EVOLUTIONARY BIOLOGY FALL 2012 WHEN: MWF 11:45 – 12:35 WHERE: DeBartolo Hall 129 INSTRUCTOR: Mike Pfrender TA: Sheina

1. EVOLUTIONARY BIOLOGY FALL 2012 WHEN: MWF 11:45 – 12:35 WHERE: DeBartolo Hall 129 INSTRUCTOR: Mike Pfrender TA: Sheina Sims 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. New candidates for oldest fossils Remains in 3.4-billion-year-old rocks hint at when cellular life arose, and how it powered itself. • Researchers have found what could be the oldest microbial fossils yet documented. The traces, discovered in 3.4-billion-year-old Australian rocks, might help to resolve the question of when cellular life arose, and how it produced energy. Wacey, D., Kilburn, M. R., Saunders, M., Cliff, J. & Brasier, M. D. Nature Geosci.http://dx.doi.org/10.1038/NGEO1238 (2011).

11. Published online 21 August 2011 | Nature | doi:10.1038/news.2011.490 News Climate change will hit genetic diversity Probable loss of 'cryptic' variation a challenge for conservationists. Virginia Gewin The stonefly Arcynopteryx compacta needs cold water and has short wings - it's not well equipped to escape rising temperatures.A. Schmidt-Kloiber/W. Graf Climate change represents a threat not only to the existence of individual species, but also to the genetic diversity hidden within them, researchers say. The finding promises to complicate assessments of how climate change will affect biodiversity, as well as conservationists' task in preserving it. DNA studies have revealed that traditional species, as defined by taxonomists, contain a vast amount of 'cryptic' diversity — such as different lineages, or even species within species. Carsten Nowak, a conservation biologist at the Senckenberg Research Institutes and Natural History Museum in Gelnhausen, Germany, and his colleagues have made a first attempt to understand how global warming might affect this form of diversity. Their findings are published in Nature Climate Change1. • Climate change represents a threat not only to the existence of individual species, but also to the genetic diversity hidden within them, researchers say. The finding promises to complicate assessments of how climate change will affect biodiversity, as well as conservationists' task in preserving it. • DNA studies have revealed that traditional species, as defined by taxonomists, contain a vast amount of 'cryptic' diversity — such as different lineages, or even species within species. Carsten Nowak, a conservation biologist at the Senckenberg Research Institutes and Natural History Museum in Gelnhausen, Germany, and his colleagues have made a first attempt to understand how global warming might affect this form of diversity. Their findings are published in Nature Climate Change1. • The team looked at aquatic insects living in the mountain streams of central Europe — seven species of caddisfly, a mayfly and a stonefly. The insects were chosen because they are likely to be especially vulnerable to rising temperatures — they need cold water, and have limited ability to travel large distances. The stonefly Arcynopteryx compacta needs cold water and has short wings - it's not well equipped to escape rising temperatures.

12. 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

13. COURSE REQUIREMENTS: • Problem Sets, Writing Assignments, etc. • Total 100 pts. • Exams • 1st Midterm 100 pts. • 2nd Midterm 100 pts. • Final 100 pts. • Total 300 pts.

14. 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!!!!

15. Recommended Textfor Evolutionary Biology • On reserve at the Library • Textbook website: • http://wps.prenhall.com/esm_freeman_evol_4/

16. #1 Question in Evolutionary Biology What material is going to be on the exams? Answer: Anymaterial in Assigned Readings, PowerPoints or discussed in lecture is fair game.

17. 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

18. 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 & Livestock improvement by selective breeding. • Evolution of pesticide resistance. • Transgenic organisms – advantages and risks.

19. 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?

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

21. 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

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

23. How do natural populations cope with environmental change?

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

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

26. 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)

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

28. 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)

29. 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

30. 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.

31. 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).

32. 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.

33. 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.

34. 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

35. 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.

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

37. 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. (BUT…..epigenetics???)