Deck 12: Microbial Evolution and Systematics

Question 1

Which of the following is an assumption used in the molecular clock approach?

A)Nucleotide changes accumulate in a sequence in proportion to time.
B)Nucleotide changes are generally NOT transferred to progeny.
C)Nucleotide changes are NOT random.
D)Nucleotide changes are subject to intense selective pressure.

Answer 1

A

Question 2

If you allowed 10 identical parallel Salmonella cultures to evolve for 10,000 generations under new growth conditions with very little nitrogen,the parallel cultures would

A)evolve identical adaptations to use the nitrogen source provided in the media.
B)not change or adapt very much over this small number of generations.
C)each accumulate different random mutations resulting in different adaptations to use the nitrogen in the media.
D)direct mutations to occur in nitrogen utilization and uptake genes in order to adapt rapidly to the culture conditions.

Answer 2

C

Question 3

A key concept in evolution is that all mutations are

A)random.
B)neutral.
C)deleterious.
D)either deleterious or beneficial.

Answer 3

A

Question 4

Chemical reactions involving ________ have been proposed as energy-yielding reactions for primitive organisms.

A)Fe,O₂,and H₂
B)S,O₂,and H₂
C)S,and O₂
D)S,and H₂

Question 5

Two tubes are inoculated from one test tube of a bacterial culture.The cultures are then transferred every day for 2 months.All of the media and growth conditions are the same in every tube.After 2 months of cultivation,the fitness and genotype frequencies of the populations in the two tubes are compared.The fitness of the two cultures is the same,but the genotype frequencies are very different in the two cultures.How is this possible?

A)Two months is not long enough for different fitness levels to evolve even if the genotype frequencies change.
B)This result is not possible because different genotype frequencies would result in different fitness levels under the same growth conditions.
C)Natural selection caused the evolution of different genotype frequencies within the separate test tubes.
D)Genetic drift within the small populations in the test tubes resulted in different genotype frequencies.

Question 6

Molecular sequencing suggests that mitochondria arose from a group of prokaryotic organisms within the

A)Crenarchaeota.
B)cyanobacteria.
C)iron-oxidizing bacteria.
D)Proteobacteria.

Question 7

What two gases were most abundant on early Earth?

A)O₂ and CO₂
B)N₂ and H₂
C)CO₂ and H₂
D)CO₂ and N₂

Question 8

LUCA is

A)the last universal common ancestor.
B)the individual ancestor of each of the three domains.
C)actually somewhat of a misnomer because it is now believed that each of the domains arose independently.
D)All of the answers are correct.

Question 9

The earliest stromatolites were probably formed by

A)anoxygenic phototrophs.
B)anoxygenic lithotrophs.
C)oxygenic phototrophs.
D)oxygenic lithotrophs.

Question 10

The most widely used molecule in sequence-based evolutionary analyses are ________ genes.

A)ATPase
B)electron transport
C)SSU rRNA
D)tRNA

Question 11

Evolution is driven by

A)random mutation.
B)novel metabolic pathways.
C)selection pressure.
D)selection pressure applied to random mutation.

Question 12

Both deletions and insertions occur during the evolution of microbial genomes.Insertions bring in new genes that may be useful for the cell,but deletions

A)may increase fitness of a microorganism by eliminating unneeded genes.
B)always result in a severe loss of fitness for the microorganism.
C)are uncommon because they are usually lethal.
D)always result in a severe loss of fitness but keep microbial genomes compact.

Question 13

The earliest RNA probably functioned in

A)catalysis.
B)self-replication.
C)both catalysis and self-replication.
D)neither catalysis nor self-replication.

Question 14

Compared with today,the temperature on Earth during its first half-billion years was probably

A)considerably warmer.
B)considerably colder.
C)about the same as today.
D)about the same as today on average,but the diurnal fluctuations were much greater.

Question 15

A sequence variant of a gene is called a(n)

A)allele.
B)mutation.
C)nucleotide polymorphism.
D)ribotype.

Question 16

A monophyletic group is a group that

A)descended from one ancestor.
B)has the same fitness level.
C)possesses one taxonomic trait that is the same.
D)shares one phylogenetic marker.

Question 17

Microorganisms were probably restricted to the oceans and subsurface environments until

A)aquatic life brought them onto land.
B)chemoorganotrophy developed.
C)phototrophy evolved.
D)the ozone layer was made.

Question 18

Which statement most closely expresses our present understanding?

A)The chloroplast is an ancestor of the cyanobacteria.
B)The cyanobacteria are descendents of the chloroplast.
C)The chloroplast arose from the incorporation of a cyanobacterial-like organism.
D)The chloroplast and the cyanobacteria are not closely (or specifically)related.

Question 19

Horizontal gene transfer

A)is so rare over evolutionary history that it is not considered when examining microbial evolution.
B)occurs within bacterial species.
C)complicates the construction of phylogenetic trees and the interpretation of specific traits in relation to evolution.
D)only affects the evolution of plasmids.

Question 20

Polyphasic taxonomy uses methods that include

A)phenotypic methods.
B)genotypic methods.
C)phylogenetic methods.
D)phenotypic,genotypic,and phylogenetic methods.

Question 21

You are studying 12 new isolates from the human skin.The isolates have 16S rRNA sequences that are 97% similar and share important phenotypic traits.Their genomes have 55% of their genes in common.The isolates would most likely be

A)classified as individual strains of the same species.
B)classified as individual species of the same genus.
C)split into different families.
D)classified as the same species if they can mate via conjugation.

Question 22

Microbial ________ studies the diversity of microorganisms and links their phylogeny with ________.

A)taxonomy / genotype
B)phylogeny / phenotype
C)taxonomy / phenotype
D)systematics / taxonomy

Question 23

The first catalytic and self-replication biological molecule was most likely

A)RNA.
B)DNA.
C)proteins.
D)ATP.

Question 24

Because DNA:DNA hybridization reveals subtle differences in genes,it is useful for differentiating organisms from different

A)domains.
B)families.
C)orders.
D)strains or species.

Question 25

Based on the phylogenetic tree below,which of the following statements is FALSE?

A)Species E is more closely related to species A than to species D.
B)Species D is more closely related to species C than to species E.
C)Species F is more closely related to species D than to species E.
D)Species C is more closely related to species B than to species D.

Question 26

What characteristics make a gene a good candidate for determining the evolutionary relationships between organisms?

A)highly conserved
B)universally distributed
C)transferred horizontally between species
D)highly conserved and universally distributed

Question 27

The early energy reactions used hydrogen,which is a powerful ________ and could have been used to form ________.

A)oxidant / the proton motive force
B)electron donor / the proton motive force
C)electron acceptor / oxygen
D)oxidant / oxygen

Question 28

The pan genome of a microbial species is constantly changing because of

A)bottleneck events.
B)horizontal gene transfer.
C)substitutions.
D)substitution and bottleneck events.

Question 29

What was produced by photosynthesis before the cyanobacterial lineage developed on Earth?

A)oxygen
B)elemental sulfur
C)ferrous iron
D)hydrogen sulfide

Question 30

Microbial species have a core genome and a pan genome.What is the difference between the two?

A)The core genome consists of all the nucleic acid polymerases and translation enzymes,while the pan genome consists of all the biosynthetic pathways.
B)The core genome is the set of genes within the mitochondria,while the pan genome is the set of genes in the nucleus of a species.
C)The core genome is a set of genes shared by all members of a species,while the pan genome includes the core genes as well as genes that are not shared by all members.
D)The core genome is the set of genes introduced by horizontal gene transfer,while the pan genome is the set of genes that is not transferred horizontally.

Question 31

________ formed the semipermeable membrane-like surfaces for the earliest life forms.

A)Proteins
B)Hydrogen sulfide
C)Lipid bilayers
D)RNA

Question 32

It is believed that phototrophy arose approximately 3.3 billion years ago in

A)Bacteria.
B)Archaea.
C)Eukarya.
D)LUCA.

Question 33

As oxygen appeared in the atmosphere,________ also accumulated,which formed a protective barrier that protects the Earth from ________.

A)ozone / UV radiation
B)elemental sulfur / volcanism
C)ferrous iron / hydroxylating radicals
D)sulfate / hydrogen sulfide

Question 34

Which taxonomic tool would scientists use if they wanted to determine if an outbreak of food poisoning was caused by a particular strain of a pathogen?

A)fluorescence in situ hybridization
B)DNA:DNA hybridization
C)multilocus sequence typing
D)fatty acid methyl ester analysis

Question 35

Oxygen did not accumulate in the early atmosphere until it reacted with reduced materials,especially ________,in the oceans.

A)hydrogen
B)elemental sulfur
C)ferrous iron
D)nitrate

Question 36

Which of the following statements is FALSE concerning the universal tree of life?

A)Previous versions of the universal tree of life were based largely on fossils and comparative biology,which overlooked the diversity of and relationships between most prokaryotes.
B)The current universal tree of life is supported by multiple genes including SSU rRNA sequences.
C)The current universal tree of life depicts three domains of life,two of which are prokaryotic.
D)The current universal tree of life is based on molecular sequences and completely changes our view of evolutionary relationships between eukaryotic species.

Question 37

Ribotyping

A)bypasses sequencing and sequence alignments.
B)exploits unique DNA restriction patterns.
C)allows discrimination between species and different strains of a species.
D)bypasses sequencing and sequence alignments,exploits unique DNA restriction patterns,and allows discrimination between species and different strains of a species.

Question 38

The oxic atmosphere created conditions that led to the evolution of various new metabolic pathways,such as

A)sulfide oxidation.
B)nitrification.
C)iron oxidation.
D)sulfide oxidation,nitrification,and iron oxidation.

Question 39

Which is NOT a characteristic of a "primitive" state of microbial evolution?

A)hyperthermophilic
B)aerobic metabolism
C)small genome
D)branching near the root of the evolutionary tree of life

Question 40

Two eukaryotic organelles that are hypothesized to be the result of endosymbiosis are the ________ and the ________.

A)nucleus / Golgi body
B)mitochondrion / chloroplast
C)endoplasmic reticulum / Golgi body
D)hydrogenosome / chloroplast

Question 41

In taxonomy,family is a more general term than order.

Question 42

At present there are four phyla in the domain Bacteria.

Question 43

Prior to rRNA sequencing and the use of molecular phylogeny,Bacteria and Archaea were classified as in a single group of simple organisms called the Monera.

Question 44

One widely used cladistic method of examining evolutionary relationships is ________,which is based on the assumption that evolution is most likely to have proceeded by the path requiring fewest changes.

A)topology
B)neighbor joining
C)parsimony
D)systematics

Question 45

Two organisms containing identical GC ratios are not necessarily related.

Question 46

Sequencing technology and molecular phylogenetic analyses have had very little impact on our understanding of the evolution and diversity of life on Earth.

Question 47

The evolutionary history of a group of organisms is called its ________ and it is inferred from ________.

A)taxonomy / phenotype
B)phylogeny / nucleotide sequence data
C)phylogeny / phenotype
D)taxonomy / morphology

Question 48

The atmosphere of primitive Earth is usually classified as an oxidizing atmosphere.

Question 49

Most bacterial phyla lack strong phenotypic cohesiveness.

Question 50

DNA:DNA hybridization is a sensitive method for revealing subtle genetic differences because it measures the degree of sequence similarity between two genomes.

Question 51

The establishment of DNA as the genome of the cell may have resulted from the need to store genetic information in a more stable form than RNA.

Question 52

Systematic analysis now commonly includes ________ to identify,characterize,and determine relationships between new strains of bacterial species.

A)whole genome analysis
B)microscopy
C)staining
D)pigments

Question 53

Multilocus sequence typing involves sequencing several different

A)genomes.
B)housekeeping genes.
C)tRNA genes.
D)rRNA genes.

Question 54

The domains of life arose as barriers between gene exchange evolved between organisms.

Question 55

The hyperthermophilic members of the Crenarchaeota branch very close to the root of the universal tree.

Question 56

Eukaryotes originated after the rise in atmospheric oxygen.

Question 57

The earliest nucleic acid was probably a simple DNA molecule.

Question 58

Microbial species are difficult to define because they are often polyphyletic.

Question 59

One phenotypic trait used for species identification and description is the analysis of the types and proportions of the fatty acids present in the cytoplasmic and outer membranes.The methodology employed is often nicknamed FAME.

Question 60

The 16S rRNA sequence is an approximately 1,500 bp linear strand of single stranded RNA.

Question 61

Lateral gene transfer is one plausible explanation as to why organisms in Archaea,Bacteria,and Eukarya still share so many genes among such distinct domains.

Question 62

Can gene frequencies change in the absence of selection? Why or why not?

Question 63

All unicellular organisms belong to the same domain of life.

Question 64

Approximately 4 billion years ago Archaea and Bacteria diverged as being distinct from each other.

Question 65

Rhodobacter cells perform photosynthesis in the presence of light and grow heterotrophically in the dark.After being cultured in total darkness for multiple generations phenotypic and genotypic changes occur.What phenotypic changes occur and what evolutionary processes are driving them?

Question 66

How does the Black Queen Hypothesis explain the effect of gene deletions on bacterial evolution?

Question 67

Draw a rooted phylogenetic tree containing seven organisms labeled A to G.Label your tree with the following terms: branches,extant taxa,nodes,last common ancestor,and an outgroup.

Question 68

You have isolated a microbe from an environmental sample.The microbe has the ability to perform a new metabolic reaction at a very low temperature,so you are excited that it could be a new species.What experiments should you perform to determine if your isolate is truly a new species? What process will you follow to officially name your isolate?

Question 69

How did cyanobacteria,oxygen,and ozone impact the evolution of eukaryotic cells?

Question 70

Why is the biological species concept useful for Eukarya but not meaningful for Archaea and Bacteria? How are prokaryotic species defined?

Question 71

Carl Woese was an important figure in microbial classification and changed our understanding of the evolution and diversity of life.What breakthrough did he make that allowed us to infer evolutionary relationships between organisms? What assumptions was his breakthrough based on?

Question 72

The primary domains were founded based on comparative ribosomal RNA gene sequencing.

Question 73

Life is believed to have originated at hydrothermal springs on the ocean floor rather than on near the surface of Earth.What conditions made the hydrothermal springs the likely place for the beginning of life? Relate the conditions of the early oceans to the likely metabolism of the first cells.

Question 74

Explain the endosymbiotic theory.What is the evolutionary value of endosymbiosis?

Question 75

Draw a graph of relative fitness and number of mutations of an evolving strain versus the ancestral strain over 20,000 generations under the same growth conditions.Explain the change in fitness and mutations over time using evolutionary concepts and terms.

Question 76

Oxygen was a driving factor in the formation of eukaryotic cells.

Question 77

Construct a chart to demonstrate the molecular features of the primary domains of life.Why are there overlapping or shared molecular features between all three domains? Relate the shared and unique molecular features of each domain to early evolution,the last universal common ancestor (LUCA),and the evolution of the three domains

Question 78

When exposed to UV light,oxygen gas produces ozone gas.

Question 79

Explain the strengths and limitations of using 16S rRNA for phylogenetic analyses.

Question 80

Describe the hydrogen hypothesis and why it is favored over other hypotheses.