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Lecture 1: Introduction to Population Genetics August 17, 2015 Instructors u Steve DiFazio 5200 Life Sciences Building Office Hours: Wed,Fri 1 to 2 pm u Ran Zhou (TA) 5206 Life Sciences Building Office Hours: Tue 2:30 to 3:30 Wed 3:30 to 4:30 u Please use office hours, or make appointment! Course Structure u Two 50-minute lectures per week Do readings before class Bring a calculator to class Be ready to participate! Handouts of lecture slides may be distributed at beginning of class (vote on this) Slides posted to website after class (please don’t print old slides) u One 2-hour lab session, 6:30-8:20 each week Grading u Exam 1, Sep 23, 120 points u Exam 2, Oct 28, 120 points u Weekly Lab Reports, 12 X 10 pts = 120 points u Final Exam, Monday, Dec 7, 2:30 pm, 3131 LSB, 120 points u Extra credit opportunities u Scale for final grades: (no curve) Class Website http://www.as.wvu.edu/~sdifazio/popgen/ or google “difazio popgen” Home page has information from syllabus: Course structure Grading Rules and policies WVU Ecampus Site Mainly for posting grades and emailing class (change your email settings if you don’t receive these) Also contains some information about texts and pdfs of background reading May see increased use during the semester Schedule Page Updated continuously during course Lecture slides available following lecture Reading assignments Exam schedule Lab schedule Required Text Hedrick, P.W. 2011. Genetics of Populations. Jones and Bartlett Available from WVU book store Also partially on Google Books (searchable) Supplemental Reading Services Three books on reserve in WVU downtown library: Hamilton, M. 2009. Population Genetics. Gillespie, J.H. 2004. Population Genetics: A Concise Guide. Falconer, D.S., and T.F.C. Mackay. 1996. Introduction to Quantitative Genetics. Supplemental Reading Search for “difazio” Other Resources Laboratory TA: Ran Zhou Tightly linked to lectures Intended as “Active Learning” modules Enhance understanding of concepts and principles Provide hands-on introduction to Population Genetics software Every Wednesday evening, 6:30 to 8:20 pm Bring your lab manual and (if you prefer) a calculator Required Lab Manual Slavov, G, E. RodgersMelnick, and S.P. DiFazio. 2015. BIOL 464/GEN 535 Population Genetics Laboratory Manual. WVU Press. 110 Pages. Available only from WVU book store (~$20) Please purchase this before the next lab Extra Credit Opportunity Find a new error in the Lab Manual or Text Typo/grammatical error: 1 point Calculation, derivation or mathematical error: 5 points First come, first served Exception: pages 1 and 2 are reversed: printer error Laboratory Web Page Schedule of lab topics Links to required software and data Due dates for lab reports Lab Reports Lab reports due at beginning of lab period 12 total, worth 10 points each Deduct 0.5 points for each day late Lab report for week 13 is optional: up to 10 pts extra credit. Due by Dec 9 at 11:59 pm, firm. Guidelines for lab report are in lab manual Submit by ecampus. Email ([email protected]) and/or paper versions are also OK Most weeks require a write-up with interpretations for each calculation or simulation Please be careful to fully answer questions, including explanations of results from biological standpoint Working Together and Academic Honesty Group work in laboratory is optional but encouraged It is fine to discuss lab problems and work on them together HOWEVER, your lab report must be your original work See academic honesty policy on class website Try Library plagiarism module http://www.libraries.wvu.edu/instruction/plagiarism/ Exams are based primarily on the lab exercises and examples worked in class Exams See samples on course website schedule page Mix of conceptual and computational questions Exam dates: Sep 23, Oct 28, Dec 7 (last week of classes/first half of final exam week) Sep 23 and Oct 28 exams are on Wednesday in computer lab (regularly scheduled lab time) Up to 2 hours to complete Final exam is in 3131 LSB and will be limited to 50 minutes Final exam is not strictly cumulative, but everything is cumulative in Population Genetics! Highlights from the Schedule Introduction to Probability Genetic variation in populations: Hardy-Weinberg Equilibrium Selection Inbreeding Genetic drift Gene Flow and population structure Genetic identity and forensic identification Linkage disequilibrium Phylogenetics Coalescence and neutral theory Quantitative genetics Connecting genotypes to phenotypes What is Evolution? Evolutionary Synthesis Fisher, Wright, and Haldane were fathers of population genetics and modern evolutionary theory Working in early 1920’s, worked out how to apply Mendel’s laws in a population context to provide mechanistic explanation for evolutionary change R.A. Fisher Sewall Wright http://www.ars.usda.gov J.B.S. Haldane http://www.york.ac.uk http://www.ucc.ie/ Population Genetics Study of heritable variation in assemblages of organisms, and how this is affected by mutation, drift, selection, and gene flow Mutation Drift + - Diversity +/Selection + Migration Population Genetics is Important Disease susceptibility, genetic testing, and personalized medicine Statistical interpretation of forensic DNA evidence Human evolution and cultural history Crop and animal improvement Traditional breeding Genetic engineering Conservation plans for plant and animal communities Responses of plant and animal communities to climate change Mathematical Tools for Population Genetics Basic algebra 1 1 fe 4Ne 1 1 Basic calculus Basic statistics Probability m P Pk k 1 PIDsibk He 1 1 1 4 2 2 2 (1 pi ) [ pi ( pi ) ] 4 2 i i i Population Genetics and Probability Probability is at the core of much of population genetics Reproduction is a sampling process Effects of mutation, gene flow, selection, and genetic drift must be seen as departures from expectations based on random processes Example: 1 genetic locus and two alleles in a forest of 20 trees determines color of foliage. Green is dominant. What proportion of offspring will have white foliage? : 4 copies : 36 copies Population Genetics and Probability Alternatively: Most of this class can be understood based on thoroughly understanding the following problem: Given a jar of M & M’s of a specified size (possibly infinite), predict how the proportions of colors will change over time under different scenarios Vote: Milk chocolate Peanut Dark chocoloate Almond Peanut butter Pretzel Other? Allergies?