Lecture 1: Introduction to Population Genetics

1. Lecture 1: Introduction to Population Genetics January 8, 2014

2. Instructors • Steve DiFazio • 5200 Life Sciences Building • Office Hours: Mon, Wed, Thurs 1 to 2 pm • Rose Strickland-Constable (TA) • 5206 Life Sciences Building • Office Hours: Mon, Fri 11:30 to 12:30 Wed 4:30 to 5:30 • Please use office hours, or make appointment!

3. Course Structure • 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 (don’t print old slides) • One 2-hour lab session, 6:30-8:20 each week

4. Grading • Exam 1, Feb 12, 120 points • Exam 2, Mar 26, 120 points • Weekly Lab Reports, 12 X 10 pts = 120 points • Final Exam, Tuesday, Apr 29, 11 am, 3306 LSB, 140 points • Extra credit opportunities • Scale for final grades: (no curve)

5. 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

6. Schedule Page • Updated continuously during course • Lecture slides available following lecture • Reading assignments • Exam schedule • Lab schedule

7. Required Text Hedrick, P.W. 2011. Genetics of Populations. Jones and Bartlett • Available from WVU book store • Also partially on Google Books (searchable)

8. Supplemental Reading Mountain Lynx 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.

9. Supplemental Reading

10. Other Resources

11. Laboratory • TA: Rose Strickland-Constable • 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

12. Required Lab Manual Slavov, G, E. Rodgers-Melnick, and S.P. DiFazio. 2014. BIOL 464/GEN 535 Population Genetics Laboratory Manual. WVU Press. 108 Pages. • Available only from WVU book store (~$20) • Please purchase this before the next lab

13. 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

14. Laboratory Web Page • Schedule of lab topics • Links to required software and data • Due dates for lab reports

15. Lab Reports • Lab reports due at beginning of lab period • 12 total, worth 10 points each • Deduct 0.5 points for each day late • Last report is optional: up to 10 pts extra credit • Guidelines for lab report are in lab manual • Email and/or paper versions are fine • 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

16. 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

17. 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 • Tying genotypes to phenotypes

18. What is Evolution?

19. Sewall Wright R.A. Fisher http://www.ars.usda.gov J.B.S. Haldane http://www.york.ac.uk http://www.ucc.ie/ 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

20. Mutation Drift + - + +/- Selection Migration Population Genetics Study of heritable variation in assemblages of organisms, and how this is affected by mutation, drift, selection, and gene flow Diversity

21. 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

22. Introductions Name Major Career goal/goal for class. Be honest!

23. Mathematical Tools for Population Genetics • Basic algebra • Basic calculus • Basic statistics • Probability

24. 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 locusand 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