Updated reading list and information about the Archaeogenetics module Lent Term 2012 A37, A38, G10

Lectures
Lecture 1 (A37, A38, G10): Archaeogenetics principles and techniques Mon 13 Feb, 10-11am, This lecture looks at how genetic methods can be used to address archaeological questions. Key concepts in biology, fundamental molecular biological techniques and DNA analysis methods used to reconstruct relationships between organisms are outlined. Sampling and reconstruction of evolutionary patterns and processes will be discussed. Lecture 2 (A38, G10): Further archaeogenetics principles and techniques Tues 14 Feb, 9-10am, Unpicking the evolutionary toolkit: methods in the lab and on the computer. Polymerase chain reaction; DNA sequencing; genotyping. Genetic analysis: sequence alignment and tree reconstruction; bioinformatics databases. Identifying genetic clusters. Lecture 3 (A37, A38, G10): Archaeogenetics and agriculture Mon 20 Feb, 10-11am This lecture looks at how we can infer the domestication and spread of plants and animals from genetic data. We will discuss case studies using data from modern samples and archaeological specimens. We will outline the signals that can be observed from non-functional and functional genetic markers. Lecture 4 (A37, A38, G10): New methods and archaeogenetics in the genomics era Tues 21 Feb, 9-10am Ancient DNA. Next generation sequencing and its applications. Expressed genes.

Practicals
Weds 15 Feb (A37, G10) 11am-1pm, Lab 3.1 DNA amplification and visualisation *NB it is likely that we will have to arrange a 2nd session for some students as the group is too large to run as a single session* Weds 29 Feb (G10 only) 2-4pm, B9 (Computer Room) 29 Feb DNA sequence analysis and phylogeny construction NB - IMPORTANT NOTE FOR FEMALE STUDENTS: The first practical, DNA amplification, uses certain chemicals that should be avoided if you are pregnant. If

you are or think you may be pregnant, please contact the course lecturer concerned in confidence to inform them of the situation. You will not be expected to do the practical, but you will not be docked marks for lack of attendance.

Seminars
Tues 14th Feb, 2-4pm (A38, G10) Interpretation of archaeogenetic data sets For discussion: how can we answer key questions about domestication using DNA studies? Select 2-3 of the case studies listed in the reading list for Lecture 3, and come prepared to talk about examples of how genetics answers archaeological questions. Tues 21st Feb 2-4pm (A38, G10) Presentation and discussion of recent case-studies Use the reading list for Lecture 4 to prepare a presentation on one of the following topics (or any other sub-field that interests you): a) Next Generation Sequencing and its role in archaeology b) Genetic Analysis of morphological changes in domesticates c) Archaeogenetics and Palaeoenvironmental studies (megafaunal extinctions, palaeoclimate etc.) d) DNA preservation and authenticating DNA sequence data from archaeological specimens Presentations can be prepared by pairs of students if you wish. Please liaise with others so we have a good spread of topics among the group.

Supervisions
Dates to be arranged. A37 one supervision is compulsory. Essay to be submitted in advance. Supervisions for A38 and G10 can be organised if desired. Essay titles (choose one) 1) How can the reconstruction of relationships between organisms from genetic data help us to answer archaeological questions? 2) What do archaeogenetic data tell us about the process of domestication? 3) How do modern and archaeological samples complement one another in archaeogenetic studies to provide information on the origin and spread of domesticated plants and animals?

Reading list
Lecture 1 (A37, A38, G10): Archaeogenetics principles and techniques Background readings some from textbooks on molecular biology and evolutionary analysis. There is substantial overlap in the basic information among these so no need to read them all. Some of you will have more background knowledge in biology than others read what you find helpful. Making a start on reading the general review papers on domestication (listed under Lecture 3 below) would also be advisable. Brown T, K Brown. 2011. Biomolecular Archaeology: an introduction. Oxford: Wiley-Blackwell. Ch. 2 (DNA) Griffiths, AJF, SR Wessler, SB Carroll, J Doebley. 2011. Introduction to Genetic Analysis (10th edition). New York: W.H. Freeman. Ch. 8 (DNA structure), ch. 18 (population genetics) Higgs, PG, TK Attwood. 2005. Bioinformatics and Molecular Evolution. Oxford: Blackwell. Ch. 2. (Nucleic acids, proteins, and amino acids) Howe, CJ. 2007. Gene cloning and manipulation (2nd edition). Cambridge: Cambridge University Press. Ch. 2 (Polymerase chain reaction) Nei, M, S Kumar. 2000. Molecular evolution and phylogenetics. Oxford: Oxford University Press. Page, RDM, EC Holmes. 1998. Molecular evolution: a phylogenetic approach. Oxford: Blackwell Science. Salemi, M, A-M Vandamme, P Lemey. 2009. The phylogenetic handbook : a practical approach to phylogenetic analysis and hypothesis testing. Cambridge: Cambridge University Press. Ch. 1. (Basic concepts of molecular evolution)

Lecture 2: Further archaeogenetics principles and techniques More material on the methodological/technical side of things. Also make a start on the material listed under Lectures 3 & 4 (you will need to do this before the first seminar in any case). Guichoux E, L Lagache, S Wagner, P Chaumeil, P Leger, O Lepais, C Lepoittevin, T Malausa, E Revardel, F Salin, RJ Petit. 2011. Current trends in microsatellite genotyping. Molecular Ecology Resources 11:591-611. Higgs, PG, TK Attwood. 2005. Bioinformatics and Molecular Evolution. Oxford: Blackwell. Ch. 2. (Nucleic acids, proteins, and amino acids), ch. 3 (Molecular evolution and population genetics) Ho, SYW, B Shapiro. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources 11:423-434. Salemi, M, A-M Vandamme, P Lemey. 2009. The phylogenetic handbook : a practical approach to phylogenetic analysis and hypothesis testing. Cambridge: Cambridge University Press. Chapter 2 (Sequence databases and data searching)

Lecture 3 (A37, A38, G10): Archaeogenetics and agriculture A mix of case studies (marked *) and review/synthesis papers. Make sure you read at least 3-4 case studies not just the reviews! *Blackman, BK, M Scascitelli, NC Kane, HH Luton, DA Rasmussen, RA Bye, DL Lentz, LH Rieseberg. 2011. Sunflower domestication alleles support single domestication center in eastern North America. Proceedings of the National Academy of Sciences of the United States of America 108:14360-14365. Brown T, K Brown. 2011. Biomolecular Archaeology: an introduction. Oxford: Wiley-Blackwell. Ch. 7 (Sources of Ancient Biomolecules), ch. 8 (Degradation of Ancient Biomolecules), ch. 13 (Studying the origins and spread of agriculture) Burger JC, MA Chapman, JM Burke. 2008. Molecular insights into the evolution of crop plants. American Journal of Botany 95:113-122. de Bruyn, M, AR Hoelzel, GR Carvalho, M Hofreiter. 2011. Faunal histories from Holocene ancient DNA. Trends in Ecology & Evolution 26:405-413. Doebley JF, BS Gaut, BD Smith. The molecular genetics of crop domestication. Cell 127:1309-1321. Driscoll, CA, DW Macdonald, SJ O'Brien. 2009. From wild animals to domestic pets, an evolutionary view of domestication. Proceedings of the National Academy of Sciences of the United States of America 106:9971-9978. Larson, G. 2011. Genetics and Domestication Important Questions for New Answers. Current Anthropology 52:S485-S495. *Lari, M, E Rizzi, S Mona, et al. 2011. The Complete Mitochondrial Genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy. Bmc Evolutionary Biology 11. *Larson, G, R Liu, X Zhao, et al. 2010. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proceedings of the National Academy of Sciences of the United States of America 107:76867691. *Lippold, S, NJ Matzke, M Reissmann, M Hofreiter. 2011. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. Bmc Evolutionary Biology 11. *Molina, J, M Sikora, N Garud, et al. 2011. Molecular evidence for a single evolutionary origin of domesticated rice. Proceedings of the National Academy of Sciences of the United States of America 108:8351-8356. Navascues, M, F Depaulis, BC Emerson. 2010. Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Molecular Ecology Resources 10:760-772. *Palmer, SA, JD Moore, AJ Clapham, P Rose, RG Allaby. 2009. Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation. Plos One 4. Purugganan, MD, DQ Fuller. 2011. Archaeological data reveal slow rates of evolution during plant domestication. Evolution 65:171-183. *Roed, KH, O Flagstad, G Bjornstad, AK Hufthammer. 2011. Elucidating the ancestry of domestic reindeer from ancient DNA approaches. Quaternary International 238:83-88. *Vaughan, DA, B-R Lu, N Tomooka. 2008. The evolving story of rice evolution. Plant Science 174:394-408.

*vonHoldt, BM, JP Pollinger, KE Lohmueller, et al. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464:898-U109. Zeder M. 2006. Central questions in the domestication of plants and animals. Evolutionary Anthropology 15:105-117. *Zhang, Y, D Vankan, JSF Barker. 2011. Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo. Animal Genetics 42:366377.

Lecture 4 (A37, A38, G10): New methods and archaeogenetics in the genomics era Adler, CJ, W Haak, D Donlon, A Cooper, C Genographic. 2011. Survival and recovery of DNA from ancient teeth and bones. Journal of Archaeological Science 38:956-964. Anderson-Carpenter, LL, JS McLachlan, ST Jackson, M Kuch, CY Lumibao, HN Poinar. 2011. Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics. Bmc Evolutionary Biology 11. Cieslak, M, M Reissmann, M Hofreiter, A Ludwig. 2011. Colours of domestication. Biological Reviews 86:885-899. Howe, CJ. 2007. Gene cloning and manipulation (2nd edition). Cambridge: Cambridge University Press. Ch. 3 (Simple cloning) Lorenzen, ED, D Nogues-Bravo, L Orlando, et al. 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479:359-U195. Matsuoka, Y. 2011. Evolution of Polyploid Triticum Wheats under Cultivation: The Role of Domestication, Natural Hybridization and Allopolyploid Speciation in their Diversification. Plant and Cell Physiology 52:750-764. McCormack, JE, SM Hird, AJ Zellmer, BC Carstens, RT Brumfield. 2012. Applications of next-generation sequencing to phylogeography and phylogenetics. 2012. Molecular Phylogenetics and Evolution (in press, available online). Ottoni, C, HEC Koon, MJ Collins, KEH Penkman, O Rickards, OE Craig. 2009. Preservation of ancient DNA in thermally damaged archaeological bone. Naturwissenschaften 96:267-278. Peng, JH, D Sun, E Nevo. 2011. Domestication evolution, genetics and genomics in wheat. Molecular Breeding 28:281-301. Rowe, KC, S Singhal, MD Macmanes, JF Ayroles, TL Morelli, EM Rubidge, K Bi, CC Moritz. 2011. Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Molecular Ecology Resources 11:1082-1092. Sakuma S, B Salomon, T Komatsuda. 2011. The domestication syndrome genes responsible for the major changes in plant form in the Tritceae crops. Plant and Cell Physiology 52:738-749. Sonstebo, JH, L Gielly, AK Brysting, et al. 2010. Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources 10:1009-1018. Winters, M, JL Barta, C Monroe, BM Kemp. 2011. To Clone or Not To Clone: Method Analysis for Retrieving Consensus Sequences In Ancient DNA Samples. Plos One 6.