1. Announcements

2. Prokaryotic diversity

3. We’re covered in germs: Lets design for that.

4. Learning outcomes
Be able to compare and contrast archaea, bacteria and eukarya
Explain the evolutionary relationships between these three domains of life and the most recent evidence for it.
Identify the major divisions of bacteria and archaea and describe the broad characteristics of each
Explain why we cannot do this for every division
Determine which traits (if any) can be used reliably to determine the relationships between microorganisms

5. How we use evolutionary relationships to discover the diversity of life
And why we don’t even know about most of it

6. Early work on prokaryotic diversity
Describe
Isolate
Study

7. Great plate-count anomaly

8. Molecular methods for diversity

9. How and why we infer relationships among species

10. We can do the same analysis with DNA
Each nucleotide is a ‘character’.
ATTCCGCTACTCCTTGAGA
ATTACGCTACTCCATGAGA

11. Phylogenetic analysis process

12. From Alignment to Tree Pairwise Distance (Divergence) Matrix (1) (2)
(3)
(4) 7 10 17
(1, 2)
(3)
(4) 10 17
((1, 2), 3)
(4) 17

13. Understanding A tree
TIP
BRANCH
NODE
(1)
(2)
(3)
(4)

14. Understanding A tree (1) (2) (3) (4) (1) (2) (3) (4) Time Time
(1) (2) (3) (4)
Time
(1)
(2)
(3)
(4)
Time
(1) (2) (3) (4)

15. Understanding A tree (1)
A. Who is Species (1) most closely related to?
B. Who is Species (3) most closely related to?
C. Species (4) is more closely related to Species (3) than it is to Species (2). True/False?
(2)
(3)
(4)

16. Understanding A tree (1) (2) (3) (4) Is this the same tree? (2) (1)

17. Understanding A tree (1) (2) (3) (4) Is this the same tree?
How about this?
(3) (1) (2) (4)
(2)
(1)
(3)
(4)

18. Which sequences should we look at in microbiology?
Goal: To determine how a particular trait has evolved
Goal: To determine evolutionary relationships between distantly related groups (i.e. bacteria domains vs archaea domains)
Goal: To identify a bacteria or archaea that you just cultured

19. Archaea and eukarya are more closely related
Comparing
Phenotype
Sequences
Lokiarchaea

20. Archaea / eukarya / bacteria
Cell wall
Cell membrane
Chromosome
Gene organization
Cell structures

21. Eukarya/archaea similarities
Gene expression machinery: Sigma factors and transcription factors
Organization of DNA within the cell

22. Competing hypotheses for euk/arch
TA Williams, et al. Nature 504, (2013) doi: /nature12779

23. Support for two domains
Archaeal links in the origin of eukaryotes.
TA Williams, et al. Nature 504, (2013) doi: /nature12779

24. Lokiarchaeota: the missing link

25. Prok diversity Scavenger hunt
Work in groups to answer the questions in your handouts.
Use the discussion thread on canvas and the pictures displayed on the phylogenetic tree

26. regroup
Based on what you found in the scavenger hunt, if you had to use one phenotype alone to determine the taxonomy of your isolate, what would you choose, if anything?
Why?
Going back to the TED talk, what do you think we can learn by characterizing environments at the phyla or division level?
Lists of favorite traits – wacky and scary