to answer the question. Humans, chimpanzees, gorillas, and orangutans are members of a clade called the great apes, which shared a common ancestor about 15 million years ago. Gibbons and siamangs comprise a clade called the lesser apes. Tree-branch lengths indicate elapsed time. Assuming chimps and gorillas are humans' closest relatives, removing humans from the great ape clade and placing them in a different clade has the effect of making the phylogenetic tree of the great apes ________. A) polyphyletic B) paraphyletic C) monophyletic D) into a new order Answer: B 38) The question refers to the following table, which compares the percent sequence homology of four different parts (two introns and two exons) of a gene that is found in five different eukaryotic species. Each part is numbered to indicate its distance from the promoter (for example, Intron I is the one closest to the promoter). The data reported for species A were obtained by comparing DNA from one member of species A to another member of species A. % Sequence Homology Species Intron I Exon I A 100% 100% B 98% 99% C 98% 99% D 99% 99% E 98% 99% Intron VI 100% 82% 89% 92% 80% Exon V 100% 96% 96% 97% 94% Based on the tabular data, and assuming that time advances vertically, which phylogenetic tree is the most likely depiction of the evolutionary relationships among these five species? A) B) C) D) Answer: D 39) The question refers to the following table, which compares the percent sequence homology of four different parts (two introns and two exons) of a gene that is found in five different eukaryotic species. Each part is numbered to indicate its distance from the promoter (for example, Intron I is the one closest to the promoter). The data reported for species A were obtained by comparing DNA from one member of species A to another member of species A. % Sequence Homology Species Intron I Exon I A 100% 100% B 98% 99% C 98% 99% D 99% 99% E 98% 99% Intron VI 100% 82% 89% 92% 80% Exon V 100% 96% 96% 97% 94% 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 Answer: D 40) In a comparison of birds and mammals, 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 Answer: A 41) To apply the principle of maximum parsimony to construction of 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, either in DNA sequences or morphology D) choose the tree with the fewest branch points Answer: C 42) 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 Answer: C 43) Use the figure to answer the following question. The phylogenetic tree shown ________. A) depicts uncertainty about whether the bryophytes or the vascular plants evolved first B) depicts an evolutionary hypothesis C) includes evolution of convergent characteristics D) indicates that seeds are a shared ancestral character of all vascular plants Answer: B 44) Concerning growth in genome size over evolutionary time, which of these is least associated with the others? A) orthologous genes B) gene duplications C) paralogous genes D) gene families Answer: A 45) Eukaryotes 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) mitochondrial genomes C) homologous genes that are poorly conserved D) homologous genes that are highly conserved Answer: D 46) 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 Answer: C 47) The lakes of northern Minnesota are home to many similar species of damselflies of the genus Enallagma. These species have apparently undergone speciation from ancestral stock since the last glacial retreat about 10 thousand years ago. Sequencing which of the following would probably be most useful in sorting out evolutionary relationships among these closely related species? A) conserved regions of nuclear DNA B) mitochondrial DNA C) amino acids in proteins D) ribosomal RNA Answer: B 48) 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? Dogs and wolves ________. A) have very similar morphologies B) belong to the same order C) are both members of the order Carnivora D) share a very recent common ancestor Answer: D 49) 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 Answer: D 50) Which of the following items is most likely to form a simple linear relationship with the number of gene-duplication events, when placed as the label on the vertical axis of the following graph? A) number of mitochondria B) number of cells/organism C) genome size D) phenotypic complexity Answer: C 51) The most important feature that permits a gene to act as a molecular clock is ________. A) a large number of base pairs B) being acted upon by natural selection C) a reliable average rate of mutation D) a recent origin by a gene-duplication event Answer: C 52) Molecular clocks are more reliable when ________. A) the surrounding pH is close to 7.0 B) most mutations of highly conserved DNA sequences should have no functional effect C) the DNA codes for amino acid sequences whose side groups (or R groups) have a neutral pH D) a significant proportion of mutations are not acted upon by natural selection Answer: D 53) Which of the following 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 Answer: D 54) The question refers to the following table, which compares the percent sequence homology of four different parts (two introns and two exons) of a gene that is found in five different eukaryotic species. Each part is numbered to indicate its distance from the promoter (for example, Intron I is the one closest to the promoter). The data reported for species A were obtained by comparing DNA from one member of species A to another member of species A. % Sequence Homology Species Intron I Exon I A 100% 100% B 98% 99% C 98% 99% D 99% 99% E 98% 99% Intron VI 100% 82% 89% 92% 80% Exon V 100% 96% 96% 97% 94% 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 Answer: C 55) Based on cladistics, which eukaryotic kingdom is polyphyletic and, therefore, unacceptable? A) Plantae B) Fungi C) Animalia D) Protista Answer: D 56) Which eukaryotic kingdom includes members that are the result of endosymbioses that included an ancient aerobic bacterium and an ancient cyanobacterium? A) Plantae B) Fungi C) Animalia D) Protista Answer: A 57) A large proportion of archaeans are extremophiles, so called because they inhabit extreme environments with high acidity, salinity, and/or temperature. Such environments are thought to have been much more common on primitive Earth. Thus, modern extremophiles survive only in places that their ancestors became adapted to long ago. Which of the following 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 the amount of genetic change, the branches of the extremophiles should be shorter than the non-extremophilic 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. Answer: B 58) Use the following information to answer the question. Paulinella chromatophora is one of the few cercozoans that is autotrophic, carrying out aerobic photosynthesis with its two elongated "chromatophores." The chromatophores are contained within vesicles of the host cell, and each is derived from a cyanobacterium, though not the same type of cyanobacterium that gave rise to the chloroplasts of algae and plants. A crucial photosynthetic gene of the cyanobacterium that gave rise to the chromatophore is called psaE. This gene is present in the nuclear genome of the cercozoan, but is not in the genome of the chromatophore. This is evidence of ________. A) reciprocal mutations in the chromatophore and nuclear genomes B) horizontal gene transfer from bacterium to eukaryotes C) genetic recombination involving a protist and an archaean D) transduction by a phage that infects both prokaryotes and eukaryotes Answer: B 59) 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) mtDNA B) rRNA genes C) morphological D) ecological Answer: B 60) The following question refers to this phylogenetic tree, depicting the origins of life and the three domains. Horizontal lines indicate instances of gene or genome transfer. A possible phylogenetic tree for the three domains of life. If the early history of life on Earth is accurately depicted by the figure, then which statement is most in agreement with the hypothesis proposed by this tree? A) The last universal common ancestor of all extant species is one individual species. B) The origin of the three domains appears as a polytomy. C) Archaean genomes should not contain genes that originated in bacteria, and vice versa. D) Eukaryotes are more closely related to archaeans than to bacteria. Answer: B 61) The following question refers to this phylogenetic tree, depicting the origins of life and the three domains. Horizontal lines indicate instances of gene or genome transfer. A possible phylogenetic tree for the three domains of life. Which of these processes can be included among those responsible for the horizontal components of the figure? A) endosymbiosis B) mitosis C) binary fission D) point mutations Answer: A 62) A phylogenetic tree is shown for the three domains of life (Eukarya, Archaea, and Bacteria). The tree branches in two directions from the first point, labeled Common ancestor of all life. One branch leads in the direction of Eukarya and Archaea, and the other branch leads to Bacteria. The branch leading to Eukarya and Archaea divide, one branch leading to each domain. The branch leading to Eukarya divides into four branches. One leads to Euglenozoans, and the other three lead to branching points. The first leads to Forams in one direction, and another branching point in the other that leads to Diatoms and Ciliates. The second branching point leads to Red algae in one direction, and a branching point that leads to green algae and land plants in the other direction. The third branching point leads to amoebas in one direction, and a branching point that leads to fungi and animals in the other direction. Land plants, Fungi and Animals are all highlighted. Cyanobacteria were once called blue-green algae because they are photosynthetic. According to the phylogeny shown, the cyanobacteria are more closely related to gram-positive bacteria than to ________. A) proteobacteria B) green algae C) euglenozoans D) crenarcheotes Answer: A 63) Which of the following statements is accurate, at least according to our present knowledge? A) Eukaryotes acquired nuclear genes only in the distant past; these genes can allow survival in anaerobic environments. B) Genes from prokaryotes have been acquired by some eukaryotes; these genes can allow survival in extreme environments. C) Prokaryotes acquired genes from eukaryotes many times; these genes can allow survival in extreme environments. D) Prokaryotes acquired genes from fungi; these genes can allow the digestion of cellulose. Answer: B 64) A phylogenetic tree is shown for the three domains of life (Eukarya, Archaea, and Bacteria). The tree branches in two directions from the first point, labeled Common ancestor of all life. One branch leads in the direction of Eukarya and Archaea, and the other branch leads to Bacteria. The branch leading to Eukarya and Archaea divide, one branch leading to each domain. The branch leading to Eukarya divides into four branches. One leads to Euglenozoans, and the other three lead to branching points. The first leads to Forams in one direction, and another branching point in the other that leads to Diatoms and Ciliates. The second branching point leads to Red algae in one direction, and a branching point that leads to green algae and land plants in the other direction. The third branching point leads to amoebas in one direction, and a branching point that leads to fungi and animals in the other direction. Land plants, Fungi and Animals are all highlighted. Examine the figure. If you were a graduate student trying to develop a thesis project that would resolve polytomies, which of the following groups would you study? A) animals and fungi B) euglenozoans, euryarcheotes, and gram-positive bacteria C) forams, red algae, and amoebas D) red algae, green algae, and cyanobacteria Answer: C 65) If additional DNA sequence evidence shows that yeast genes for synthesizing proteins are more similar to protein-synthesizing genes in bacteria than those in archaea, a modern systematist would ________. A) redraw the phylogeny to show eukaryotes sharing a more recent common ancestor with bacteria than archaea B) redraw the phylogeny to show more recent common ancestry between archaea and yeast than between eukaryotes and archaea C) retain the phylogeny that shows a more recent common ancestor between eukaryotes and archaea D) retain the phylogeny that shows a more recent common ancestor between bacteria and archaea Answer: A 66) Which of the following statements about horizontal gene transfer is accurate? A) Horizontal gene transfer was quite common in the early stages of evolution of life on Earth. B) Horizontal gene transfer among organisms does not occur today. C) Horizontal gene transfer moves only genes that play a role in metabolism. D) Horizontal gene transfer occurs only among closely related organisms. Answer: A 67) The kingdom Monera was dismantled because of which of the following reasons? A) Some Monera contained nuclei in their cells. B) The Monera, as originally constituted, contained both plants and animals. C) The Monera, as originally constituted, was monophyletic. D) Some, but not all, of the organisms in Monera contained DNA sequences that were similar to those of eukaryotes. Answer: D 68) Imagine that you discovered the following information: Feature RNA polymerase Introns Antibiotic sensitivity Membrane Lipids Bacteria small, simple absent sensitive C chains unbranched Archaea complex present insensitive C chains branched Eukaryotes complex present insensitive C chains branched These data would support which of the following conclusions? A) Eukaryotes share a more recent common ancestor with bacteria than with archaea. B) Bacteria are the only one of the three groups that lacks a nucleus. C) Archaea are more similar to bacteria than to eukaryotes. D) Eukaryotes are more similar to archaea than to bacteria. Answer: D Student Edition End-of-Chapter Questions 1) 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. Answer: A 2) 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. Answer: C 3) 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 Answer: B 4) 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. Answer: C 5) 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. Answer: D 6) 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 Answer: A 7) 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. Answer: D