UPTEC X 12 012 Examensarbete 30 hp Juni 2012 Origin of the Egyptian Domestic Cat Carolin Johansson Molecular Biotechnology Programme Uppsala University School of Engineering UPTEC X 12 012 Date of issue 2012-06 Author Carolin Johansson Title (English) Origin of the Egyptian Domestic Cat Title (Swedish) Abstract This study presents mitochondrial genome sequences from 22 Egyptian house cats with the aim of resolving the uncertain origin of the contemporary world-wide population of Domestic cats. Together with data from earlier studies it has been possible to confirm some of the previously suggested haplotype identifications and phylogeny of the Domestic cat lineage. Moreover, by applying a molecular clock, it is proposed that the Domestic cat lineage has experienced several expansions representing domestication and/or breeding in pre-historical and historical times, seemingly in concordance with theories of a domestication origin in the Neolithic Middle East and in Pharaonic Egypt. In addition, the present study also demonstrates the possibility of retrieving long polynucleotide sequences from hair shafts and a time-efficient way to amplify a complete feline mitochondrial genome. Keywords Feline domestication, cat in ancient Egypt, mitochondrial genome, Felis silvestris libyca Supervisors Anders Götherström Uppsala University Scientific reviewer Jan Storå Stockholm University Project name Sponsors Language Security English Classification ISSN 1401-2138 Supplementary bibliographical information Pages 123 Biology Education Centre Biomedical Center Husargatan 3 Uppsala Box 592 S-75124 Uppsala Tel +46 (0)18 4710000 Fax +46 (0)18 471 4687 Origin of the Egyptian Domestic Cat Carolin Johansson Populärvetenskaplig sammanfattning Det är inte sedan tidigare känt exakt hur, när och var tamkatten domesticerades. Traditionellt har teorier fokuserat på ett fornegyptiskt ursprung då ett stort antal ikonografiska, arkeologiska och historiska källor vittnar om den speciella betydelse katten hade i det fornegyptiska samhället. Det har också föreslagits att katten domesticerades långt tidigare, kanske i samband med de första jordbrukssamhällena i området kring den så kallade bördiga halvmånen i Mellanöstern. I denna studie samlades pälsprover in från Egyptiska tamkatter i syfte att på molekylär nivå jämföra de Egyptiska katterna med tidigare studier av katter från andra delar av världen. För att göra detta kartlades hela uppsättningen av det genetiska materialet som bara ärvs på mödernet (mitokondriellt DNA) för 22 av de provtagna kattindividerna. Den stora mängden genetisk information gjorde att resultat av tidigare studier kunde fastställas med större säkerhet men också att utvidgningar av tamkattslinjen kunde anas i både förhistorisk och historisk tid. Detta skulle kunna tolkas som att katten genomgått flera av varandra oberoende domesticeringar, möjligen både i yngre stenålderns Mellanöstern och i det faraoniska Egypten. Studien visar därtill på hur man på ett förhållandevis enkelt sätt kan utvinna långa sekvenser av sådant genetiskt material från katthår, en typ av vävnad som vanligen anses innehålla relativt lite och relativt trasiga DNA-molekyler. Examensarbete 30 hp Civilingenjörsprogrammet Molekylär bioteknik Uppsala universitet, juni 2012 Contents 1. Introduction .................................................................................................................................... 9 1.1. The Felidae Family ....................................................................................................................... 9 1.1.1. The Felis .............................................................................................................................. 10 1.1.1.1. Phylogeny and Systematics .......................................................................................... 10 1.1.1.2. Pre-adaptations for Domestication within the Felis .................................................... 12 1.2. The Cat as a Domesticated Animal ............................................................................................ 16 1.2.1. The Domestic Cat ................................................................................................................ 16 1.2.1.1. Classifications ............................................................................................................... 16 1.2.1.2. Cat Breeds .................................................................................................................... 17 1.2.1.3. The Domestic Cat and its Wild Relatives...................................................................... 18 1.2.1.3.1. Characterisation Schemes ..................................................................................... 19 1.2.1.3.2. Problem of Hybridisation ...................................................................................... 20 1.2.1.4. Definition of Terms and Domestication Criteria .......................................................... 21 1.2.1.5. The Domesticated Status of the Cat ............................................................................ 24 1.3. Suggested Mechanisms for the Domestication of the Cat ........................................................ 26 1.3.1. Passive Domestication ........................................................................................................ 26 1.3.2. Actively Initiated Domestication ......................................................................................... 26 1.4. The Cat in the Ancient World ..................................................................................................... 27 1.4.1. Early Archaeological Sources of Cats .................................................................................. 27 1.4.2. Early Iconographical Sources of Cats .................................................................................. 30 1.4.3. The Cat in Ancient Egypt ..................................................................................................... 31 1.4.3.1. Felids in Egypt .............................................................................................................. 32 1.4.3.2. Predynastic Time, Early Dynastic Period, Old Kingdom and the First Intermediate Period (before 2055 BCE) .......................................................................................................... 32 1.4.3.3. Middle Kingdom and the Second Intermediate Period (2055 - 1550 BCE) .................. 33 1.4.3.4. New Kingdom and the Third Intermediate Period (1550 – 664 BCE) .......................... 35 1.4.3.5. Late Period and Greco-Roman Times (664 BCE – 395 CE) ........................................... 36 1.4.3.6. Cats in the Religion ...................................................................................................... 36 1.4.3.7. Cat Mummies ............................................................................................................... 38 1.4.4. Etymological Parallels ......................................................................................................... 43 1.4.5. The Cat in Antiquity and Beyond ........................................................................................ 44 1.5. Suggested Scenarios for the Domestication of the Cat ............................................................. 48 2. Aim and Project Design ................................................................................................................. 53 3. Material and Methods .................................................................................................................. 55 3.1. Sample Collection ...................................................................................................................... 55 3.2. Sample Preparation and DNA Extraction ................................................................................... 55 3.3. Amplification .............................................................................................................................. 56 3.4. Sequencing ................................................................................................................................. 58 3.5. Data Analyses ............................................................................................................................. 59 3.5.1. Phylogeny and Population Genetics ................................................................................... 59 3.5.2. Simulations .......................................................................................................................... 62 4. Results ........................................................................................................................................... 65 4.1. Success Rates ............................................................................................................................. 65 4.2. Sequencing and Coverage .......................................................................................................... 65 4.3. Phylogeny ................................................................................................................................... 71 4.4. Simulation Outcome .................................................................................................................. 86 5. Discussion ...................................................................................................................................... 87 5.1. Sample set .................................................................................................................................