Announcements Seminar today after class! Seminar Wednesday!

Microbial evolution II Population genetics of HGT

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

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

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

Studying evolution: Experimental evolution

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

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)

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

Long-term E. coli evolution: parallel evolution Lenski, Rose, Simpson, and Tadler. 1991. Long-term experimental evolution in E. coli I. Adaptation and divergence during 2000 generations. American naturalist. 138:1315-1341

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:10.1038/nature08480

Comparison of genetic variation in microbial populations Homologous recombination HGT mutation

Homologous recombination and evolution 3 4 RecA finds region of homology: 5 6 Sometimes

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

Genome rearrangements in citrate utilization

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

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?)

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

How often does HGT occur? A comparison of homologous recombination rates in bacteria and archaea. 2009. ISME journal Michiel Vos and Xavier Didelot

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)

HGT plus gene loss can cause variation in gene frequency

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

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?

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;107:18634-18639 ©2010 by National Academy of Sciences

* = 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;107:18634-18639 ©2010 by National Academy of Sciences

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?

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

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

How and why we infer relationships among species

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

Phylogenetic analysis process

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

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

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) http://guestblog.scientopia.org/wp-content/uploads/sites/35/2012/07/Fred2a.gif

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)

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

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