Deborah A. Bolnick

This course surveys the patterns of biological variation within and between human populations.  We will examine physical, genetic, and behavioral traits, and consider both the microevolutionary and cultural processes that influence those traits.  We will also discuss how studies of human variation have impacted society in the past and present.  Topics include:  an overview of the principles of genetics and evolution, race, sex differences, human variability in behavior, eugenics and contemporary genetic issues, human plasticity, and disease.

This course explores the intersection of genetics and anthropology.  We will cover the basic principles of molecular genetics and population genetics as relates to the study of humans and other primates.  We will examine the ways in which genetics can contribute to the field of anthropology, as well as how anthropological knowledge can illuminate genetic findings.  Students will gain hands-on experience in genetic analysis, and will learn to understand and evaluate molecular anthropology research.  Topics to be covered include: human genetic diversity, human evolution and migration, ancient DNA, primate evolution and behavior, genetic ancestry and identity, genetic essentialism, admixture, eugenics, and the ethical, legal, and social implications of human genetics research.

This course surveys the patterns of biological variation within and between human populations.  We will examine physical, genetic, and behavioral traits, and consider both the microevolutionary and cultural processes that influence those traits.  We will also discuss how studies of human variation have impacted society in the past and present.  Topics include:  an overview of the principles of genetics and evolution, race, sex differences, human variability in behavior, eugenics and contemporary genetic issues, human plasticity, and disease.

Ancient DNA can be obtained from the remains of organisms that have long been dead (and may now be extinct), and it can be retrieved from a variety of sources — human and animal remains, coprolites, seeds and other plant material, soil, and even some cultural artifacts.  The study of ancient DNA makes it possible to directly assess genetic variation in the past, allowing us to track evolutionary changes over time and to reconstruct long-term population dynamics.  Furthermore, when ancient DNA is considered in conjunction with archaeological evidence, it can help clarify the social structure, mating and postmarital residence patterns, kinship systems, and burial practices of ancient populations.  It can also shed light on prehistoric population movements and interactions.   While ancient DNA studies have the potential to provide important and unique insights about evolution and human prehistory, there are significant challenges associated with the recovery and analysis of ancient DNA.  This graduate course will explore the prospects and problems of ancient DNA research, and will consider applications of such research in anthropology, evolutionary biology, archaeology, and paleontology.  Topics to be covered may include:  post-mortem DNA degradation and preservation; sources of ancient DNA; laboratory methods for analyzing ancient DNA; contamination and authentication issues; phylogenetic, demographic, and anthropological inferences from ancient DNA; the Neandertal/Denisovan genomes and human evolution; biomolecular archaeology; prehistoric human migration; plant and animal domestication; paleopathology, disease, and ancient microbial studies; animal ancient DNA studies; the rate of molecular evolution; plant archaeogenetics.

 

This course explores the intersection of genetics and anthropology.  We will cover the basic principles of molecular genetics and population genetics as relates to the study of humans and other primates.  We will examine the ways in which genetics can contribute to the field of anthropology, as well as how anthropological knowledge can illuminate genetic findings.  Students will gain hands-on experience in genetic analysis, and will learn to understand and evaluate molecular anthropology research.  Topics to be covered include: human genetic diversity, human evolution and migration, ancient DNA, primate evolution and behavior, genetic ancestry and identity, genetic essentialism, admixture, eugenics, and the ethical, legal, and social implications of human genetics research.

This course explores the intersection of genetics and anthropology.  We will cover the basic principles of molecular genetics and population genetics as relates to the study of humans and other primates.  We will examine the ways in which genetics can contribute to the field of anthropology, as well as how anthropological knowledge can illuminate genetic findings.  Topics to be covered include the genetic structure of human populations, race and gender issues, primate evolution and behavior, ancient DNA, gene/language/culture co-evolution, behavioral genetics, genetic testing/counseling, the Human Genome Project, identity and genetic essentialism, and the ethical, legal, and social implications of human genetics research.

Prerequisite: Upper-division standing and Anthropology 301.

 

This course will examine the scientific study of race. We will trace the history of racial scientific racism, and we will explore the ways that race is constructed and understood in anthropology, biology, psychology, and medicine. We will also evaluate both the nature and significance of human biological diversity. This approach will make it possible for us to understand why some recent scientific research reifies race as genetic, and it will help us develop effective strategies for conveying the complex nature of race.

Anthropology 348K

ANTHROPOLOGICAL GENETICS-W

Spring 2010

 

Course Information:            Unique #30440

                                                                                                                        TTh 2:00-3:30 pm, JES A215A

 

Course Instructor:                        Dr. Deborah Bolnick

                                                                                                                            E-mail: deborah.bolnick@mail.utexas.edu

                                                                                                                        Phone: (512) 471-7532

                                                                                                                        Office Hours: EPS 1.106, Thursday 11:30am-1:30pm or by appointment

 

Teaching Assistant:                        Gabrielle Russo

                                                                                                                        E-mail: gabrielle.russo@mail.utexas.edu

                                                                                                                        Office Hours: EPS 2.104, Friday 9:00-10:50am 

 

Course Description:           

This course explores the intersection of genetics and anthropology.  We will cover the basic principles of molecular and population genetics as relates to the study of humans and non-human primates.  We will discuss the ways in which genetics can contribute to the field of anthropology, as well as how anthropological knowledge can illuminate genetic research.  This class will be a mix of lecture, discussion, and laboratory work.  Tuesdays will be mostly lecture, whereas Thursdays will be devoted to discussions of the assigned readings or lab work.  You will gain some hands-on experience in genetic analysis and will learn to understand and evaluate molecular anthropology research.  This course is also a substantial writing component course, so we will work to improve your writing skills through short, informal writing assignments and a longer research paper.

 

Course Requirements:

1.            Exam 1 (20%).  The first exam on February 25 will cover material from lectures, discussions,

labs, and readings.  The exam may include multiple choice, short answer, and essay questions.

2.       Exam 2 (20%).  The second exam on April 15 will cover material presented after the first exam.  Exam format will be similar to that of the first exam.

3.       Short Writing Assignments (10%).  Five short writing assignments (1 pg each, double-spaced) will be given over the semester.  In some assignments, you will reflect on the assigned readings before coming to a class discussion; in others, you will apply what you learned in class to analyze a genetic dataset.  These assignments will be graded based on the thought and effort you put into the assignment, and will give you the chance to receive some informal feedback on your writing.

4.            Class Participation (15%).  This portion of your grade will be based on your participation in

class activities and discussions.  On one discussion day, you will be responsible for (a) orally

summarizing the main points of the readings for the class, and (b) providing questions to help

guide the class discussion. This activity will make up 1/3 of your class participation grade.   

5.  Research Paper (30%).  The research paper (10-12 pages, double-spaced) will allow you to

explore a relevant topic of your choice.  A 2-page proposal and bibliography (5%) is due on

March 23.  Part 1 of the paper (10%) is due on April 8.  After receiving feedback, you will

submit your final research paper (15%) on May 6.  Paper instructions will be handed out later.

6.  Research Presentation (5%).  Each student will give a 10-minute presentation on the subject of

their research paper on May 6 or 15.

Required Readings:

1.             Relethford, John H. 2003. Reflections of Our Past. Boulder: Westview Press.

2.             A packet of other required readings is available at Abel’s Copies (University Towers, 715D West

23^rd Street, 472-5353).

 

Course Website: 

Class information, handouts, and a discussion forum will be available at the course website on Blackboard (http://www.courses.utexas.edu).  Course updates will also be sent to your university e-mail account.  Please check both regularly. 

 

Grading Policies:

If an assignment is turned in late, the assignment grade will be lowered by 10% for each day that the assignment is late.  If a serious issue (i.e. illness, family death, etc.) arises that may prevent you from attending class, turning in an assignment on time, or taking an exam, contact Dr. Bolnick by e-mail or telephone as soon as possible to discuss an assignment extension or to schedule a make-up exam.

 

Final letter grades will be assigned using the following scale: A (90-100%), B (80-89%), C (70-79%), D (60-69            %), F (0-59%).

 

Re-grading Policy:  If you believe that an exam or assignment has been graded incorrectly, submit a written request for a re-grade to Dr. Bolnick within one week of when the graded exam or assignment was returned.  The written request should include an explanation of your position and be attached to the graded exam or assignment.  If you suspect that a simple addition error was made, speak to Dr. Bolnick to have the error corrected. 

 

Credit/No-Credit Policy:  To receive credit for this course if you enrolled on the pass/fail basis, you must 1) take the two exams, 2) turn in a paper proposal, part 1 of the research paper, and final research paper, 3) complete at least three of the short writing assignments, and 4) receive the equivalent of a D or higher in this class.

 

Cheating/Plagiarism Policy:  If you cheat or plagiarize, the university guidelines for disciplinary action will be followed.  Any cheating or plagiarism will be reported to the Dean of Students and will result in failure of this course.  For more information, see http://deanofstudents.utexas.edu/sjs (especially the sections on Academic Integrity, Plagiarism, and Discipline Procedures).

 

Accommodations:  I encourage students with disabilities to meet with me at the beginning of the semester to discuss any needs.  Any student with a documented disability (e.g. physical, learning, psychiatric, vision, hearing, etc.) may arrange accommodations with Services for Students with Disabilities, which is located in the Student Services Building (see http://deanofstudents.utexas.edu/ssd or call 471-6259 or TTY 471-4641 for more information).

 

Attendance:  I do not take formal attendance, but I am aware of who consistently comes to class and who does not.  Attendance is necessary to earn the points for class participation, and consistent attendance can help to raise your grade if you end up with a borderline final grade.  Whether or not you come to class, you are responsible for keeping up with what happens in class.
Schedule of Topics, Readings, and Important Dates:

 

            (D) = class discussion; SWA = Short Writing Assignment

* indicates readings that must be completed BEFORE coming to class

 

Date                                                                        Topic and Readings

Tues., Jan. 19                                    Introduction and History   

Reading: O’Rourke; Marks (A)   

 

Th            urs., Jan. 21                                    (D) Folk Heredity and Eugenics; SWA 1 Due

                                                                               Reading: *Scheinfeld, *Allen, *Sinnott & Dunn, *Kalb             

 

Tues., Jan. 26                                    DNA, Genes, and Mutations                                                                       

Reading: Stone & Lurquin; Dolgin    

 

Th            urs., Jan. 28                                    DNA Extraction and Polymerase Chain Reaction (PCR) Lab (in PAT 609)  

                                                                               Reading: Hartl & Jones (A)                         

 

Tues., Feb. 2                                    Genome Complexities     

                                                                                                Reading: Commoner, Ledford, Gibbs, Pray, Zimmer                         

 

Th            urs., Feb. 4                                    (D) Genetic Essentialism; SWA 2 Due

Reading: *Nelkin & Lindee, *Turney, *Wald, *Taussig    

 

Tues., Feb. 9                                    Population Genetics I 

                                                                                                Reading: Mielke et al.            

 

Thurs., Feb. 11                                    Gel Electrophoresis and RFLP Lab (in PAT 609)

                                                                                                Reading: Hartl & Jones (B)                         

 

Tues., Feb. 16                                    Population Genetics II; SWA 3 Due

                                                                                                Reading: Fix, Mielke & Fix                       

 

Thurs., Feb. 18                                    (D) Admixture; Overview of Research Paper Assignment                                                           

                                                                                                Reading: *Reflections of Our Past chapter 10; Hafner                                     

 

Tues., Feb. 23                                    Population Genetics III; Review for Exam; SWA 4 Due

 

Th            urs., Feb. 25                                    Exam 1    

 

Tues., Mar. 2                                    Humans and Apes 

Reading: *Marks (B), Reflections of Our Past chapter 2, Cohen     

 

Th            urs., Mar. 4                                    DNA Sequence Analysis Lab                          

 

Tues., Mar. 9                                    Primate Evolution

                                                                                                Reading: Surridge et al.

 

 

Date                                                                        Topic and Readings

Thurs., Mar. 11                                    (D) Primate Behavior 

                                                                                                Reading: *Utami et al., *Ross et al., *Mitani et al.                       

 

Mar. 16/18                                                SPRING BREAK

 

Tues., Mar. 23                                    Ancient DNA; Research Paper Proposal and Bibliography Due

                                                                                                Reading: Kaestle & Horsburgh                        

 

Thurs., Mar. 25                                    (D) Neandertals                       

Reading: *Reflections of Our Past chapter 4, *Clark, *Krause et al., *Herrera et al.

 

Tues., Mar. 30                                    Modern Human Origins

  Reading: Reflections of Our Past chapter 3, Weaver & Roseman                

 

Thurs., Apr. 1                                    (D) Human Genetic Diversity                                                                                                                       

Reading: *Reflections of Our Past chapter 5, *Campbell & Tishkoff                             

 

Tues., Apr. 6                                    Prehistoric Migration I: Colonization of the Americas; SWA 5 Due 

  Reading: Reflections of Our Past chapter 6, Goebel et al.                

 

Thurs., Apr. 8                                    (D) Culture, Language, and Genes; Research Paper Part 1 Due

                                                                                                Reading: *Nettle & Harriss, *Nettle, *Bolnick et al. (A)

 

Tues., Apr. 13                                    Prehistoric Migration II: Europe and the Pacific

Reading: Reflections of the Past chapters 7 & 8         

 

Thurs., Apr. 15                                    Exam 2

 

Tues., Apr. 20                                    Film: Motherland             

 

Thurs., Apr. 22                                    (D) Genomics, Ancestry, and Identity

  Reading: *Bolnick et al. (B), *Rotimi, *Nelson                

 

Tues., Apr. 27                                    Guest Lecturer: John Relethford (SUNY-Oneonta)

Reading: Reflections of the Past chapter 9

 

Thurs., Apr. 29                                    (D) Genetic Kinship

                                                                                                Reading: *Tallbear, *Nash                                   

 

Tues., May 4                                    (D) DNA Databases

                                                                                                Reading: *Pálsson & Hardardóttir, *Obasogie

 

Thurs., May 6                                    Student Presentations; Final Research Paper Due

 

Sat., May 15                                                Student Presentations (9am – noon)                       
Contents of the Course Reader:

O’Rourke DH. 2003. Anthropological genetics in the genomic era: a look back and ahead.

American Anthropologist 105:101-109.

Marks, J. (A) 2008. The construction of Mendel’s laws. Evolutionary Anthropology 17:250-253.

Scheinfeld A. 1944. The Kallikaks after thirty years. Journal of Heredity 259-264.

Allen, GE. 1997. The social and economic origins of genetic determinism: a case history of the

American eugenics movement, 1900-1940 and its lessons for today. Genetica 99:77-88.

Sinnott EW, Dunn LC. 1925. The problems of eugenics. Principles of Genetics: An

Elementary Text, with Problems. New York: McGraw-Hill Book Co. pp 402-415.

Kalb C. 2004. Brave new babies. Newsweek January 26:44-52.

Stone L, Lurquin PF. 2007. Genes, Culture, and Human Evolution: A Synthesis. Malden, MA: Blackwell

Publishing. pp 48-72.

Dolgin E. 2009. The genome finishers. Nature 462:843-845.

Hartl DL, Jones EW. (A) 2001. Genetics. Fifth edition. Sudbury, MA: Jones and Bartlett Publishers.

pp 58-64.

Commoner B. 2002. Unraveling the DNA myth. Harper’s Magazine February: 39-47.

Ledford H. 2008. Human genes are multitaskers. Nature.

Gibbs WW. 2003. The unseen genome: gems among the junk. Scientific American 289:46-53.

Pray LA. 2004. Epigenetics: genome, meet your environment. The Scientist 18:14-20.

Zimmer C. 2008. Now: the rest of the genome. New York Times (November 11).

Nelkin D, Lindee MS. 1995. The DNA Mystique. New York: W.H. Freeman and Co. pp 1-16.

Taussig K-S. 2005. The molecular revolution in medicine: promise, reality, and social organization.

In: MicKinnon S, Silverman S, editors. Complexities: Beyond Nature and Nurture. Chicago: University

of Chicago Press. pp 223-250.

Mielke JH, Konigsberg LW, Relethford JH. 2005. Human Biological Variation. Oxford: Oxford

University Press. pp 47-85.

Hartl DL, Jones EW. (B) 2001. Genetics. Fifth edition. Sudbury, MA: Jones and Bartlett Publishers.

pp 50-58, 65-76.

Fix AG. 1999. Migration and Colonization in Human Microevolution. Cambridge: Cambridge University

Press. pp 51-74.

Mielke JH, Fix AG. 2007. The confluence of anthropological genetics and anthropological

demography. In: Crawford MH, editor. Anthropological Genetics. Cambridge: Cambridge University

Press. pp 112-140.

Hafner K. 2007. Seeing corporate fingerprints in Wikipedia edits. New York Times (August 19).

Marks J. (B) 2002. What It Means to Be 98% Chimpanzee. Berkeley: University of California Press. pp 7-

50.

Cohen J. 2007. Relative differences: the myth of 1%. Science 316:1836.

Surridge AK, Osorio D, Mundy NI. 2003. Evolution and selection of trichromatic vision in

primates. TRENDS in Ecology and Evolution 18:198-205.

Utami SS, Goossens B, Bruford MW, de Ruiter JR, van Hooff JARAM. 2002. Male bimaturism

and reproductive success in Sumatran orang-utans. Behavioral Ecology 13:643-652.

Ross CN, French JA, Orti G. 2007. Germ-line chimerism and paternal care in marmosets (Callithrix

kuhlii). Proceedings of the National Academy of the Sciences USA 104:6278-6282.

Mitani JC, Merriwether DA, Zhang C. 2000. Male affiliation, cooperation, and kinship in wild

chimpanzees. Animal Behaviour 59:885-893.

Kaestle FA, Horsburgh KA. 2002. Ancient DNA in anthropology: methods, applications, and

ethics. Yearbook of Physical Anthropology 45:92-130.

Clark AG. 2008. Genome sequences from extinct relatives. Cell 134:388-389.

Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin J-J, Hänni C,

Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Pääbo S. 2007. The derived FOXP2 variant of

modern humans was shared with Neandertals. Current Biology 17:1908-1912.

Herrera KJ, Somarelli JA, Lowery RK, Herrera RJ. 2009. To what extent did Neanderthals and

modern humans interact? Biological Reviews 84:245-257.

Weaver TD, Roseman CC. 2008. New developments in the genetic evidence for modern human

origins. Evolutionary Anthropology 17:69-80.

Campbell MC, Tishkoff SA. 2008. African genetic diversity: implications for human demographic

history, modern human origins, and complex disease mapping. Annual Review of Genomics and

Human Genetics 9:403-433.

Goebel T, Waters MR, O’Rourke DH. 2008. The late Pleistocene dispersal of modern humans in the

Americas. Science 319:1497-1502.

Nettle D, Harriss L. 2003. Genetic and linguistic affinities between human populations in Eurasia

and West Africa. Human Biology 75:331-344.

Nettle D. 1999. Linguistic diversity of the Americas can be reconciled with a recent colonization.

Proceedings of the National Academy of the Sciences USA 96:3325-3329.

Bolnick DA, Bolnick DI, Smith DG. (A) 2006. Asymmetric male and female genetic histories in

Native Americans from eastern North America. Molecular Biology and Evolution 23:2161-2174.

Bolnick DA, Fullwiley D, Duster T, Cooper RS, Fujimura JH, Kahn J, Kaufman JS, Marks J,

Morning A, Nelson A, Ossorio P, Reardon J, Reverby SM, TallBear K. (B) 2007. The science and

business of genetic ancestry testing. Science 318:399-400.

Rotimi CN. 2003. Genetic ancestry tracing and the African identity: a double-edged sword?

Developing World Bioethics 3: 151-158.

Nelson A. 2008. Bio science: genetic genealogy testing and the pursuit of African ancestry. Social

Studies of Science 38:759-783.

TallBear K. 2008. Native-American-DNA.com: in search of Native American race and tribe. In:

Koenig BA, Lee SS, Richardson SS, editors. Revisiting Race in a Genomic Age. New Brunswick:

Rutgers University Press. pp 235-252.

Nash C. 2004. Genetic kinship. Cultural Studies 18:1-33.

Pálsson G, Hardardóttir KE. 2002. For whom the cell tolls. Current Anthropology 43:271-301.

Obasogie OK. 2009. Playing the Gene Card?: A Report on Race and Biotechnology. Oakland: Center for

Genetics and Society. pp 31-44.

 

 

 

PDFs Available on the Course Website:

Turney J. 2009. Interview with the gene: genetic metaphors in journalism. GeneWatch 22(6):8-11.

Wald P. 2009. Myth, Mendel, and the movies. GeneWatch 22(6):11-13.

 

Anthropology 388

HUMAN/PRIMATE EVOLUTIONARY GENETICS

Spring 2010

 

Course Information:            Unique Number: 30520

                                                                                                                        Meeting Time: Tuesdays 9:00 am-12:00 pm

Meeting Location: EPS 1.130KA

 

Course Instructor:                        Dr. Deborah Bolnick

                                                                                                                            E-mail: deborah.bolnick@mail.utexas.edu

                                                                                                                        Phone: (512) 471-7532

                                                                                                                        Office Hours: EPS 1.106, Thursday 11:30am-1:30pm or by appointment

 

Course Description:           

This course will examine the evolutionary history of human and non-human primates from a genetic perspective.  The first third of the course will provide an overview of genomics, population genetics, and evolutionary genetic theory as pertains to the study of humans and other primates.  Students will gain hands-on experience with laboratory techniques and the quantitative methods used to analyze genetic data.  The second two-thirds of the course will focus on applications of molecular data to questions and current issues in the study of human evolution/migration and primatology.  Emphasis will be placed on the critical analysis and discussion of recent literature, so students are expected to complete required readings before class and come prepared to actively participate in class discussion.

 

Course Requirements:

1.        Seminar Coordination (25%). Each student will organize and help lead two classes.  The student leader is expected to (a) briefly present the core ideas found in the readings (PowerPoint slides or handouts may be prepared if you think they would be helpful), and (b) prepare a set of topics and questions to help guide the class discussion.  You should consult with Dr. Bolnick in office hours or by email the week before you are scheduled to help lead class.

2.       Class Participation (25%).  Each student is expected to (a) complete all readings before class, (b) bring questions/comments to class, and (c) participate fully in all discussions.  The participation grade will also include grades for two short presentations on February 9 and 16 (instructions given in class at a later date).

3.       Weekly Commentaries (15%). A one page (double-spaced) commentary on the readings is due in class when you are not giving an in-class presentation.  This assignment is intended to facilitate careful, critical thought about the topic before class.  Your commentary may focus on one or several readings, and it may raise questions or concerns, discuss a point that seems particularly important, synthesize material from different sources, suggest additional research that is needed to resolve an issue, etc.  Your commentary should not simply be a summary of the readings.

4.       Genetics Exercises (10%). Three homework exercises will be assigned that involve the analysis of hypothetical or real molecular data.  Exercises will be graded on both accuracy and effort.

5.       Research Proposal and Presentation (25%). Each student will write a 15-20 page research proposal (double-spaced) on a relevant topic of your choice and in the format of a NSF Dissertation Improvement Grant proposal (guidelines will be distributed at a later date).  The first part of the proposal (5%) is due on April 6.  After receiving feedback from Dr. Bolnick and other students, each student will complete their proposal and turn in the final product on April 27 (15%).  Each student will also give a 20-minute presentation of their proposal on that day (5%).

Required Readings:

1.             Jobling MA, Hurles ME, and Tyler-Smith C. 2004. Human Evolutionary Genetics: Origins, Peoples, and

Disease. New York: Garland Science.

2.            Other required readings are available on the course website (see below).

 

If you do not understand a concept, method, or other topic, you are expected to follow up with additional readings.  Additional reading suggestions can be found at the end of each chapter in the textbook, in the references listed in the journal articles, or by talking to Dr. Bolnick.

 

Course Website: 

Class information, readings, assignments, handouts, and a discussion forum will be available at the course website on Blackboard (http://www.courses.utexas.edu).  Course updates will also be sent to your university e-mail account.  Please check both regularly. 

 

Grading Policies:

If an assignment is turned in late, the assignment grade will be lowered by 10% for each day that the assignment is late.  If a serious issue (i.e. illness, family death, etc.) arises that may prevent you from attending class or turning in an assignment on time, contact Dr. Bolnick by e-mail or telephone as soon as possible to discuss a make-up assignment or a change in an assignment’s due date.

 

Final letter grades will be assigned using the following scale:

A                      90-100%

B                      80-89%

C                      70-79%

D                      60-69%

F                      below 59%

 

Re-grading Policy:  If you believe that an assignment has been graded incorrectly, submit a written request for a re-grade within one week of when the graded assignment was returned.  The written request should include an explanation of your position and be attached to the graded assignment.

 

Cheating/Plagiarism Policy:  If you cheat or plagiarize, the university guidelines for disciplinary action will be followed.  Any cheating or plagiarism will be reported to the Dean of Students and will result in failure of this course.  For more information, see http://deanofstudents.utexas.edu/sjs (especially the sections on Academic Integrity, Plagiarism, and Discipline Procedures).

 

Accommodations:  I encourage students with disabilities to meet with me at the beginning of the semester to discuss any needs.  Any student with a documented disability (e.g. physical, learning, psychiatric, vision, hearing, etc.) may arrange accommodations with Services for Students with Disabilities, which is located in the Student Services Building (see http://deanofstudents.utexas.edu/ssd or call 471-6259 or TTY 471-4641 for more information).
Schedule of Topics, Readings, and Due Dates:

 

January 19                                    Introduction and History; DNA/PCR Lab

 

January 26                                    Human/Primate Genomes                       

Required Readings:

Human Evolutionary Genetics chapters 1 and 2.

Pennisi E. 2000. Human Genome Project: And the gene number is…? Science 288:1146-1147.

Pennisi E. 2007. Working the (gene count) numbers: finally, a firm answer? Science 316:1113.

Kaiser J. 2008. A plan to capture human diversity in 1000 genomes. Science 319:395.

Zimmer C. 2008. Now: the rest of the genome. The New York Times (November 11).

Monroe D. 2009. Genomic clues to DNA treasure sometimes lead nowhere. Science 325:142-143.

Li WH, Saunder MA. 2005. The chimpanzee and us. Nature 437:50-51.

Marques-Bonet T, Ryder OA, Eichler EE. 2009. Sequencing primate genomes: what have we

learned? Annual Review of Genomics and Human Genetics 10:355-386.

 

February 2                                    Genetic Variation; Gel Electrophoresis/RFLP Lab                       

Required Readings:

Human Evolutionary Genetics chapters 3 and 4.

Perry GH, et al. 2007. Diet and the evolution of human amylase gene copy number variation.

Nature Genetics 39:1256-1260. 

Willerslev E, Cooper A. 2005. Ancient DNA. Proceedings of the Royal Society Series B 272:3-16.

Millar CD, et al. 2008. New developments in ancient genomics. Trends in Ecology and Evolution

23:386-393.

 

February 9                                    Processes Shaping Genetic Diversity                       

Exercise 1 Due

Required Readings:

Human Evolutionary Genetics chapter 5.

Tishkoff SA, et al. 1996. Global patterns of linkage disequilibrium at the CD4 locus and modern

human origins. Science 271:1380-1387.

Amos W, Hoffman JI. 2010. Evidence that two main bottleneck events shaped modern human

genetic diversity. Proceedings of the Royal Society Series B 277:131-137.

Tishkoff SA, et al. 2007. Convergent adaptation of human lactase persistence in African and

Europe. Nature Genetics 39:31-40.

Oota H, et al. 2001. Human mtDNA and Y-chromosome variation is correlated with matrilocal

versus patrilocal residence. Nature Genetics 29:20-21.

Wilder JA, et al. 2004. Global patterns of mitochondrial DNA and Y-chromosome structure are

not influenced by migration rates of females than males. Nature Genetics 36:1122-1125.

 

February 16                        Genetic Inferences; DNA Sequence Analysis Lab                        

Required Readings:

Human Evolutionary Genetics chapter 6.

Underhill PA, Kivisild T. 2007. Use of Y chromosome and mitochondrial DNA population

structure in tracing human migrations. Annual Review of Genetics 41:539-564.

 

 

February 23                        Human/Primate Evolution                                    

Exercise 2 Due

Required Readings:

Human Evolutionary Genetics chapter 7.

Chatterjee HJ, et al. 2009. Estimating the phylogeny and divergence times of primates using a

supermatrix approach. BMC Evolutionary Biology 9:259.

Fischer A, et al. 2006. Demographic history and genetic differentiation in apes. Current Biology

16:1133-1138.

Cohen J. 2007. Relative differences: the myth of 1%. Science 316: 1836.

Patterson N, et al. 2006. Genetic evidence for complex speciation of humans and chimpanzees.

Nature 441:1103-1108. (also Brief Communications Arising)

Khaitovich P, et al. 2005. Parallel patterns of evolution in the genomes and transcriptomes of

humans and chimpanzees. Science 309:1850-1854.

 

March 2                                                Molecular Primatology                       

Required Readings:

Di Fiore A. 2003. Molecular genetic approaches to the study of primate behavior, social

organization, and reproduction. Yearbook of Physical Anthropology 46:62-99.

Utami SS, et al. 2002. Male bimaturism and reproductive success in Sumatran orang-utans.

Behavioral Ecology 13:643-652. 

Charpentier M, et al. 2005. Constraints on control: factors influencing reproductive success in

male mandrills (Mandrillus sphinx). Behavioral Ecology 16:614-623.

Rodriguez-Llanes JM, Verbeke G, Finlayson C. 2009. Reproductive benefits of high social status

in male macaques (Macaca). Animal Behaviour 78:643-649.

Ross CN, French JA, Orti G. 2007. Germ-line chimerism and paternal care in marmosets

(Callithrix kuhlii). Proceedings of the National Academy of the Sciences USA 104:6278-6282. 

Bradley BJ, Doran-Sheehy DM, Vigilant L. 2007. Potential for female kin associations in wild  

western gorillas despite female dispersal. Proceedings of the Royal Society Series B 274:2179-2185.

 

March 9                                                Origins of Modern Humans                                   

Required Readings:

Human Evolutionary Genetics chapter 8.           

Evans PD, et al. 2006. Evidence that the adaptive allele of the brain size gene microcephalin

introgressed into Homo sapiens from an archaic Homo lineage. Proceedings of the National Academy

of the Sciences USA 103:18178-18183. 

Garrigan D, Kingan SB. 2007. Archaic human admixture: a view from the genome. Current

Anthropology 48:895-902.

Herrera KJ, et al. 2009. To what extent did Neanderthals and modern humans interact? Biological

Reviews 84:245-257.

Pennisi E. 2009. Tales of a prehistoric human genome. Science 323:866-871.

Caramelli D, et al. 2003. Evidence for a genetic discontinuity between Neandertals and 24,000-

year-old anatomically modern Europeans. Proceedings of the National Academy of the Sciences USA

100:6593-6597.

Abbott A. 2003. Anthropologists cast doubt on human DNA evidence. Nature 423:468.

Barbujani G, Bertorelle G. 2003. Were Cro-Magnons too like us to tell? Nature 424:127.

 

March 16                                    Spring Break

 

March 23                                    Global Diversity Patterns                                   

Required Readings:

Human Evolutionary Genetics chapter 9.

Bolnick DA. 2008. Individual ancestry inference and the reification of race as a biological

phenomenon. In: Koenig B, Lee S, Richardson S, editors. Revisiting Race in a Genomic Age. New

Brunswick: Rutgers University Press. pp 70-88.

Novembre J, et al. 2008. Genes mirror geography within Europe. Nature 456:98-101.

Long JC, Li J, Healy ME. 2009. Human DNA sequences: more variation and less race. American

Journal of Physical Anthropology 139:23-34.

Hunley KL, Healy ME, Long JC. 2009. The global pattern of gene identity variation reveals a

history of long range migrations, bottlenecks, and local mate exchange: implications for

biological race. American Journal of Physical Anthropology 139:35-46.

DeGiorgio M, Jakobsson M, Rosenberg NA. 2009. Explaining worldwide patterns of human

genetic variation using a coalescent-based serial founder model of migration outward from

Africa. Proceedings of the National Academy of the Sciences USA 106:16057-16062.

The HUGO Pan-Asian SNP Consortium. 2009. Mapping human genetic diversity in Asia. Science

326:1541-1545.

 

March 30                                    Correlating Genes, Language, and Culture I: Population Expansions            

Exercise 3 Due

Required Readings:

Human Evolutionary Genetics chapters 10 and 11.

Barbujani G, Chikhi L. 2006. DNAs from the European Neolithic. Heredity 97:84-85.

Schroeder KB, et al. 2007. A private allele ubiquitous in the Americas. Biology Letters 3:218-223.

O’Rourke DH. 2009. Human migrations: the two roads taken. Current Biology 19:R203-R205.

 

April 6                                                Correlating Genes, Language, and Culture II: Admixture                        

                                                                        Research Proposal Part I Due

Required Readings:

Human Evolutionary Genetics chapter 12.

Hammer MF, et al. 2000. Jewish and Middle Eastern non-Jewish populations share a common

pool of Y-chromosome biallelic haplotypes. Proceedings of the National Academy of the Sciences

USA 97:6769-6774.

Fullwiley D. 2008. The biologistical construction of race: ‘admixture’ technology and the new

genetic medicine. Social Studies of Science 38:695-735.

Pena SDJ, et al. 2009. DNA tests probe the genomic ancestry of Brazilians. Brazilian Journal of

Medical and Biological Research 42:870-876. 

Halder I, et al. 2009. Measurement of admixture proportions and description admixture structure

in different U.S. populations. Human Mutation 30:1299-1309.

 

April 13                                                Phenotypic Variation and Adaptation                                   

Required Readings:

Human Evolutionary Genetics chapter 13.

Balter M. 2005. Are humans still evolving? Science 309:234-237.

Lamason RL, et al. 2005. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish

and humans. Science 310:1782-1786.

Gibbon A. 2007. European skin turned pale only recently, gene suggests. Science 316:364.

Culotta E. 2007. Ancient DNA reveals Neandertals with red hair, fair complexions. Science

318:546-547.

Yu L, et al. 2010. Adaptive evolution of digestive RNASE1 genes in leaf-eating monkeys

revisited: new insights from ten additional colobines. Molecular Biology and Evolution 27:121-131.

Surridge AK, Osorio D, Mundy NI. 2003. Evolution and selection of trichromatic vision in

primates. TRENDS in Ecology and Evolution 18:198-205.

Verrelli BC, et al. 2008. Different selective pressures shape the molecular evolution of color

vision in chimpanzee and human populations. Molecular Biology and Evolution 25:2735-2743.

 

April 20                                                Topic/Readings to Be Determined

 

April 27                                                Student Presentations                                   

Final Research Proposal Due 

 

May 4                                                No Class (Dr. Bolnick at SAR conference)