1 EVOLUTIONARY BIOLOGY FALL 2016WHEN: MWF 11:30 – 12:20 WHERE: 283 Galvin Life Science Center INSTRUCTOR: Mike Pfrender Course webpage:

2 “Nothing in biology makes sense except in light of evolution”Theodosius Dobzhansky 1973 “Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science.”

3 Managing Evolving Fish StocksEvolutionary impact assessment is a framework for quantifying the effects of harvest-induced evolution on the utility generated by fish stocks. Conover, Nature : Jorgensen et al. Science 318:

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 Is there an evolutionary theory to explain aging and senescence?

9 A Greenland shark (Somniosus microcephalus)A Greenland shark (Somniosus microcephalus). These creatures are among the worlds largest carnivorous sharks and are distributed throughout Arctic waters. For decades, the longevity of this slow-growing species has remained a mystery. Using well-established radiocarbon dating techniques applied on Greenland shark eye lens tissue, Nielsen et al. estimate that these animals are the longest-living vertebrates known to date. This species is large yet slow-growing. The oldest of the animals that they sampled had lived for nearly 400 years, and they conclude that the species reaches maturity at about 150 years of age.

10 What are the evolutionary consequences of small population size?

11 MAJOR GOALS IN THIS COURSE:Describe major evolutionary events and patterns in the history of biological diversity on Earth Develop analytical frameworks to describe the process of evolutionary change in natural populations Apply these frameworks to understand evolutionary dynamics – especially with regard to human populations

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

13 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 review sessions & office hours!!!!

14 Text for Evolutionary BiologyOn reserve at the Library (soon!)

15 #1 Question in Evolutionary BiologyWhat material is going to be on the exams? Answer: Any material in Assigned Readings, PowerPoints or discussed in lecture is fair game.

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 & Livestock improvement by selective breeding. Evolution of pesticide resistance. Transgenic organisms – evaluating the 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. Avoiding the loss of adaptive variation. Identification of minimal population size for viability. Predicting the response to global change.

20 How do natural populations and communities cope with environmental change?

21 Physically move to track a beneficial habitatResponse to Environmental Challenges Natural populations faced with a changing environment can: Physically move to track a beneficial habitat Accommodate the altered environment with phenotypic plasticity (direct response to the environment) Adapt to the altered environment through genetic changes Go extinct!

22 Even populations capable of rapid evolution may face a high risk of extinction due to reductions in population size during the initial period of adaptation. FROM: Gomulkiewicz & Holt When does evolution by natural selection prevent extinction. Evolution 49:

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24 WELL CHARACTERIZED ECOLOGY KNOCKOUT - RNAi - TRANSGENIC LINESModel Systems For Evolutionary & Ecological Genomics? WELL CHARACTERIZED ECOLOGY KNOCKOUT - RNAi - TRANSGENIC LINES QTL PANELS GENOME SEQUENCE GENETIC MAP GENE EXPRESSION ?

25 Mt. Mendel Darwin Lakes Rapid Ecosystem ChangesIn the Sierra Nevada ecosystem, the recent introduction of salmonids is a dramatic and rapid change in the environment. UNIVERSITY OF NOTRE DAME

26 Undisturbed Daphnia Populations in the Sierra Nevada4 mm High elevation populations of Daphnia melanica are typically highly pigmented and have large body size. Lower Skelton Lake Elevation ~3,000 meters. Yosemite Natl. Park Dark pigmentation is due to the elevated levels of incident UV-B radiation at these extreme elevations No vertebrate predators leads to large body size UNIVERSITY OF NOTRE DAME

27 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 UNIVERSITY OF NOTRE DAME

28 Changes in PigmentationDaphnia exposed to predation from introduced fish have reduced pigmentation Scoville & Pfrender 2009

29 Genetic Basis of Changes in PigmentationTyrosine DOPA Dopamine melanin NADA Sclerotin NBAD TH pale DDC Ddc DAT aaNAT HYDROLASE tan SYNTHASE ebony PO yellow -alanine 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)

30 - Up-regulated (28°C) - Down-regulated (28°C)The complexity of organismal responses to their environment requires an understanding of regulatory networks. Transcriptional response of Daphnia to thermal stress - Up-regulated (28°C) - Down-regulated (28°C)

31 Our Current Understanding of the Genetic Basis of AdaptationUnderstanding how genomic and regulatory variation contribute to phenotypic variation in natural environments is a major challenge. On one side of the equation we are making piles of genome level data and on the other side we have the organism interacting with its environment. Putting these pieces together and completing the map from genotype to phenotype to environment will likely occupy us over the next ten years.

32 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.

33 WHAT IS EVOLUTION? Darwin: descent with modificationFutuyma: 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).

34 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.