“Nothing makes sense but in the light of evolution” --Theodosius Dobzhansky

1. “Nothing makes sense but in the light of • evolution” • --Theodosius Dobzhansky

2. 1. Outline of course grading organization 2. Talk about domestication disease evolution

3. Grading Three exams: Exam 1 Exam 2 Exam 3 (Final) 30% 30% 40% 30% 10% (comprehensive) 100 pts 100 pts 133 pts 100pts 33pts

4. Grading There will be multiple choice questions ~2/3 There will be problem or short answer questions as the material permits The average grade on exams is ~ 50 The numerical grade tells you little about the letter grade Grades will be ‘standardized’ in a way that allows for differences in test difficulty, etc. There is always a normal distribution of grades I standardize the scores using a ‘z-statistic’ Your standardized score will depend on the mean and the variance of the test scores The mean grade for this course will be in the C range

5. Genetic Mechanisms of Evolution population genetics quantitative genetics Theory of Adaptation Speciation Macroevolution Organization of Topics in the Course

6. Genetic Mechanisms of Evolution population genetics quantitative genetics

7. Genetic Mechanisms of Evolution population genetics quantitative genetics Theory of Adaptation Speciation Macroevolution

8. Theory of Adaptation

9. Genetic Mechanisms of Evolution population genetics quantitative genetics Theory of Adaptation Speciation Macroevolution

10. Speciation

11. Genetic Mechanisms of Evolution population genetics quantitative genetics Theory of Adaptation Speciation Macroevolution

12. Macroevolution

13. Genetic Mechanisms of Evolution population genetics quantitative genetics Theory of Adaptation Speciation Macroevolution

14. Domestic dogs are extremely variable “Domesticated” from wolves

15. When were dogs domesticated? Where were they domesticated? How many times were they domesticated? Dogs are the first domesticated species The oldest remains of true dogs are ~12-14,000 years old from Eurasia and 9-10,000 from N. America

16. Phylogeny of dogs clades Genetic Evidence for an East Asian Origin of Domestic Dogs Peter Savolainen, Ya-ping Zhang, Jing Luo, Joakim Lundeberg, and Thomas Leitner Science Nov 22 2002: 1610-1613.

18. Coyote

19. Phylogeny from pre-Columbian dog remains Latin American Alaskan Eurasian Wolves, lu American Wolves, lu Modern dogs, D Humans colonizing America ~12-14,000 years ago brought dogs with them Ancient DNA Evidence for Old World Origin of New World Dogs. Jennifer A. Leonard, Robert K. Wayne, Jane Wheeler, Raúl Valadez, Sonia Guillén, and Carles Vilà Science Nov 22 2002: 1613-1616.

20. When were wolves domesticated? Before 14,000 BP Where were they domesticated? East Asia How many times were they Once, with occasional domesticated?wolf (female) hybrids

21. What happens during domestication? 1. Animal/plant ‘chosen’ for advantageous traits. 2. Animal/plant deliberately bred for traits. How do dogs differ from wolves? Bark They wag tails Their tails are curved Jaw differences They are hunting ‘companions’

22. Dogs are highly attuned to the behavior of people Social cues about the location of food The Domestication of Social Cognition in Dogs. Brian Hare, Michelle Brown, Christina Williamson, and Michael Tomasello. Science Nov 22 2002: 1634-1636.

25. Corn is not so simple

26. There are variants that occur naturally The variants can be inherited Some variants perform better in some environments Better variants become more common

27. why should we care about evolution? -- emergent diseases -- antibiotic resistance in bacteria -- pesticide resistance of mosquitoes

28. 1.Transformation of a lineage over time -- usually short time scale -- test with experiments or the comparative method 2. Diversification of one lineage into several -- often long time scale -- usually not experimentally tractable -- phylogeny reconstruction

29. HIV as an evolutionary case study Adaptation - how populations change through time in response to environmental change (lineage transformation) -- AZT resistance -- evolution of lethality Diversification - how new forms arise -- origins of HIV -- evolution of lethality

31. HIV retrovirus (RNA) attacks T cells (immune system) normal: 800-1000 cells/ml AIDS: <200 cells/ml death by secondary infection b/c immune system destroyed } reduce recognition of virus as foreign destruction of T cells changes in virus

32. HIV is a retrovirus -- reverse transcriptase AZT: azidothymidine vs normal thymidine = stop codon is AZT resistance due to infection with a different HIV ? 1. resistant individuals often have the same change in the reverse transcriptase 2. stopping AZT causes resistance to decline

33. HIV quickly becomes resistant to drug treatments

34. Evolution of resistance to AZT reverse transcriptase errors non-mutant mut1 mut2 mut3 mut4 mut5 killed by X slightly X X X AZT resistant non- resistant mut2.1 mut2.2 mut2.3 X X X

35. AZT resistance is an example of evolution by Natural Selection 1. mutations by reverse transcriptase produce variant HIV molecules 2. mutants are passed to ‘offspring’ of resistant genotypes 3. differential survival in AZT environment resistance is costly (slow growth). Mutants differ in enzyme function 4. resistance becomes typical effectiveness and speed of process -- rate of mutation (m ~1%/yr) -- strength of selection

36. Influenza RNA virus Spreads rapidly Human immune system affects flu Time period 1985-1996 HA1 gene (Hemagglutinin) Type A subtype H3