1. Announcements
Seminar today after class!
Seminar Wednesday!

2. Microbial evolution II Population genetics of HGT

3. Review: Evolution of antibiotic resistance on a solid surface
Steps of evolution =
What is needed for evolution to occur?

4. How can we determine relationships in this figure?
What if there was horizontal gene transfer?

5. Learning outcomes
Be able to explain two approaches to studying evolution in microorganisms
Distinguish between impacts of HGT and mutation on microbial evolution
Be able to identify variation likely to occur from HGT vs mutation vs recombination
Apply knowledge of evolutionary process to constrain rates of evolution by HGT
Explain how HGT and gene loss cause variation in gene frequency in a population
Be able to explain how DNA sequences are used to determine evolutionary history of species
Use diverse phylogenetic trees to determine the relationships among species

6. Studying evolution: Experimental evolution

7. Experimental evolution in E. coli
Ancestor
Frequent dilution into fresh media, many generations of evolution
Several replicate starter populations
Several replicate evolved populations

8. Benefits of experimental evolution with microorganisms
Identical genetic backgrounds (clonal) – chance vs natural selection
Many generations of evolution (short generation time)
Ability to directly compare ancestors and evolved lines (- 80 degree fossil record)
Control ecology – have treatments with only one variable changing
Natural selection vs random factors (large population sizes)

9. Long-term E. coli evolution: Dr. Rich Lenski

10. Long-term E. coli evolution: parallel evolution
Lenski, Rose, Simpson, and Tadler Long-term experimental evolution in E. coli I. Adaptation and divergence during 2000 generations. American naturalist. 138:

11. Mutations in Long-term E. coli evolution
Mutations found by sequencing genomes sampled between
2,000 and 20,000 generations from an evolution experiment with E. coli.
JE Barrick et al. Nature 000, 1-5 (2009) doi: /nature08480

12. Comparison of genetic variation in microbial populations
Homologous recombination
HGT
mutation

13. Homologous recombination and evolution3 4
RecA finds region of homology: 5 6
Sometimes

14. Example: Homologous recombination and E. coli
Zachary Blount studies evolution of citrate utilization in the Lenski lab

15. Genome rearrangements in citrate utilization

16. Review of horizontal gene transfer
Mechanism
How?
What?
With whom?

17. Possibilities and limitations of HGT
What kind of genetic changes can occur through horizontal gene transfer?
What are the limits?
(hint for one = how does DNA get into the genome?)

18. Which of the following is least likely to be transferred horizontally?  
A. gene for the DNA polymerase between bacteria and archaea
B. gene for DNA polymerase between two individuals of the same species
C. antibiotic resistance gene transferred between two different species
D. antibiotic resistance gene transferred between two individuals of the same species

19. How often does HGT occur?
A comparison of homologous recombination rates in bacteria and archaea ISME journal
Michiel Vos and Xavier Didelot

20. HGT and evolutionary rate
If you wanted to calculate the rate at which HGT can take over a population, how would you do it? What would change in the list below for mutations?
Calculating rates for beneficial mutations
Step 1: Generation of variation (mutation supply rate)
Step 2: Escaping drift
Step 3: Calculating rate of fixation (Tau)

21. HGT plus gene loss can cause variation in gene frequency

22. Example: changes in gene freq/time
Prochlorococcus (phototroph, cyanobacterium)
Pelagibacter (heterotroph)
Ocean
Remarkable variation in gene content : Why?
Genetic drift?
Natural selection?

23. Example: changes in gene freq/time
Sequenced community DNA in two ocean regions: HOTS (near Hawaii) and BATS (near Bermuda)
BATS = more mixing and higher nutrient inputs, higher iron and other metals
HOTS = higher phosphate levels
Does gene content variation reflect habitat?

24. Genes more common at BATS than HOTS
Relative gene frequency among Prochlorococcus and Pelagibacter populations in the oligotrophic North Pacific (HOT) and North Atlantic (BATS) subtropical ocean gyres.
Genes more common at BATS than HOTS
* = upregulated in response to P starvation
HOTS
Coleman M L , Chisholm S W PNAS 2010;107:
©2010 by National Academy of Sciences

25. * = upregulated in response to P starvation
Relative gene frequency among Prochlorococcus and Pelagibacter populations in the oligotrophic North Pacific (HOT) and North Atlantic (BATS) subtropical ocean gyres.
* = upregulated in response to P starvation
Coleman M L , Chisholm S W PNAS 2010;107:
©2010 by National Academy of Sciences

26. Example: changes in gene freq/time
Sequenced community DNA in two ocean regions: HOTS (near Hawaii) and BATS (near Bermuda)
BATS = more mixing and higher nutrient inputs, higher iron and other metals – phosphate metabolism genes more frequent for phototroph and heterotroph
HOTS = higher phosphate levels
Does gene content variation reflect habitat?

27. Summary: How do each of the following affect evolution?
Mutation
Genome rearrangements
Horizontal gene transfer
Nature of changes
Rate of evolution

28. Comparing DNA sequences to infer evolutionary relationships (molecular systematics)
Why compare?
How?

29. How and why we infer relationships among species

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

31. Phylogenetic analysis process

32. 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

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

34. 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)

35. 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)

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

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