Durham E-Theses Morphological Variation in Wild and Domestic Suids OWEN, JOSEPH,THOMAS,DAVID How to cite: OWEN, JOSEPH,THOMAS,DAVID (2013) Morphological Variation in Wild and Domestic Suids, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/6950/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk Morphological Variation in Wild and Domestic Suids Joseph Thomas David Owen PhD Thesis Department of Anthropology Department of Archaeology Durham University 2012 Table of Contents Content Page Number Declaration vi Statement of Copyright vi Acknowledgements vii 1.1 Introduction 1 1.1.1 Structure of the Thesis 3 1.1.2 Pigs Exploitation 8 1.1.3 The Extreme Relationships between Pigs and 9 People 1.1.4 Pigs and Social Status 12 1.2 The Biology of Pigs 13 1.2.1 Current Taxonomy 13 1.2.2 Geography, Ecology and Habitat of the Suids 15 Studied 1.2.3 The Evolutionary History of Suids 17 1.2.4 Known Biogeographic variation within Sus 18 scrofa 1.2.5 Known constraints on Sus scrofa range 20 1.2.7 Suids and Insularity 21 1.3 Domestication 24 1.3.1 Defining the Process of Domestication 27 1.3.2 Defining what a ‘Domestic’ Animal is 29 1.3.3 How do Animals Become Domesticated? 32 1.3.4 Domestication Pathways 34 1.3.5 Cultural and Biological processes of 36 domestication 1.3.5.1 Cultural processes 36 1.3.5.2 Biological processes 36 1.3.6 Changes seen in Domesticated Animals 39 1.3.7 Wild Progenitors 42 1.3.8 The Domestication of Pigs: When, Where and 42 How Many Times? 1.3.9 The Study of Domestication 46 1.3.10 Methods used in the Study of Domestication 46 1.3.11 Methodological Issues 47 1.3.12 Alternative Methodologies 50 Bibliography 56 2 Methodology 67 2.1 Material 67 2.1.1 The Suid Cranium 67 2.1.2 Materials 71 2.1.3 Covariates 73 2.1.4 Ageing Methods 74 i 2.1.5 Biometrics, and issues associated with them 75 2.2 Methods 77 2.2.1 Geometric Morphometrics 77 2.2.2 Generalised Procrustes Analysis 77 2.2.3 Kendall’s shape space and tangent space 79 2.2.4 Size 80 2.2.5 Procrustes distances 80 2.2.6 Visualisation techniques 81 2.2.7 Landmarks 82 2.2.8 Data Collection 84 2.2.9 Landmarks used and explanation for choice 84 2.2.10 Estimating intra-observer error 88 2.2.11 Sexual dimorphism 89 2.2.12 Allometry 91 2.3 Methods of Analysis 92 2.3.1 Principal Components Analysis 92 2.3.2 Canonical Variates Analysis 93 2.3.3 Permutation Tests 95 2.3.4 Discriminant Functions 95 2.3.5 Cross Validation 96 2.3.6 Student’s and Hotelling’s t-tests 97 2.3.7 ANOVA and MANOVA 98 2.3.8 Regression 99 2.3.9 Cluster Analysis and Neighbour Joining Trees 100 2.3.10 Mode of Evolution 101 Bibliography 104 Results Chapters 3 Manuscript 1: 109 Resolving genetic and morphological phylogenies within Suidae Abstract 110 Introduction 111 Materials and Methods 113 Results 114 Discussion 116 Conclusion 117 Bibliography 118 4 Manuscript 2: 130 Pigs in Space: Biogeographic variation in Sus scrofa Abstract 131 ii Introduction 132 Materials 138 Methods 143 Results 145 Discussion 150 Conclusion 152 Bibliography 154 5 Manuscript 3 161 Quantifying cranial shape differences between wild boar and domestic pigs (Sus scrofa) using 3D geometric morphometrics and its application to zooarchaeology Abstract 162 Introduction 163 Materials 165 Methods 166 Results 168 Discussion 170 Conclusion 173 Bibliography 174 6 Manuscript 4 179 Domestication and Heterochrony in Sus scrofa Abstract 180 Introduction 181 Materials 183 Methods 184 Results 185 Discussion 189 Conclusion 190 Bibliography 192 Supporting Information List of landmarks and Image S1 196 Table S2 199 7 Conclusion 202 7.1. Evolutionary relationships in suids 202 7.2 Biogeographic variation in suids 202 7.3 Discrimination between wild and domestic suid 203 morphology 7.4 Domestication and Heterochrony in Sus scrofa 204 7.5 Strengths, weaknesses and recommendations for 205 future work Bibliography 205 iii List of Figures Figure # Content Page Number Introduction 1 Excerpt from Linnaeus’ Systema Naturae 2 2 Hair or clothing pins made from pig fibula 9 3 Distribution of Sus haplotypes 19 4 Representation of the scale of interaction 31 between animals and humans 5 Summary of the main types of domestication 35 6 Arrival dates and approximate geographical 44 expansions of defined Early Neolithic cultures 7 The introduction, introgression and expansion 45 of pig haplotypes into Europe Methodology 8 Depiction of the pig skull a Lateral view 68 b Basicranium 69 c Dorsal view 71 9 Map showing distribution of samples 73 10 Pig crania depicting landmark positions a Position of landmarks on the cranium 86 b Position of landmarks on the basicranium 87 11 PCA showing error assessment 89 Manuscript 1 1 Map showing distribution of samples 125 2 Genetic and Morphological NJ trees 125 3 PCA and CVA showing group differences 126 4 Maximum Likelihood estimate of the rate and 127 tempo of evolution in suids and Ancestral node scores of suids Manuscript 2 1 Map of samples 158 2 Box plot of centroid sizes 159 3 PCA and CVA of Sus scrofa 160 Manuscript 3 1 PCA of wild and domestic pigs 177 2 PCAs of cranial landmark subsets 178 Manuscript 4 1 PCA of wild and domestic ontogenetic series 195 iv List of Tables Table # Content Page Number Methodology 1 Test results for sexual dimorphism 91 Manuscript 1 1 List of recognised suid taxa and samples used 123 in the analysis S2 Distance matrix of procrustes distances 129 between taxa in Figure 2b S3 Discriminant function scores 129 Manuscript 2 1 List of Samples and Covariates 140 2 Discriminant function results 146 Manuscript 3 1 Procrustes distances and discriminant 169 functions 2 Cross validation results between domestic 170 breeds Manuscript 4 1 Distances between wild and domestic groups 186 for complete crania for all age stages 2 Distances between wild and domestic groups 186 for complete crania for different age stages 3 Angles between ontogenetic trajectories 187 4 Tests for paedomorphism: distances between 187 different ages stages for wild and domestic pigs 5 Distances between wild and domestic pigs for 188 partial crania 6 Angles between ontogenetic crania for 189 separate parts of the crania v Declaration All work submitted within this thesis was conducted and written by the author, with the following exceptions. The analysis of the mode of evolution in manuscript 2, which was jointly conducted by the author and Prof. P.David Polly (University of Illinois), and the computation of angles between regression trajectories in manuscript 4, which was collaborative work between the author and Prof. Kieran McNulty (University of Minnesota). Statement of Copyright The copyright of this thesis rests with the author. No quotation should be published without the author’s prior written consent and information derived from it should be acknowledged. vi Acknowledgements 'The time has come,' the Walrus said, 'To talk of many things: Of shoes - and ships - and sealing wax - Of cabbages - and kings - And why the sea is boiling hot - And whether pigs have wings.' (Lewis Carroll – 1871) It is a pleasure to thank the many, many people who made this thesis possible. It is difficult to overstate my gratitude to my PhD supervisor, Dr. Una Strand Viðarsdóttir. Her constant enthusiasm, inspiration, patient and repeated efforts to clearly (and simply) explain things (especially with regard to grammar) helped to make statistics fun and interesting for me. Throughout my PhD, she has provided encouragement, sound advice, good teaching and good company – both in Durham and away on data collection, with lots of good ideas. I consider it a privilege to have been able to work with her, and look forward to many years of collaboration. I am indebted to my other supervisors, Prof. Keith Dobney, Dr. Greger Larson and Prof Peter Rowley-Conwy. All three have provided great encouragement and counsel, both inspiring me to pursue an academic career whilst spurring me on to achieve. They have mentored me through my formative academic years, affording me many opportunities for which I am exceedingly grateful. I would also like to thank my colleagues on the research project, Dr Allowen Evin, Dr Thomas Cucchi and Dr Linus Girdland Flink. Their assistance and advice, especially Allowen with statistics, has helped me enormously throughout the PhD. Their companionship during data collection led to some great experiences which I will always treasure. Also, Helgi Pétur Gunnarsson, husband of Una Strand Viðarsdóttir, thank you for digging me out of numerous statistical dead ends, although he did fail the Vienna rib challenge. vii I am indebted to my fellow students and good friends for providing such a stimulating and fun atmosphere in which to work and play.