Adaptation

1. Adaptation 713/813, Lecture 7

2. The most conspicuous evidence of evolution by natural selection is the fit of organisms to their environment. Yet quantifying adaptation continues to elude biologists.

3. How do you measure adaptation? • We mean the process that leads to the greater fitness of an organism to its environment; its outcome is also an adaptation • Break into groups of three and discuss, come up with three alternative methods • Also please briefly consider 1 strength and 1 weakness of the class thus far (of knowledge or approach)

4. 2010 methods Class answers: • Experimental evolution of transplanted populations, measure change in morphology or physiology • Change abiotic conditions, observe community response • Look for specific traits in a specific environment (in parallel) • Measure “success/failure” rate of a likely adaptive trait (eg birds eating nuts, bacteria eating food) • Correlate population size with success (or perhaps better, reproductive rate) • Transplant expt with no evolution; measure predation/prey responses • Swap symbionts and measure symbiotic phenotypes (eg light) • Correlate phylogenetic branch lengths (of multiple lineages) in specific environments • Force competition in a common environment (cage match); see who wins

5. 2012 methods • Knockouts -> loss of adaptation? • Artificial selection  look for correlated effects • Growth rate/output in environmental proxy of “reality” • Rate or efficiency of consumption of resources • Long-term observation focusing on change in phenotypes related to reproductive success • Look for examples of parallelism and/or convergence • Read functional output of a genome, link to environment • Change environment, measure change in expression • Experimentally increase competition for a limiting resource • Look for homogeneity of alleles over time (evidence of competitive advantage) • Look for positive/negative effects of plasticity via manipulation • Manipulate pairwise interactions among species (commensal/symbiosis) • Extent of genetic variation might be a proxy for selection • Manipulate other community members, test for effect on one population or individual

6. Course pluses and minuses so far Pluses • Blogs b/c it reveals thought process of peers • Class and recitation discussion of articles • Diverse background among classmates • Forces active learning and discussion/engagement • Paper dissection • New tabs from browsing Minuses • Iack of focus on blog assignment • Intimidiation re: background • Reading primary literature can be overwhelming • Not enough time to read work of peers • No textbook • Limited sense of structure • Lack of printed syllabus • Chaotic website • Need PPT ahead of time

7. One method is Comparative • It MUST be grounded in phylogeny to as to guarantee the comparison of like things, if not strict homologssee: http://en.wikipedia.org/wiki/Phylogenetic_comparative_methods • If two species share the same ancestor, and one has a trait that improves its fit to its home environment that the other lacks, you may infer it is an adaptation

8. Another: convergent evolution • Repeated evolution of the same trait in replicate populations is a hallmark of adaptation

9. Whats best? Measure it directly! • Compare performance (fitness) of two genotypes and measure difference • Ideal: compare ancestor with evolved directly (head-to-head competition) • Both of these are often impractical

10. Fitness = Ln [ N 1 (Day 1) / N1 (Day 0) ] Ln [ N 2 (Day 1) / N2 (Day 0) ] Adaptation may be quantified directly Day 0 Day 1 Evolved Ancestor Determine 1 :2 Plate on agar to determine the ratio of 1 :2 Ratio of realized growth

11. Experimental evolution Studying evolution, and usually adaptation, in action

13. The outcome of selection for high and low oil content in the Illinois corn experiment.

14. William Dellinger 1880-1886 Selected for thermotolerance of microorganisms 60 F  158 F Unfortunately incubator destroyed along with samples

16. - + Generation 0 ------------------------- Generation 20,000+ è • Lenski Long-term Experimental • Conditions • 12 replicate cultures • single genotype of Escherichia coli B • daily serial transfer • single resource and temperature • no sex

19. Mutation rate itself evolves in certain populations Non-mutator Mutator Population Generations Sniegowski et al., Nature 387, 703-705 (1997)

20. More on the mechanics of microbial experimental evolution • Batch (serial) culture = open system • Chemostat = closed system • Turbidostat = closed • Static culture (liquid or solid) = closed

22. Chemostat

23. Chemostats select for nutrient affinity

24. Static culture

25. What are the key variables? (brainstorm) • Population size (N), and effective population size (Ne) • Mutation rate • Recombination? • Parasites? • Constant or fluctuating environment? • Mass-action or structured environment?

26. Some questions addressed by experimental evolution • What is the tempo and mode of evolution? (gradual or punctuated, limits, etc?) • What factors promote or constrain adaptation? • What are the consequences of adaptation? • What are the mechanisms of adaptation? • Is the mutation rate optimal or minimal? • How do mutations interact?

27. Is evolution repeatable? “I call this experiment ‘replaying life’s tape.’ You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past – say to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original.” “The bad news is that we cannot possibly perform the experiment…” -S.J. Gould, Wonderful Life: the Burgess Shale and the nature of history (1989)

28. We CAN replay evolution Replicate populations evolving under identical conditions address whether evolution is repeatable. Do you predict phenotypic repeatability (parallelism)? Do you predict genetic repeatability?