COPYRIGHT AND CITATION CONSIDERATIONS FOR THIS THESIS/ DISSERTATION o Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. o NonCommercial — You may not use the material for commercial purposes. o ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. How to cite this thesis Surname, Initial(s). (2012). Title of the thesis or dissertation (Doctoral Thesis / Master’s Dissertation). Johannesburg: University of Johannesburg. Available from: http://hdl.handle.net/102000/0002 (Accessed: 22 August 2017). GENETIC BUILDING BLOCKS OF HUMAN COGNITION: HOMO NEANDERTHALENSIS VS. HOMO SAPIENS A Dissertation Submitted to the DEPARTMENT OF ANTHROPOLOGY AND DEVELOPMENT STUDIES of the FACULTY OF HUMANITIES at the UNIVERSITY OF JOHANNESBURG by SHANNON KIM PERUCATTI 2011 03 150 In Fulfilment of the Requirements for the Degree of MASTER OF ARTS IN ANTHROPOLOGY September 2019 Johannesburg, South Africa Supervised by PROF. M. LOMBARD Co-supervised by ASSOCIATE PROF. C.M. SCHLEBUSCH i ACKNOWLEDGMENTS I wish to thank the many people who assisted me and contributed in one way or another with the completion of my dissertation. First and foremost, I would like to thank my supervisor, Professor Marlize Lombard, for her unwavering support and guidance. Your time, wise words, and encouragement will always be appreciated. Thank you also to my co- supervisor, Associate Professor Carina Schlebusch, for your motivational and academic assistance. It has been a great honour to have both of you as my supervisors and I will be forever grateful for the opportunities you have provided me. Thank you both for believing in me, even when there were times when I was ready to give up. My research would not have been possible without the financial support of the National Research Fund grant-holder-linked bursary and the UJ supervisor-linked bursary that I received from Professor Marlize Lombard. Nor would it have been possible without the institutional support of the Palaeo-Research Institute (formerly the Centre for Anthropological Research) at the University of Johannesburg. Thank you to my family, friends, and partner (Stephen) for your continued support. Your patience and confidence in me are greatly appreciated. To all that took the time to read my dissertation, thank you. I hope you find/found it as enjoyable and invigorating as I did when writing it. Lastly, thank you to everyone at Research House 10 — Anzel, Charlotte, Charné, Dipuo, Justin, Nonny, and Steph. iii ABSTRACT The cognitive differences and similarities between Homo neanderthalensis (Neanderthals) and Homo sapiens have long been a point of study and debate, especially in the palaeoneurological and archaeological fields. Here, I revisit the controversy with the help of genetic interpretations by assessing whether there is an overrepresentation of genes associated with cognition as well as brain morphology in Homo sapiens (us). To do this, I performed a functional enrichment analysis utilising gene and phenotype ontologies on combined data (encapsulating 6545 genes) from eleven genomic studies that either tested for the predictions of functional consequences of gene variants between Neanderthals, Denisovans, and Homo sapiens, and/or attempted to capture positive selective events that occurred in the ancestral population branch of all present-day humans. Functional enrichment analysis provides a uniform way to describe the functions of genes by computationally modelling biological reality (i.e., statistically evaluating and identifying patterns within gene groups). The gene ontology enrichment results suggest that an excess of biological processes related to cell-cycle related functions, signalling pathways, and general nervous system developmental processes were prominently modified by genetic changes in Homo sapiens. Phenotypes in brain growth trajectories and cognitive traits are likely influenced by these biological processes (among other cellular and molecular functions). Some of the medically associated phenotypes related to brain function and cognition also seem to have co-evolved with Homo sapiens material culture. Yet, the trajectory of change associated with both stone tools and genetic variation in my project suggests that our ability to think about materiality is probably what differentiates us from Neanderthals. Further experiments are required to identify and confirm genetic changes, particularly their expression, in Neanderthals. Keywords: cognition, ancient DNA, functional enrichment, Homo neanderthalensis, Homo sapiens iv TABLE OF CONTENTS AFFIDAVIT ......................................................................................................................... ii ACKNOWLEDGEMENTS ................................................................................................... iii ABSTRACT ........................................................................................................................ iv TABLE OF CONTENTS ...................................................................................................... v LIST OF FIGURES ............................................................................................................ viii LIST OF TABLES ............................................................................................................... ix GLOSSARY ........................................................................................................................ x CHAPTER ONE: INTRODUCTION...................................................................................... 1 1.1 Contextualisation ......................................................................................................... 1 1.2 Problem statement ....................................................................................................... 3 1.3 Aims and objectives .................................................................................................... 3 1.4 Structure of the dissertation ....................................................................................... 4 CHAPTER TWO: HOMO NEANDERTHALENSIS AND HOMO SAPIENS’ SKULL MORPHOLOGY, PALAEONEUROLOGY, AND COGNITION ............................................ 5 2.1 Introduction .................................................................................................................. 5 2.2 Key characteristics of cranio-facial morphology ...................................................... 6 2.2.1. The neurocranium ............................................................................................... 6 2.2.2. The basicranium .................................................................................................. 8 2.2.3. The facial skeleton and dentition ......................................................................... 9 2.3 Key characteristics of brain morphology ................................................................ 11 2.4 Inferring differences and similarities in brain function and cognition .................. 12 2.4.1. The frontal lobe .................................................................................................. 13 2.4.2. The parietal lobes .............................................................................................. 16 2.4.3. The temporal lobes ............................................................................................ 19 2.4.4. The olfactory bulbs ............................................................................................ 21 2.4.5. The occipital lobes ............................................................................................. 21 2.4.6. The cerebellum .................................................................................................. 22 2.5 Summary .................................................................................................................... 22 CHAPTER THREE: GENETIC MECHANISMS OF THE HUMAN BRAIN AND COGNITIVE EVOLUTION ................................................................................................. 25 3.1 Introduction ................................................................................................................ 25 3.1.1. The basics of the human genome ..................................................................... 25 3.1.2. Mutation, recombination, and selection events .................................................. 26 3.2 Genetic variation between Homo sapiens, Homo neanderthalensis, and Denisovans ....................................................................................................................... 30 3.2.1. Changes influencing gene function .................................................................... 30 3.2.2. Epigenetic variation ........................................................................................... 33 3.2.3. Genes possibly targeted by selection ................................................................ 34 3.3 Effects of admixture from Homo neanderthalensis and Denisovans in Homo sapiens ............................................................................................................................. 38 3.4 Functional enrichment .............................................................................................