ANG 6460L, ADVANCED MOLECULAR ANTHROPOLOGY LABORATORY

Prof. Connie J. Kolman

Class meets in B103 Turlington Hall

Contact information:

Turlington Hall, B119

(352)392-2253

Office hours: Tues and Thurs, 10:30-12:00

The purpose of this class is to examine current applications of molecular data to questions of anthropological interest through class discussions and original laboratory research. Approximately 1/3 of class time will be spent on oral presentations and class discussions of journal articles (chosen by the student) and lab results. The remaining 2/3 of class time will be spent on original laboratory research focused on the student’s PhD research topic. All research will be conducted in Dr. Mulligan’s laboratory.

All students will present at least two 15-30 min oral presentation of either 1) a journal article of molecular anthropological interest or 2) their own laboratory results. All students will be responsible for reading all articles assigned for each week and generating at least 2-3 questions or comments for articles that the student is not presenting. Students will also design laboratory experiments that address a specific question within the broad area of their thesis research. The oral presentation and questions/comments plus regular class participation will account for 25% of the course grade. Experimental design, performance of experiments, and maintenance of a laboratory notebook will account for 75% of the course grade.

Journal articles and topics to be presented and discussed will be chosen by the student, but, in the past, have included the following papers:

Use of genetic data to define human populations and track migrations, eg. colonization of the New World

Mitochondrial DNA and the peopling of the New World, Schurr 2000, Amer Scientist, 88:246-253

Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations, Torroni et al 1992, Genetics, 130:153-162.

Origin and evolution of Native American mtDNA variation: A reappraisal, Forster et al 1996, Am J Hum Genet, 59:935-945.

mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America? Brown et al 1998, Am J Hum Genet, 63:1852-1861.

Origin of New World colonizers

mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans, Torroni et al 1993, Am J Hum Genet, 53:591-608.

Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders, Kolman et al 1996, Genetics, 142:1321-1334.

Ancestral Asian source(s) of New World Y-chromosome founder haplotypes, Karafet et al 1999, Am J Hum Genet, 64:817-831.

History of Oceanic populations

MtDNA and language support a common origin of Micronesians and Polynesians in Island Southeast Asia, Lum and Cann 1998, Am J Phys Anthropol, 105:109-119.

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations, Lum et al 1998, Am J Hum Genet, 63:613-624

Polynesian origins: Insights from the Y chromosome, Su et al 2000, Proc Natl Acad Sci USA, 97:8225-8228.

MtDNA and Native Americans: A southern perspective, Cann 1994, Am J Hum Genet, 55:7-11 and responses Lack of ancient Polynesian-Amerindian contact, Bonatto et al 1996, Am J Hum Genet, 59:253-256 and Mitochondrial myopia: Reply to Bonatto et al, Cann and Lum 1996, Am J Hum Genet, 59:256-258

Estimating 1) admixture levels and 2) historical demographics of human populations

Mitochondrial versus nuclear admixture estimates demonstrate a past history of directional mating, Merriwether et al 1997, Am J Phys Anthropol, 102:153-159.

Estimating African American admixture proportions by use of population-specific alleles, Parra et al 1998, Am J Hum Genet, 63:1839-1851.

The genetic structure of ancient human populations, Harpending et al 1993, Curr Anthropol, 34:483-496

Human evolution: Out-of-Africa or something more complicated?

Mitochondrial DNA sequences in single hairs from a southern African population, Vigilant et al 1989, Proc Natl Acad Sci USA, 86:9350-9354.

Global patterns of linkage disequilibrium at the CD4 locus and modern human origins, Tishkoff et al 1996, Science, 271:1380-1387 and responses Interpretations of multiregional evolution, Wolpoff 1996 and Tishkoff et al 1996, Science, 274 and Genetic data and the African origin of humans, Pritchard and Feldman 1996 and Risch et al 1996, Science, 274:1648-1549.

X chromosome evidence for ancient human histories, Harris and Hey 1999, Proc Natl Acad Sci USA, 96:3320-3324.

Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation, Hammer et al 1998, Mol Biol Evol, 15:427-441.

Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa, Quintana-Murci et al 1999, Nature Genetics, 23:437-441.

Colonization of Europe: Significant Neolithic contribution or not?

Paleolithic and Neolithic lineages in the European mitochondrial gene pool, Richards et al 1996, Am J Hum Genet, 59:185-203

Paleolithic and Neolithic lineages in the European mitochondrial gene pool, Cavalli-Sforza and Minch 1997, Am J Hum Genet, 61:247-251 and response Richards et al 1997, Am J Hum Genet, 61:251-254.

Evidence for Paleolithic and Neolithic gene flow in Europe, Barbujani et al 1998, Am J Hum Genet, 62:488-491 and response Richards and Sykes 1998, Am J Hum Genet, 62:491-492.

The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y chromosome perspective, Semino et al 2000, Science, 290:1155-1159.

Analysis of ancient DNA to reconstruct human history

Ancient DNA analysis of human populations, Kolman and Tuross 2000, Am J Phys Anthropol, 111:5-23.

mtDNA analysis of a prehistoric Oneota population: Implications for the peopling of the New World, Stone and Stoneking 1998, Am J Hum Genet, 62:1153-1170.

Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake wetlands, Parr et al 1996, Am J Hum Genet, 99:507-518.

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

Analysis of DNA from ethnoarchaeological stone scrapers, Kimura et al, J Arch Sci, in press

Forensic DNA analysis

Ethnic-affiliation estimation by use of population-specific DNA markers, Shriver et al., 1997, Am J Hum Genet, 60:957-964.

Application of mtDNA sequence analysis in forensic casework for the identification of human remains, Bender et al 2000, Forensic Sci Int, 113:103-107 and Efficiency of forensic mtDNA analysis: Case examples demonstrating the identification of traces, Szibor et al 2000, Forensic Sci Int, 113:71-78.

Short tandem repeat methodology for genotypic identification of single-person versus multi-person use of syringes, Shrestha et al 2000, AIDS, 14:1507-1513.

Identifying genetic mutations responsible for human diseases

Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene, Dean et al 1996, Science, 273:1856-1862.

Polymorphisms in genes involved in folate metabolism as maternal risk factors for Down syndrome, Hobbs et al 2000, Am J Hum Genet, 67:623-630.

Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits, Kittles et al 1999, Proc Natl Acad Sci USA, 96:4204-4209.