!! ! " # $ %&'%(&)% $ * +(+%(''()%(& , - ,,, .(%)/)&% ! " # $% % %&%%' ' ' ( )* + ) , -)$% %) , , . / , ( ). ) 0!1)22 ) )3,40154 566!501$ 52) . %%%% + + + ). ++ ' )* 2$0 ' 7 + )" + + ' ' ). + 4 ' ' ' '+ / + ) * ' + '' ) 5 8 ' 9 . 3 '' : + $%%%%51%%%% + + ).9 ,( + + '8 ' ' ) * + 7 )3 ,( + + + ' )* ' + +' ' 4 ) .,( 8 ! !" ! # !$ %&'( ! !)*+,-. ! ;-, $% % 3,, 26 52$ ! 3,40154 566!501$ 52 & &&& 5 $<$2 = &>> )7)> ? @ & &&& 5 $<$2 A Till mamma Art work on front page by Lotta Tomasson List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Svensson, E.M., Axelsson, E., Vretemark, M., Makowiecki, D., Gilbert, M.T.P., Willerslev, E., Götherström, A. Insights into Y chromosomal genetic variation and effective population size in the extinct European aurochs Bos primigenius. Manuscript II Svensson, E., Götherström, A., (2008) Temporal fluctuations of Y-chromosomal variation in Bos taurus. Biology Letters, 4(6):752-754 III Svensson, E.M., Götherström, A., Vretemark, M. (2008) A DNA test for sex identification in cattle confirms osteometric results. Journal of Archaeological Science 35(4):942-946 IV Telldahl, Y., Svensson, E.M., Götherström, A., Storå, J. Typing late prehistoric cows and bulls-osteology and genetics of cattle at the Eketorp fortification and settlement on Öland, Sweden. Submitted V Svensson, E.M., Anderung, C., Baubliene, J., Persson, P., Malmström, H., Smith, C., Vretemark, M., Daugnora, L., Götherström, A. (2007) Tracing genetic change over time using nuclear SNPs in ancient and modern cattle. Animal Genetics, 38(4):378-383 VI Svensson, E.M., Jakobsson, M., Vretemark, M., Telldahl, Y., Persson, P., Malmborg, G., Götherström, A. Signs of contrast- ing selection in medieval and modern North European cattle. Manuscript Reprints were made with permission from the respective publisher. Additional papers not included in the thesis I Ala-Poikela, M., Svensson, E., Rojas, A., Horko, T., Paulin, L., Valkonen, J., Kvarnheden, A. (2005) Genetic diversity and mixed infections of begomoviruses infecting tomato, pepper and cucurbit crops in Nicaragua. Plant pathology, 54(4):448– 459 II Malmstrom, H., Svensson, E.M., Gilbert, M.T., Willerslev, E., Gotherstrom, A., Holmlund, G. (2007) More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA. Molecular Biology and Evolution, 24(4):998-1004 III Gilbert, M.T.P., Jenkins, D.L., Higham, T.F.G., Rasmussen, M., Malmström, H., Svensson, E.M., Sanchez, J.J., Cummings, L.S., Yohe, I.I. R.M., Hofreiter, M., Götherström, A., Willer- slev, E., (2009) Response to comment by Poinar et al. on "DNA from pre-clovis" human coprolites in Oregon, North America. Science, 325:148 IV Eklund, D.M., Svensson, E., Kost, B. (2010) Physcomitrella patens: a model to investigate the role of RAC/ROP GTPase signaling in tip growth. Journal of Experimental Botany, 2010 In press Contents Introduction ................................................................................................... 11 Domestication........................................................................................... 11 Why study domesticates ...................................................................... 12 Domestic animals................................................................................. 12 Farming throughout history ...................................................................... 14 The spread of farming .......................................................................... 14 Prehistoric animal husbandry .............................................................. 15 The history of breeding ........................................................................ 16 Modern breeds and effects of breeding................................................ 18 Genetic effects from domestication and breeding .................................... 19 Signatures of selection in domesticates ............................................... 19 The cattle genome under selection ...................................................... 20 Methods ........................................................................................................ 22 Ancient DNA as a tool to access temporal data ....................................... 22 Properties of ancient DNA ................................................................... 22 Genetic markers ........................................................................................ 26 Single nucleotide polymorphisms ........................................................ 27 Mitochondrial DNA ............................................................................. 27 Y chromosomal DNA .......................................................................... 28 Sequencing and Genotyping ..................................................................... 28 Pyrosequencing .................................................................................... 29 SNPstream ........................................................................................... 31 454/FLX ............................................................................................... 33 Analysing temporal data ........................................................................... 35 Ascertainment bias............................................................................... 36 Research aims ............................................................................................... 38 General aims ............................................................................................. 38 Specific aims ............................................................................................ 38 Summaries of papers ..................................................................................... 39 Paper I: Insights into Y chromosomal genetic variation and effective population size in the extinct European aurochs Bos primigenius. .......... 39 Paper II: Temporal fluctuations of Y-chromosomal variation in Bos taurus. ....................................................................................................... 40 Paper III: A DNA test for sex identification in cattle confirms osteometric results. ................................................................................... 40 Paper IV: Typing Late Prehistoric cows and bulls-osteology and genetics of cattle at the Eketorp fortification and settlement on Öland, Sweden. ........................................................................................ 42 Paper V: Tracing genetic change over time using nuclear SNPs in ancient and modern cattle. ........................................................................ 43 Paper VI: Signs of contrasting selection in medieval and modern North European cattle ............................................................................... 44 Conclusions and future prospects ................................................................. 46 Svensk sammanfattning ................................................................................ 48 Acknowledgements ....................................................................................... 51 References ..................................................................................................... 54 Abbreviations aDNA Ancient DNA bp Base pair(s) BP/BC Before present/Christ DNA Deoxyribonucleic acid dN Non-synonymous substitution rate dS Synonymous substitution rate kb Kilobase (103 base pairs) LD Linkage disequilibrium MRCA Most recent common ancestor mtDNA Mitochondrial DNA Ne Effective population size PCR Polymerase chain reaction SNP Single nucleotide polymorphism TRB Trichtbächer kultur Introduction Domestication of animals like goat, sheep, pig, horse and cow laid the foun- dation for the modern sedentary society (Diamond, 2002). Going from a hunter-gatherer lifestyle to a farming lifestyle is perhaps the most revolution- ising process in our species history. Throughout the time since domestication major changes have occurred in all of the major farm animals. Humans have selected for traits that were beneficial for us, resulting in the multitude of breeds seen today. Already at the time of Moses, key concepts in cattle breeding were recognized. Ye shall keep my statutes. Thou shalt not let thy cattle gender with a diverse kind: thou shalt not sow thy field with two kinds of seed: neither shall there come upon thee a garment of two kinds of stuff mingled together. (Holy Bi- ble, Leviticus 19:19) In this thesis I have investigated genetic signs of breeding in ancient remains of domestic cattle (Bos Taurus), and the Y chromosomal genetic diversity in extinct European aurochs (Bos primigenius). Domestication Domestication can be seen as the adaptation of a wild animal to human soci- ety (Price, 2002), this process is likely to confer phenotypic changes to the animals. It is likely that wild animals were selected for traits like tameness and docility, selection for these traits have also been shown to confer mor- phological changes to the animal (Price, 1999; Trut, 1999; Vonholdt BM, 2010). This is also seen in the archaeological record,