ANT 3930 (0832) HONORS MOLECULAR GENETICS AND EVOLUTION
Prof. Connie J. Mulligan
Class meets in 117 Little
Class time: Tuesday, periods 3-5, with a 15 min break
Prof. Connie Mulligan
B119 Turlington Hall
(352)392-2253, ext 248
Office hours: Mon and Thurs, 10:30-12:00
Course summary: ANT 3930 will examine the use of molecular genetic data to investigate the evolution and history of humans. The completion of the human genome sequence has greatly facilitated the application of molecular genetic data to questions of human prehistory. Specifically, variant sites in the human genome sites can now be identified through a computer search rather than spending weeks or months in the laboratory. These variant sites can then be used in a number of investigations, such as the reconstruction of past migration events or the detection of admixture or gene flow in a population. Specific topics to be discussed include the emergence of anatomically modern humans in Africa (out-of-Africa vs. multiregionalism theories), Neanderthal genetics (did we interbreed?), colonization of Europe, and the use of ancient DNA to study human evolution.
Reading and course format: Two textbooks (The Seven Daughters of Eve by Brian Sykes and Genetics and the Search for Modern Human Origins by John Relethford) will be used to present the fundamentals of molecular genetics and how these data are applied to anthropological questions. Relevant journal articles will be used to highlight the major contributions in the field of molecular anthropology. A course packet of journal articles and related material is available at Custom Copies (309 NW 13th St, across from Krispy Kreme Donuts, 352-375-2707). The course meets once a week for three hours and the course format is lecture plus discussion with substantial class participation. Evaluation of student performance is based on class participation, weekly quizzes, problem sets, an oral presentation, and an exam. Although basic molecular biology concepts will be reviewed, some knowledge of DNA structure, Mendelian genetics, and molecular biology is expected. Additional information is provided by several websites:
http://www.clas.ufl.edu/users/mulligan/Webpage/3930.2004/3930home.html website for class
http://www.uflib.ufl.edu/ej/ - UF database of available electronic journals (may only be available from a campus computer)
http://www.ncbi.nlm.nih.gov/PubMed - National Library of Medicine database of over 11 million journal articles dating back to the 1960s
http://www.genome.gov/glossary.cfm NIH-maintained glossary of genetic terms
http://www.genomesonline.org/ - status of genome sequencing projects
http://www.genome.gov/LegislativeDatabase - Database of federal and state laws focused on genetic issues, such as genetic testing and counseling, insurance and employee discrimination, etc.
http://www.gene.ucl.ac.uk/hugo/ - Human Genome Organisation
http://www.stanford.edu/group/morrinst/hgdp.html Human Genome Diversity Project (dated, good for historical perspective)
Grading: Final grades will be determined by the following five categories, each of which contributes 100 points to the final grade: participation (100 pts), 10 quizzes or set of questions/comments (10 pts each), 4 homework exercises (25 pts each), oral presentation (100 pts), exam (100 pts). Possible points total 500. Grades will be based on the following point percentages: 90-100%=A, 87-89%=B+, 80-86%=B, 77-79%=C+, 70-76%=C, 67-69%=D+, 60-66%=D, < 59%=E.
- Participation in class discussions is required of all students and will be based on each students contribution of original discussion, comments, questions, etc. to the class.
- Each class, either a quiz will be given or students will hand in at least three original comments or questions based on the reading material. Quizzes will cover the days reading material and will be closed-book. The lowest grade (of quizzes or comments/questions) will be dropped. Missed quizzes or comment/questions cannot be made up.
- There will be four homework exercises involving the analysis of hypothetical or actual molecular data. The exercises are intended to give students an opportunity to perform data analyses similar to those conducted in the discussion papers and will be graded on effort and accuracy. Exercises must be turned in two weeks after they are assigned. Students who miss the class in which an exercise is assigned are expected to turn the exercise in on time, i.e. two weeks after the missed class.
- Each student will present a 15-20 min oral presentation of one journal article that will be chosen by the student from articles in the course packet. The presentation must use MS PowerPoint. All students will read all articles being presented and be prepared to participate in discussions of the articles.
- The exam will consist of problems similar to the homework exercises and essay questions. Questions must be answered during the exam period without reference to books or notes of any kind. Calculators may be used, but no palm pilots or similar devices will be allowed. Make-up exams will be scheduled only in extenuating circumstances and will require a doctors note, police report, or similar supporting documentation.
Class attendance policy: Because the class meets only one time per week and because the class format is mainly discussion, it is very difficult to make up missed classes by borrowing notes, etc. Therefore, students are required to attend all classes. Computers are allowed in class for taking notes, but are not allowed during exams. Class discussions/lectures cannot be recorded in any manner without special permission.
Accommodations for students with disabilities: If you require accommodation due to a disability, please make an appointment during my office hours so that we may discuss your needs. Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation.
Academic honesty: As a result of completing the registration form at the University of Florida, every student has signed the following statement: I understand that the University of Florida expects its students to be honest in all their academic work. I agree to adhere to this commitment to academic honesty and understand that my failure to comply with this commitment may result in disciplinary action up to and including expulsion from the University. An excellent website that discusses plagiarism (provides a definition and many useful examples) is http://www.csubak.edu/ssric/Modules/Other/plagiarism.htm. All students should read this material at least once.
UF Counseling Services: On-campus services are available for students having personal problems or lacking clear career and academic goals. They include:
Video The Gene Hunters (example of studies conducted under the Human Genome Diversity Program)
1) The recent African genesis of humans, Wilson and Cann, April, 1992, Scientific American, 68-73
Exercise #1 Restriction site mapping and investigation
September 14 Lecture How to read a scientific journal article, sample PubMed search, colonization of the New World
Skim Genetics and the Search for Modern Human Origins (MHO) Chapter 2
1) Extensive mitochondrial diversity within a single Amerindian tribe, Ward et al., 1991, Proc Natl Acad Sci USA, 88:8720-8724
2) Population genetics, history, and health patterns in Native Americans, Mulligan et al., 2004, Annu Rev Genomics Hum Genet, 5:295-315
Questions on Exercise #1
Sign up for oral presentations (any articles in course packet after Sept 14)
September 21 Lecture Sample oral presentation, molecular genetic identification of Russian Tsar, colonization of Polynesia
Reading assignment - SDE Chapters 5, 6, 7 case study of the Russian Tsar and molecular analysis of Pacific Island populations
1) Identification of the remains of the Romanov family by DNA analysis, Gill et al., 1994, Nature Genetics, 6:130-135
2) Press release AND Molecular, forensic and haplotypic inconsistencies regarding the identity of the Ekaterinburg remains, Knight et al., 2004, Ann Hum Bio, 31:129-138
Exercise #1 due
September 28 Lecture colonization of Europe, replacement by modern humans or interbreeding with Neanderthals?
Reading assignment - SDE Chapters 8, 9 colonization of Europe and Neanderthals
1) DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen, Krings et al., 1999, Proc Natl Acad Sci USA, vol 96, pp 5581-5585
2) The Neandertal type site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany, Schmitz et al., Proc Natl Acad Sci USA, 99:13342-1347
Exercise #2 assigned
October 5 Lecture hunter-gatherers/pastoralism, minimum spanning networks, recombination
Reading assignment - SDE Chapters 10,11 controversies surrounding theories on first Europeans
1) Genetics and the population history of Europe, Barbujani and Bertorelle, 2001, Proc Natl Acad Sci USA, 98:22-25
2) Genetic evidence for different male and female roles during cultural transitions in the British Isles, Wilson et al., 2001, Proc Natl Acad Sci USA, 98:5078-5083
October 12 - Lecture analysis of Y chromosome genetic variants, comparison with mtDNA results
Reading assignment - SDE Chapter 13 Adam Joins the Party
1) Press release AND The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y chromosome perspective, Semino et al., 2000, Science, 290:1155-1159
2) Y chromosomes traveling south: The Cohen modal haplotype and the origins of the Lemba the Black Jews of the Southern Africa, Thomas et al., 2000, Am J Hum Genet, 66:674-686
3) Founding mothers of Jewish communities: Geographically separated Jewish groups were independently founded by very few female ancestors
Exercise #2 due
October 19 - Lecture ads and disads of ancient DNA
Reading assignment - SDE Chapters 1, 12, 14 ancient DNA
Reading assignment - SDE Chapters 15-23 (just for fun, not quiz or exam) fictional accounts of original European founding women
1) DNA sequence from Cretaceous period bone fragments, Woodward et al., 1994, Science, 266:1229-1232 AND Comments by Hedges and Schweitzer, Henikoff, Allard et al., Zischler et al., and Woodward, 1995, Science, 268:1191-1194
2) Analysis of ancient DNA from a prehistoric Amerindian cemetery, Stone and Stoneking, 1999, Phil Trans R Soc Lond B, 354;153-159
Exercise #3 assigned
October 26 - Lecture Genetic drift, similarities/differences of mt, Y, and autosomal DNA, primate phylogeny
Reading assignment - Genetics and the Search for Modern Human Origins (MHO) Chapters 1, 2 molecular analysis of human evolution
1) Y genetic data support the Neolithic demic diffusion model, Chikhi et al., 2002, Proc Natl Acad Sci USA, 99:11008-11013
2) Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo, Wildman et al., 2003, Proc Natl Acad Sci USA, 100:7181-7188
November 2 - Lecture Evolution of genus Homo, replacement and multiregional theories of human origins, origin and timing of our most recent common ancestor
Reading assignment - MHO Chapters 3 ,4 The Modern Human Origins Debate & In Search of our Common Ancestor
AND Course packet: Genetic and fossil evidence for the origin of modern humans, Stringer and Andrews, 1988, Science, 239:1263-1268
1) Press release AND Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans, Caramelli et al., 2003, Proc Natl Acad Sci USA
2) Press releases AND X chromosome evidence for ancient human histories, Harris and Hey, 1999, Proc Natl Acad Sci USA, 96:3320-3324.
3) Press release AND Comments AND Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins, Adcock et al., 2001, Proc Natl Acad Sci USA, 98:537-542
Exercise #3 due
November 9 - Lecture Patterning of genetic diversity
Reading assignment - MHO Chapters 5, 6 measurement and geographic distribution of genetic diversity, genetic distances
1) Press release AND Comments AND Global patterns of linkage disequilibrium at the CD4 locus and modern human origins, Tishkoff et al., 1996, Science, 271:1380-1387
2) Alu insertion polymorphisms and human evolution: Evidence for a larger population size in Africa, Stoneking et al., 1997, Genome Res, 7:1061-1071
Exercise #4 assigned
November 16 Lecture population size, population history
Reading assignment - MHO Chapter 7 How Many Ancestors?
1) Genetic evidence for larger African population size during recent human evolution, Relethford and Jorde, 1999, Am J Phys Anthropol, 108:251-260
2) Genetic traces of ancient demography, Harpending et al., 1998, Proc Natl Acad Sci USA, 95:1961-9167
November 23 Lecture Neanderthal genetic diversity, relationship to modern humans
Reading assignment - MHO Chapters 8, 9 Neanderthal DNA
1) A reanalysis of the ancient mitochondrial DNA sequences recovered from Neandertal bones, Gutierrez et al., 2002, Mol Biol Evol, 19:1359-1366
2) Absence of regional affinities of Neandertal DNA with living humans does not reject multiregional evolution, Relethford, 2001, Am J Phys Anthropol, 115:95-98
1) The deltaccr5 mutation conferring protection against HIV-1 in Caucasian populations has a single and recent origin in Northeastern Europe, Libert et al., 1998, Hum Mol Gen, 7:399-406
2) Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum, Mu et al., 2002, Nature, 418:323-326
3) Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance, Tishkoff et al., 2001, Science, 293:455-462
December 7 - Exam