Question 1

Which of the following best describes the primary method for constructing a phylogenetic tree among prokaryotes?

Accepted Answer

Analyzing sequence differences due to mutations (substitutions) in conserved genes.

Question 2

Why is the small subunit ribosomal RNA (SSU rRNA) gene commonly used in phylogenetic studies of prokaryotes?

Accepted Answer

It is present in all organisms, highly conserved, and has a similar mutation rate across taxa.

Question 3

Given the following SSU rRNA sequence similarities between four bacterial strains: (1) and (2) = 93%, (1) and (3) = 90%, (1) and (4) = 83%, what is the percent divergence between strain (1) and strain (4)?

Accepted Answer

$$100\% - 83\% = 17\%$$

Question 4

Which of the following is NOT a characteristic of a good gene for building a phylogeny?

Accepted Answer

It should primarily be acquired through horizontal gene transfer.

Question 5

What is the main advantage of using phylogenomics (multiple genes) over single-gene phylogenies?

Accepted Answer

It buffers against differences in evolutionary rates among individual genes, providing a more robust phylogeny.

Question 6

Which metabolic process is unique to Archaea and absent in Bacteria?

Accepted Answer

Methanogenesis.

Question 7

A newly discovered microbe has a circular chromosome, ether-linked membrane lipids, and can survive in high-salt environments. To which domain does it most likely belong?

Accepted Answer

Archaea

Question 8

Which of the following best explains the concept of a bacterial pangenome?

Accepted Answer

The total gene repertoire of a microbial species, including both core and accessory genes.

Question 9

Which statement correctly distinguishes core genes from accessory genes in a bacterial pangenome?

Accepted Answer

Core genes are found in all strains and are essential for basic functions, while accessory genes are found in some strains and provide specialized, adaptive traits.

Question 10

Which of the following is a major challenge in defining microbial species compared to eukaryotic species?

Accepted Answer

Microbes do not reproduce sexually, so species cannot be defined by the ability to produce fertile offspring.

Question 11

A scientist is studying two bacterial isolates. Their SSU rRNA sequences are 99% identical, and their average nucleotide identity (ANI) score is 96%. According to the provided criteria, how should these isolates be classified?

Accepted Answer

They are the same species.

Question 12

Which of the following best describes convergent evolution in microbial taxonomy?

Accepted Answer

Traits that arise independently in unrelated lineages due to adaptation to similar environments, leading to analogous (polyphyletic) traits.

Question 13

Which group of bacteria is responsible for producing the majority of Earth's oxygen through photosynthesis?

Accepted Answer

Cyanobacteria

Question 14

A bacterium is found to have a thick peptidoglycan layer, is resistant to antibiotics, and forms spores. To which group does it most likely belong?

Accepted Answer

Firmicutes

Question 15

Which of the following is a defining feature of Euryarchaeota?

Accepted Answer

They are the only Archaea capable of methanogenesis.

Question 16

What makes Asgardarchaeota particularly significant in evolutionary studies?

Accepted Answer

Their close evolutionary relationship to eukaryotes, containing eukaryotic-like genes.

Question 17

Which of the following membrane lipid types is characteristic of Archaea and contributes to their stability in extreme environments?

Accepted Answer

Ether-linked isoprenoids

Question 18

A newly discovered archaeon has a highly reduced genome, lacks many biosynthetic pathways, and is found attached to another archaeal cell in a deep-sea vent. Which group does it most likely belong to?

Accepted Answer

Nanoarchaeota

Question 19

Which of the following best explains why machine learning applied to archaeal proteomes is promising for antibiotic discovery?

Accepted Answer

Archaeal proteins have distinct compositional traits, and machine learning can identify novel antimicrobial peptides not found in bacteria.

Prokaryotes: Origins, Diversity, and Phylogenetic Analysis

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