2. Microbial Evolution Ecology and Evolution are inextricably connected

3. Ecology = the study of interactions between organisms and their environment (physical, chemical and biological conditions) Evolution = changes in the genetic composition of a population with the passage of each generation = change in allelic frequency in populations over time (alleles are different versions of the same gene)

4. Consider how the amount of genetic divergence (change) forms a continuum: Microevolution Macroevolution small changes large changes Microevolution = adaptation Macroevolution = speciation

5. Four distinct mechanisms generate evolution (change in allelic frequency in populations over time): 1. mutation 2. gene flow 3. genetic drift 4. selection (natural and artificial)

6. 1. Mutation = a heritable change in the nucleotide sequence of the genetic nucleic acid, resulting in an alteration in the products coded for by the gene

7. 2. Gene flow = introduction or loss of new alleles into the population through immigration or emigration. Wilson & Bossert, 1971

8. 3. Genetic drift =stochastic shifts in allele frequencies in small populations Wilson & Bossert, 1971

9. 4. Selection = change in allele frequencies over generations due to differential survival and reproductive success of genotypes Darwinian evolution is evolution by natural selection

10. Natural selection leads to adaptive radiation and speciation

11. What is the mechanism of natural selection? 1. Genotypes within populations vary and this variability is heritable. 2. Biotic and abiotic components of an organisms environment act as selection pressures. 3. Genotypes that are best adapted to these selection pressures leave the most offspring.

12. Closely examine these three premises: 1.What introduces variability among genotypes?

13. Closely examine these three premises: 1.What introduces variability among genotypes? Mutations introduce new genetic variation

14. Closely examine these three premises: 1.What introduces variability among genotypes? Mutations Plasmids Transformation Transduction Conjugation …can all introduce genetic variability to bacterial populations Horizontal gene transfer

16. Closely examine these three premises: 1.What introduces variability among genotypes? Mutations Anastomosis …can introduce genetic variability to fungal populations

17. Populations with diverse gene pools have a lot of variation in alleles. How is this variability passed on (heritable)?

18. genotypes pass on this variability through reproduction

19. In sexually reproducing organisms (eg. many species of algae, zooplankton, fungi, and protozoa), recombination occurs with reproduction (the genetic deck of cards gets shuffled every generation). That means that novel alleles that arise through mutations are immediately placed in a diversity of genetic environments.

20. genotypes pass on this variability through reproduction In contrast, recombination is not tied to reproduction in asexual organisms (e.g. bacteria, archaea, many species of algae, fungi....). Recombination happens in asexual organisms, but it is not necessarily tied with reproduction.

21. genotypes pass on this variability through reproduction Recombination has major ramifications on how natural selection acts on variance in the populations. Although sexual recombination is rare in bacteria (Cohen, 1996), horizontal gene transfer appears to be more common than previously thought (Pennisi 2004)

22. 2. What are selection pressures in an organisms environment?

23. Examples of biotic factors: predators competitors mutualists Examples of abiotic factors: resource availability physical conditions chemical conditions

25. Selection can be… natural or anthropogenic…

26. 3. Genotypes that are best adapted to these selection pressures leave the most offspring Premise 3 leads to the concept of adaptation and fitness

27. 3. Genotypes that are best adapted to these selection pressures leave the most offspring Premise 3 leads to the concept of adaptation and fitness Adaptation = a genetically determined characteristic that improves an organisms ability to survive and reproduce in a particular environment.

28. Premise 3 leads to the concept of adaptation and fitness Adaptation = a genetically determined characteristic that improves an organisms ability to survive and reproduce in a particular environment. Adapt = the evolutionary process by which organisms become better suited to their environments

29. Fitness =

30. the relative contribution by an individuals descendants to future generations.

31. Some important properties of fitness: Consider both the biotic and abiotic environment)Fitness is specific to a particular environment.(Consider both the biotic and abiotic environment). As the environment changes, so do the fitness values of the genotypes Notice the connection between ecology and evolution.

32. Some important properties of fitness: Fitness is a property of a genotype, not of an individual or a population. Individuals with the same genotype share the same fitness within the same environment. Fitness is measured over one generation or more.

33. New genotypes and alleles enter the population through mutation, immigration (horizontal gene transfer) etc. A new genotype that is fitter than the current one will gradually replace it. If the current genotype cannot be replaced by an invading one, it is said to represent the evolutionarily stable strategy or ESS (Maynard Smith and Price, 1973).

34. The concepts of fitness and adaptation are relevant ONLY in a particular ecological context. There is no such thing as fitness in an absolute sense.

35. Which of the 4 evolutionary mechanisms generates adaptation? 1. mutation 2. gene flow 3. genetic drift 4. selection

36. Only natural selection, the other mechanisms generate change, but the change has no linkage to improved survival in the environment

37. There can be multiple paths to higher fitness in response to many but not all types of natural selection (e.g. Contrast the results of Lenskis experiments of glucose starvation in E. coli with Bulls experiments with high-temperature stress in a bacteriophage

39. The role of genetic exchange (recombination of alleles) in evolution. geographic speciation The paradigm of geographic speciation was developed from studies of sexually reproducing populations This paradigm assumes: Allelic combinations are reshuffled every generation. Successful mating only occurs between individuals that are closely related.

40. geographic speciation = allopatric speciation

41. This paradigm falls apart with bacteria and other asexual organisms because: 1. Allelic combinations are NOT reshuffled every generation. Only a small amount of genetic material is exchanged (via conjugation, transformation, transduction, plasmid transfer). Cohan suggests this exchange happens at a low frequency (10 -8 to 10 -7 exchanges per gene segment per genome per generation). But Pennisi suggests this exchange rate is MUCH higher, particularly in stressful environments.

42. This paradigm falls apart with bacteria and other asexual organisms because: 2. Successful genetic exchange occurs between individuals that are NOT closely related ("promiscuous genetic exchange").

43. The process of periodic selection in bacteria purges diversity in populations gene pools. (Figure 3 in Cohan, 1996)

44. Even with relatively low levels of recombination, there is enough genetic exchange, so that diverse allelic combinations can arise. (Figure 4 in Cohan, 1996)

45. Cohan (1996) concluded that: 1. Recombination does NOT preserve genetic diversity in bacteria. 2. Genetic exchange does NOT threaten the integrity of population adaptations. 3. Genetic exchange can transfer adaptations across bacterial taxa.

46. Implications of this: 1.Adaptive mutations in bacteria have the potential to purge diversity from the populations. In contrast, in sexually reproducing organisms, adaptive mutation is transferred into many genetic backgrounds and does not follow the entire genome of the individual carrying the original mutation.

47. Implications of this: 2. At recombination rates > 10 -5 exchanges per gene segment per genome per generation, ecologically distinct populations may be indistinguishable (variance within populations is as great as variance between populations ) because of sufficient neutral sequence variance.

48. Implications of this: 3. Adaptive gene sequences can go ANYWHERE