Chapter 16 Lec. 2

Question 1

Evolutionary analysis: Phylogeny

Answer 1

Phylogeny:

• evolutionary history of a group of organisms.
• Can be inferred from nucleotide sequence.

Question 2

Molecular clocks (chronometers)

Answer 2

Certain genes and proteins can act as measures of evolutionary change.
Major assumptions of the approach:
-Mutations-occur at constant rate, neutral or random.

Question 3

Evolutionary analysis: Molecular clocks

Answer 3

Most widely used molecular clocks are small subunit ribosomal RNA genes.

• Found in all domains of life.
• functionally constant
• sufficiently conserved
• sufficient length
• has more and less conserved regions

Question 4

Evolutionary analysis: Carl Woese

Answer 4

Pioneered the use of SSU rRNA for phylogenetic studies in 1970’s.
Established the three domains of life:
-bacteria, archaea and eukaryotes.
Provided phylogenic framework for bacteria.

Question 5

Evolutionary analysis: database project

Answer 5

The ribosomal database project

• Collection of rRNA sequences
• contains >409,00 sequences
• provides variety of analytical programs

Question 6

Evolutionary analysis: Comparative rRNA sequencing

Answer 6

Comparative rRNA sequencing is a routine procedure that involves the following

• amplification of gene rRNA
• sequencing amplified genes
• analysis of sequence

Question 7

Evolutionary analysis: 1st step

Answer 7

1st step: Aligning sequence of interest with sequences from homologous genes from other strains or species.

Question 8

Evolutionary analysis: BLAST

Answer 8

Basic local alignment search tool.

• Aligns query sequence with those in GenBank.
• Helpful for identifying gene sequences.

Question 9

Microbial phylogeny: Domain bacteria

Answer 9

At least 80 major evolutionary groups.
Many groups defined from environmental sequences alone— no cultured reps.
Many groups are phenotypically diverse—physiology and phylogeny not necessarily linked.

Question 10

Microbial phylogeny: eukaryotes and archaea

Answer 10

Eukaryotic organelles originated within bacteria. 
-mitochondria arose from proteobacteria 
-chloroplasts arose from cyanobacteria. 
Archaea consist of two major groups:
-crenarchaeota
-euryarchaeota

Question 11

The species concept in microbiology

Answer 11

Biological species concept not meaningful as prokaryotes are haploid and do not undergo sexual reproduction.
Genealogical species concept is an alternative.
-Prokaryotes are distinct from other groups.

Question 12

The species concept in microbiology: prokaryotes

Answer 12

No universally accepted concept of species for prokaryotes.
Current definition of prokaryotic species
-collection of strains sharing a high degree of similarity in several independent traits.

Question 13

The species concept in microbiology 3: 16s rRNA gene

Answer 13

Lack of divergence of 16S rRNA gene limits effectiveness in discriminating at species level.
Multigene or whole genome approach can be used:
-genome structure: size and number of chromosomes.
-gene content
-geen order

Question 14

The species concept in microbiology: HOW?

Answer 14

Ecotype
-population of cells that share a particular resource.
-different ecotypes can coexist in a habitat.
Bacterial speciation may occur from a combination of repeated periodic selection for a favorable trait

Question 15

The species concept in microbiology: How many?

Answer 15

No firm estimate on the number of prokaryotic species.

Nearly 7000 species of bacteria and archaea currently known.

Question 16

Horizontal gene transfer

Answer 16

Changes everything.