Microbial Diversity and Molecular Evolution (Ch. 17,
Lec. 15)
Wednesday, November 11, 2020 1:07 AM
• Most of the tree of life is microbial-- only part that isn't is part of Eukarya.
17.1: Origins of Life
• Conditions required to grow cells: essential elements, continua source of energy, temp
range permitting liquid water.
• Stromatolites: bacterial communities that are our earliest forms of life via fossil evidence.
• When earth formed 4billion years ago, microbes came to life 3.8bil yrs ago. When oxygen
abundance was sufficient, environment supported metabolism of microorganisms.
○ Gradually evolved from only cyanobacteria to multicellular organisms.
17.3: Evolution: Phylogeny and Gene Transfer
• Clade: branches of group of related organisms.
○ Each clade is a monophyletic group--share a common ancestor not shared by
outside organisms. -> … -> Species
• Phylogeny: branching divergence for a species.
• Mechanisms of evolution: random mutations, natural selection and adaptation, and
reductive (degenerative) evolution: loss/mutation of DNA encoding unselected traits.
• Molecular clock: based on the acquisition of new random mutations in each round of DNA
replication, we can infer how much time has passed. AKA based on mutation rate!
○ Most widely used clock is the gene that encodes the small subunit rRNA (SSU
rRNA). -> 16S rRNA or 18S rRNA (eukaryotes)
○ Clock requires alignment of homologous sequences in divergent species or strains.
• 16S rRNA has variable and conserved regions-- can design primers against those.
○ Variable regions used to determine bacterial taxonomy.
• Data comparing multiple sequences are calculated by computer programs. Standard
assumptions of these programs: minimum # of changes, functional sequences change more
slowly, 3rd-base codon positions show more random change.
• Phylogenetic tree are based on freq of differences in 16S rRNA (and other homologous)
sequences among species. AKA based on sequence similarity!
○ Divergence data can be used to infer the length of time since 2 species shared a
common ancestor.
• Rooted trees indicate position of the common ancestor (comparison w/ an outgroup);
unrooted trees do not.
• Carl Woese first used SSU (small subunit) rRNA phylogeny to reveal the existence of
Archaea.
• Horizontal/lateral gene transfer: acquiring a piece of DNA from another cell.
○ In prokaryotes, DNA is transferred horizontally by plasmids, transposable elements,
and bacteriophages.
○ Horizontally-transferred DNA can be identified using differences in GC/AT ratio.
○ This type of transfer is so prevalent among microbes that it obscures monophyletic
distinctions among taxa.
• Vertical gene transfer: acquiring of an entire genome from parent to offspring.
• Genomes contains 2 kinds of genes:
1. Informational genes: encode products essential for transcription/translation.
a. Interact w/ many cellular components.
b. Tend to be transferred vertically.
2. Operational genes: encode products that govern metabolism, stress response,
pathogenicity.
a. Tend to be transferred horizontally.
17.4 NS and Adaptation
• Natural selection: functions that help an organisms survive become selected for and
enriched.
○ Mechanisms of NS include: genomic analysis, strongly-selective environments, and
experimental evolution.
• Gene duplications allow paralogous genes or paralogs, to evolve w/ different functions.
• Degenerative (reductive) evolution: occurs when unneeded genes are lost from the
genome.
○ Host-dependent organisms save energy by avoiding their replication/expression.
• Environments under intense selective pressure reveals rapid evolution: antibiotic exposure,
high-temp.
• After exposure to antibiotics-> small-colony variants that show up are resistant to said
antibiotic.
• (Slide 30) The higher the tetracycline (antibiotic) conc, the more resistant generations
grow.
• Experimental evolution: founds a bacterial pop and then grows it under a chosen set of
environmental conditions (to see how it evolves).
○ Typically pop is grown in liquid medium, then diluted into a fresh medium daily.
• Lensky's expt: 1/12 pop became more denser-- had evolved the ability to grow aerobically
on citrate. -> Cit+
○ Data fit model of stages of evolving a new trait: (1) potentiation to achieve useful
mutations, (2) actualization of a novel mutant phenotype, and (3) refinement/INCing
degree of the phenotype.
17.5: Microbial Species and Taxonomy
• Taxonomy: description of life forms and organization into dif categories based on shared
traits. Involves classification, nomenclature, and identification.
• Phylogeny: relationships are based on DNA relatedness.
• Ecology: relationships are based on share traits and ecological niche.
• Working definition of species:
○ SSU rRNA similarity >95% share the same genus.
○ Avg nucleotide identity (ANI) of orthologs >95%.
Lec. 15)
Wednesday, November 11, 2020 1:07 AM
• Most of the tree of life is microbial-- only part that isn't is part of Eukarya.
17.1: Origins of Life
• Conditions required to grow cells: essential elements, continua source of energy, temp
range permitting liquid water.
• Stromatolites: bacterial communities that are our earliest forms of life via fossil evidence.
• When earth formed 4billion years ago, microbes came to life 3.8bil yrs ago. When oxygen
abundance was sufficient, environment supported metabolism of microorganisms.
○ Gradually evolved from only cyanobacteria to multicellular organisms.
17.3: Evolution: Phylogeny and Gene Transfer
• Clade: branches of group of related organisms.
○ Each clade is a monophyletic group--share a common ancestor not shared by
outside organisms. -> … -> Species
• Phylogeny: branching divergence for a species.
• Mechanisms of evolution: random mutations, natural selection and adaptation, and
reductive (degenerative) evolution: loss/mutation of DNA encoding unselected traits.
• Molecular clock: based on the acquisition of new random mutations in each round of DNA
replication, we can infer how much time has passed. AKA based on mutation rate!
○ Most widely used clock is the gene that encodes the small subunit rRNA (SSU
rRNA). -> 16S rRNA or 18S rRNA (eukaryotes)
○ Clock requires alignment of homologous sequences in divergent species or strains.
• 16S rRNA has variable and conserved regions-- can design primers against those.
○ Variable regions used to determine bacterial taxonomy.
• Data comparing multiple sequences are calculated by computer programs. Standard
assumptions of these programs: minimum # of changes, functional sequences change more
slowly, 3rd-base codon positions show more random change.
• Phylogenetic tree are based on freq of differences in 16S rRNA (and other homologous)
sequences among species. AKA based on sequence similarity!
○ Divergence data can be used to infer the length of time since 2 species shared a
common ancestor.
• Rooted trees indicate position of the common ancestor (comparison w/ an outgroup);
unrooted trees do not.
• Carl Woese first used SSU (small subunit) rRNA phylogeny to reveal the existence of
Archaea.
• Horizontal/lateral gene transfer: acquiring a piece of DNA from another cell.
○ In prokaryotes, DNA is transferred horizontally by plasmids, transposable elements,
and bacteriophages.
○ Horizontally-transferred DNA can be identified using differences in GC/AT ratio.
○ This type of transfer is so prevalent among microbes that it obscures monophyletic
distinctions among taxa.
• Vertical gene transfer: acquiring of an entire genome from parent to offspring.
• Genomes contains 2 kinds of genes:
1. Informational genes: encode products essential for transcription/translation.
a. Interact w/ many cellular components.
b. Tend to be transferred vertically.
2. Operational genes: encode products that govern metabolism, stress response,
pathogenicity.
a. Tend to be transferred horizontally.
17.4 NS and Adaptation
• Natural selection: functions that help an organisms survive become selected for and
enriched.
○ Mechanisms of NS include: genomic analysis, strongly-selective environments, and
experimental evolution.
• Gene duplications allow paralogous genes or paralogs, to evolve w/ different functions.
• Degenerative (reductive) evolution: occurs when unneeded genes are lost from the
genome.
○ Host-dependent organisms save energy by avoiding their replication/expression.
• Environments under intense selective pressure reveals rapid evolution: antibiotic exposure,
high-temp.
• After exposure to antibiotics-> small-colony variants that show up are resistant to said
antibiotic.
• (Slide 30) The higher the tetracycline (antibiotic) conc, the more resistant generations
grow.
• Experimental evolution: founds a bacterial pop and then grows it under a chosen set of
environmental conditions (to see how it evolves).
○ Typically pop is grown in liquid medium, then diluted into a fresh medium daily.
• Lensky's expt: 1/12 pop became more denser-- had evolved the ability to grow aerobically
on citrate. -> Cit+
○ Data fit model of stages of evolving a new trait: (1) potentiation to achieve useful
mutations, (2) actualization of a novel mutant phenotype, and (3) refinement/INCing
degree of the phenotype.
17.5: Microbial Species and Taxonomy
• Taxonomy: description of life forms and organization into dif categories based on shared
traits. Involves classification, nomenclature, and identification.
• Phylogeny: relationships are based on DNA relatedness.
• Ecology: relationships are based on share traits and ecological niche.
• Working definition of species:
○ SSU rRNA similarity >95% share the same genus.
○ Avg nucleotide identity (ANI) of orthologs >95%.
