ASM 494/598 Genetic Perspectives on Modern Human Origins

Wednesday 1:40-4:30

Course Description:

            This course will discuss human evolutionary history from a genetic perspective.  In particular, we will examine the different models that have been proposed for recent human evolution, the types of genetic markers that have been analyzed and what they indicate, and the current debates in the field. Did the most recent common ancestors of modern humans exist 1 million, 500,000 or 50,000 years ago? Where did they live, and did they interbreed with other hominins? Do the available genetic data enable us to distinguish between the competing theories of the origin of modern humans? What kinds of data are necessary for testing these hypotheses? Emphasis is on critical reading and discussion of recent literature. Students will also get some hands on experience with basic analyses of data. The course web site is: http://www.public.asu.edu/~acstone/Genetic_Perspectives/

 Grading:

The final grade for the course will be based on homework consisting of problem sets (60%), class discussion (15%) and a  research paper (25%). Extra credit will not be offered in this course.

 Course Reading Material:

Articles for the class will be placed on the course link in myASU.

Week 1: Introduction

Week 2: Early research on human evolution from a genetic perspective

Sarich, VM and Wilson AC (1967) Immunological time scale for hominid evolution. Science 158:1200-1203.

Lewontin, R. C. (1972) The apportionment of human diversity. Evolutionary Biology 6:381-398

Nei, M. and Roychoudhury, A. K. (1974) Genic variation within and between the three major races of man, Caucasoids, Negroids, and Mongoloids. American Journal of Human Genetics 26:421-443.

Cavalli-Sforza, L. L. (1974) The genetics of human populations. Scientific American 231(3):80-89.

Mountain, J. (1998) Molecular evolution and modern human origins. Evolutionary Anthropology 7:21-37.

Week 3: Mitochondrial DNA

Cann, R et al. (1987) Mitochondrial DNA and human evolution. Nature 325: 31-36.

Vigilant, L et al. (1991) African populations and the evolution of human mitochondrial DNA. Science 253:1503-1507.

Templeton, AR (1993) The “Eve” hypothesis: a genetic critique and reanalysis. American Anthropologist 95:51-72

Stoneking, M (1994) In defense of “Eve” - a response to Templeton’s critique. American Anthropologist 96:131-141.

Week 4: Mitochondrial DNA (part II), Neandertals and us

Harpending et al. (1993) The genetic structure of ancient human populations. Current Anthropology 34:483-496.

Krings et al. (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19-30.

Ingman, M et al. (2000) Mitochondrial genome variation and the origins of modern humans. Nature 408: 708-713.

Gutierrez, G. et al. (2002) A reanalysis of the ancient mitochondrial DNA sequences recovered from Neandertal bones. Molecular Biology and Evolution 19:1359-1366.

Week 5: The Y chromosome

Hammer, MF (1995) A recent common ancestry for human Y chromosomes. Nature 378:376-378

Hammer, MF and Zegura, SL (1996) The role of the Y chromosome in human evolutionary studies. Evolutionary Anthropology 5:116-134

Underhill, PA et al. (2001) The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Annals of Human Genetics 65:43-62

Week 6: Other markers

Sherry S. and Batzer M. (1997) Modeling human evolution: to tree or not to tree? Genome Research 7:947-949.

Stoneking M. et al. (1997) Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Research 7:1061-1071.

Tishkoff S. et al. (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271:1380-1387.

Garrigan et al. (2005) Deep haplotype divergence and long-range linkage disequilibrium at Xp21.1 provide evidence that humans descend from a structured ancestral population. Genetics 170:1849-1856.

Week 7: Patterning in modern humans (language)

Sokal R. et al. (1990) Genetics and language in European populations. American Naturalist 135:157-175

Barbujani G. (1997) Invited Editorial: DNA variation and language affinities. American Journal of Human Genetics 61:1011-1014.

Poloni E. S. et al. (1997) Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics. American Journal of Human Genetics 61:1015-1035.

Rosser Z. H. et al. (2000) Y-chromosomal diversity in Europe is clinal and influenced primarily by geography rather than by language. American Journal of Human Genetics 67:1526-1543.

Week 8: no class

Week 9: spring break

Week 10: Patterning in modern humans (mating patterns)

Stoneking, M (1998) Women on the move. Nature Genetics 20:219-220

Seielstad, M. (1998) Genetic evidence for a higher female migration rate in humans. Nature Genetics 20:278-280.

Oota H. et al. (2001) Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nature Genetics 29:20-21.

Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, Zhu S, Qamar R, Ayub Q, Mohyuddin A, Fu S, Li P, Yuldasheva N, Ruzibakiev R, Xu J, Shu Q, Du R, Yang H, Hurles ME, Robinson E, Gerelsaikhan T, Dashnyam B, Mehdi SQ, and Tyler-Smith C. (2003) The genetic legacy of the Mongols. American Journal of Human Genetics 72:717-721.

Wooding S., Ostler C, Prasad BVR, Watkins WS, Sung S, Bamshad M, and Jorde LB (2004) Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data. Human Genetics 115:221-229.

Week 11: The genome (us and chimpanzees)

The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87

Li W-H and Saunders MA (2005) The chimpanzee and us. Nature 437:50-51

Feuk L et al. (2006) Structural variation in the human genome. Nature Reviews Genetics 7:85-97

Week 12: phenotypic variation

Harding RM et al. (2000) Evidence for variable selective pressures at MC1R, American Journal of Human Genetics, 66:1351-1361

Frudakis T et al. (2003) Sequences associated with human iris pigmentation. Genetics: 165-2071

Sturm RA and Frudakis TN (2004) Eye colour: portals into pigmentation genes and ancestry. Trends in Genetics 20(327-332

Week 13: What makes us human? (part I)

Carroll S. (2003) Nature 422:849-857

Bamshad and Wooding (2003) Signatures of Natural Selection in the Human Genome, Nature Reviews Genetics 4:99-111.

Voight et al. (2006) A map of recent positive selection in the human genome. PLOS 4:446-458

Week 14: What makes us human? (part II)

Fisher SE and Marcus GF (2006) The eloquent ape: genes, brains and the evolution of language. Nature Reviews Genetics 7:9-20

Lai CSL et al. (2001) A forkhead-domain gene is mutated in a severe speech and language disorder. Nature 413:519-523.

Enard W et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language, Nature 418:869-872.

Bond J et al. (2002) ASPM is a major determinant of cerebral cortical size. Nature Genetics 32:316-320.

Kouprina N et al. (2004) Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLOS Biology 2:126-136.

Week 15: Expression patterns

Enard W et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296:340-3.

Gilad Y et al (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245

Fraser HB et al. (2005) Aging and gene expression in the primate brain. PLoS Biol 3:1654-1661