EVOLUTIONARY BIOLOGY FALL 2011 WHEN: MWF 11:45 – 12:35 WHERE: DeBartolo Hall 140

1. EVOLUTIONARY BIOLOGY FALL 2011 WHEN: MWF 11:45 – 12:35 WHERE: DeBartolo Hall 140 INSTRUCTOR: MIKE PFRENDER TAs: Sayanty Roy, Kerry Regan Course webpage: http://www.nd.edu/~mpfrende/

2. “Nothing in biology makes sense except in light of evolution” Theodosius Dobzhansky 1973

3. Managing Evolving Fish Stocks • Evolutionary impact assessment is a framework for quantifying the effects of harvest-induced evolution on the utility generated by fish stocks. Conover, Nature 2007 450:179-180 Jorgensen et al. Science 318:1247- 8

4. How do complex organisms evolve?

5. What explains these exaggerated phenotypes???

6. What happened to these organisms?

7. How does social behavior evolve?

8. How do host – pathogen relationships change through time? Human HIV Protein Structure

9. What are the evolutionary consequences of small population size?

10. MAJOR GOALS IN THIS COURSE: • Describe major evolutionary events and patterns in the history biological diversity on Earth • Develop an analytical frame work to describe the process of evolutionary change in natural populations • Apply this framework to understand evolutionary dynamics – especially with regard to human populations

11. COURSE REQUIREMENTS: • Problem Sets, Writing Assignments, and an occasional Quiz • Total 100 pts. • Exams • 1st Midterm 100 pts. • 2nd Midterm 100 pts. • Final 100 pts. • Total 300 pts.

12. ACHIEVING HIGH FITNESS IN EVOLUTIONARY BIOLOGY: • Attend lectures regularly. • Take detailed notes. • Read over material before lecture. • Ask lots of questions and discuss the material with instructor and classmates. • Take advantage of office hours!!!!

13. Recommended text for Evolutionary Biology • On reserve at the Library • Textbook website: • http://wps.prenhall.com/esm_freeman_evol_4/

14. #1 Question in Evolutionary Biology What material is going to be on the exams? Answer: Anymaterial in the Assigned Readings, PowerPoints or mentioned in lecture is fair game.

15. Some Practical Applications of Evolutionary Biology: • Human Health: • Evolution of pathogens and antibiotic resistance. • Understanding gene function through comparative study. • Tracing the origin and spread of infectious diseases. • Detection of nucleotide changes responsible for genetic disorders from gene genealogies. • Long-term consequences of medical intervention. SARS Coronavirus

16. Some Practical Applications of Evolutionary Biology: • Pharmaceutical Industry: • Drug design by in vitro or in vivo evolution. • Targeted searches for natural products; bio-prospecting. • Agriculture: • Crop improvement by selective breeding. • Evolution of pesticide resistance. • Transgenic organisms – advantages and risks.

17. Some Practical Applications of Evolutionary Biology: • Fisheries Biology: • Genetic consequences of selective harvesting. • How does selective harvesting affect the future of fisheries? • Genetic consequences of hatcheries. • How do hatchery raised fish affect wild stocks?

18. Some Practical Applications of Evolutionary Biology: • Conservation Biology: • Identification of evolutionary significant units (ESUs). • Avoidance of inbreeding depression in captivity. • Avoidance of loss of adaptive variation. • Identification of minimal population size for viability. • Predicting the response to global change.

19. Adaptation in a Changing World: Genetic Approaches to Understanding Phenotypic Evolution in Natural Populations Michael E. Pfrender Evolutionary and Ecological Genomics Lab Department of Biology

20. Tools for Ecological Genomics WELL CHARACTERIZED ECOLOGY COMPLETE GENOME SEQUENCE GENETIC MAP KNOCKOUT / TRANSGENIC LINES GENE EXPRESSION ARRAYS QTL PANELS

21. How do natural populations cope with environmental change?

22. STUDY SYSTEM IN HIGH ELEVATION LAKES OF THE SIERRA NEVADAS

23. Introduced salmonids are a rapid change in the environment leading to local extinction and/or adaptation of native invertebrates.

24. Rates of Adaptation • From these data we can estimate the rate of adaptation • Do Sierra Nevada Daphnia show high rates of evolutionary change in response to introduced predators? r2=0.33 p<0.0001 r2=0.08 p<0.01 Fisk et al. (2007)

25. Changes in Pigmentation • Daphnia exposed to predation from introduced fish have reduced pigmentation Scoville et al. In preparation

26. Tyrosine TH pale yellow DOPA melanin DOPA DDC Ddc PO Dopamine melanin Dopamine -alanine DAT aaNAT -alanine NBAD SYNTHASE ebony NBAD HYDROLASE tan NADA NBAD PO PO NADA Sclerotin NBAD Sclerotin Genetic Basis of Changes in Pigmentation • Data from other arthropod systems provides a set of candidate genes involved in pigmentation • We are examining these gene for structural and functional changes as well as examining the patterns of gene expression Insect Melanin Biosynthesis Pathways (Melanin pathway modified from True 2003)

27. Gene 4 Gene 5 Gene 2: 5’– 3’ Gene 1: 3’– 5’ Gene 3 Gene Coding Exon Female Male Transcriptional Response to Environmental Stimulus: Defense structures in response to predator chemical cues • How do organisms respond to their environment? Functional genomic approaches using whole genome tiling arrays

28. Primary Goals of Evolutionary Biology: • To document evolutionary history. • To understand the mechanisms that drive biological change through time. • To apply this knowledge to understand the genetic underpinnings of biological diversity, and to solve practical problems in the life sciences.

29. WHAT IS EVOLUTION? Darwin: descent with modification Futuyma: changes in the properties of populations that transcend the lifetime of a single individual. F & H: changes in allele frequencies over time. • Key Ingredients: • Change that is heritable across generations. • A property of populations, not individuals. • Includes the possibility of cultural evolution (not in our genes).

30. All evolving systems have the following properties: • POPULATIONS: Groups of entities. • VARIATION: Members of the population differ from one another with respect to some characteristic. • HEREDITARY SIMILARITY: Offspring resemble parents.

31. Historical Background Plato (427-347 BC) – Believed in 2 worlds: the real world (ideal and eternal), and an illusionary world (imperfect and perceived through the senses). Typological view of nature – individual variation as the imperfect manifestation of ethos. Aristotle (384-322 BC) – Believed that all living organisms could be arranged in a “scale of nature” or GreatChain of Being. The ladder of life consists of graduation from inanimate material through plants, through lower animals and humans to other spiritual beings.

32. Carolus Linnaeus (1707-1778) – Established the modern system of taxonomy in an attempt to discover order in the diversity of life “for the greater glory of God”. • Groupings based on similarity • Hierarchal relationships of organisms

33. Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck 1809 Philosophie Zoologique • First articulated theory of evolution: • Organisms continually arise by spontaneous generation. • “Nervous fluid” acts to move each species up the “great chain of being”. • Organisms develop adaptations to changing environment through the use and disuse of organs. (Heavy use attracts more “nervous fluid”.) • Acquired characteristics are inherited.

34. “Chain of Being” SCALE OF ORGANIZATION TIME LAMARCKIAN EVOLUTION

35. Problems with Lamarck’s ideas: • There is no evidence of spontaneous generation. • There is no evidence of an innate drive toward complexity. • - E. coli - Parasites - Cave dwelling organisms • 3) There is no evidence of inheritance of acquired characteristics.