Mimmie Kgaditse 344142 the Evolution and Diversification of Diet
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Mimmie Kgaditse 344142 The evolution and diversification of diet in elapids A dissertation submitted to the School of Animal, Plant and Environmental Sciences, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa in fulfilment of the requirements of the degree of Masters of Science. Johannesburg, South Africa July, 2016 1 DECLARATION I declare that this dissertation is my own, unaided work unless specifically acknowledged in the text. It has not been submitted previously for any degree or examination at any other university, nor has it been prepared under the aegis or with the assistance of any other body or organization or person outside of the University of the Witwatersrand, Johannesburg, South Africa. Mimmie Kgaditse, 22 July 2016 2 “In any study of evolutionary ecology, food relations appear as one of the most important aspects of the system of animate nature. There is quite obviously much more too living communities than the raw dictum “eat or be eaten,” but in order to understand the higher intricacies of any ecological system, it is most easy to start from this crudely simple point of view.” - G. E. Hutchinson (1959) Homage to Santa Rosalia or why are there so many kinds of animals? 3 ABSTRACT A central goal in macroecology is understanding the factors that have shaped broad-scale patterns among extant natural communities. Diet is widely cited as a key factor involved in shaping snake diversification. Amongst serpents, the adaptive radiation of elapids is unparalleled in terms of their sheer global distribution. My study was aimed at evaluating the variation in diet and how trends evolved throughout the radiation of the elapids. Based on the published natural history data of 303 elapid species, a cluster analysis revealed seven groups of species within which diet types were similar. The broad diet clusters included snake consumption, feeding on fish, ectotherms, endotherms, lizards, a generalist diet and lastly, a terrestrial invertebrate group that was the least prevalent diet type. Maximum Parsimony, Maximum Likelihood and Stochastic Character Mapping were used to trace the ancestral dietary condition in the Elapidae. Reconstructions demonstrated that starting from an ophiophagous ancestor, elapids still largely retain their early feeding habits. Despite the emergence of novel feeding patterns in the group, the predominantly conservative diet patterns suggest that niche conservatism has shaped elapid foraging dynamics. Members of the lineage characteristically feed on elongate ectothermic prey (e.g., squamates, caecilians, eels, earthworms) possibly owing to morphologically-mediated gape constraints. Phylogenetically corrected comparative methods were used to assess the influence of differences in body size, lifestyle and global scale spatial distribution of diet evolution. While lifestyle and distribution considerably influenced how diet patterns evolved, body size was not a significant determinant of the prey types taken. The lack of body size-diet association may be because larger-bodied elapids also opportunistically supplement their diet with smaller prey items. Overall, the findings indicate that recent ecological factors (e.g., lifestyle) coupled with long established factors (phylogeny, biogeography) have shaped elapid natural history patterns. This study is the first of its kind to offer a family-level, phylogenetically- based analysis on the evolutionary and contemporary feeding dynamics of the world’s most widespread snake family. 4 ACKNOWLEDGEMENTS I extend my gratitude to Prof. Graham Alexander and Dr. Bryan Maritz for their knowledgeable and patient supervision throughout the compilation of the manuscript. Dr. Kelsey Glennon and Prof. Glynis Goodman Cron gave helpful suggestions regarding the early stages of data analysis. Conversations with Prof. Harry Greene were invaluable in facilitating the interpretation of the findings. Rose Shepton Poultney generously provided much needed computers to expedite data analysis. I had several useful conversations with current and former members of the Alexander Herp Lab (Ashadee Kay Miller, Hiral Naik, Ishvara Singh, Shivan Parusnath, Bianca Fizzotti and Ryan Thomas) which aided in producing the manuscript at various stages of this endeavour. The National Research Foundation funded the project from start to finish, while additional tuition fees were provided by the University of the Witwatersrand in the form of the Post Graduate Merit Scholarship. The staff at the Wartenweiler library of the University of the Witwatersrand facilitated access to numerous articles of literature from around the world. 5 CONTENTS 1. ABSTRACT………………………………………………………………………...…3 2. ACKNOWLEDGEMENTS ........................................................................................... 4 3. INTRODUCTION ......................................................................................................... 9 3.1. General overview ....................................................................................... 9 3.2. Aims and objectives ................................................................................. 14 3.3. Description of the elapid family ............................................................... 15 3.3.1. Taxonomy and origin ................................................................ 15 3.3.2. Biology and ecology ................................................................. 16 4. MATERIALS AND METHODS ................................................................................. 18 4.1. Species traits ............................................................................................. 18 4.2. Ancestral state reconstruction .................................................................. 19 5. RESULTS.....................................................................................................................22 5.1. Diet clusters of extant elapids .................................................................. 22 5.2. Model selection ........................................................................................ 25 5.3. Parsimony ................................................................................................. 25 5.4. Maximum likelihood ................................................................................ 29 5.5. Stochastic character mapping (Bayesian inference) ................................. 32 5.6. Differences in the diets of elapids among biogeographic regions ............ 33 5.7. Evolutionary differences in diet types across biogeographic regions ...... 34 5.8. Differences in the diet characteristics in relation to lifestyle ................... 37 6 5.9. Lifestyle and diet ...................................................................................... 39 5.10. Body size and diet .................................................................................... 43 6. DISCUSSION .............................................................................................................. 43 6.1. Diet evolution ........................................................................................... 43 6.2. Diet and the biogeographic regions .......................................................... 45 6.3. Diet and lifestyle ...................................................................................... 47 6.4. Body size and diet .................................................................................... 50 7. CONCLUSION ............................................................................................................ 53 8. REFERENCES ............................................................................................................ 57 9. APPENDIX .................................................................................................................. 73 7 LIST OF TABLES Table 1. The Maximum Likelihood estimate; number of free parameters; AIC, AIC, AIC and AICc values for the ER, SYM and ARD models of parameter values for various diet types in Elapidae.…………………………………………………………………..…...........26 Table 2. The scaled probabilities of seven diet clusters occurring at the root node of elapid phylogeny..………………………………………………………………………………..….33 Table 3. The number of trees from of the 100 stochastically mapped histories which supported a particular diet groups as the possible ancestral condition………………………33 Table 4. The numbers of transitions which occurred between diet types in 100 stochastically mapped trees. On average trees had 110.38 changes between states.………………………..34 Table 5. The mean raw and proportional amount of time spent consuming seven diet types within the elapid snake family..…………………………………………………...………….34 Table 6. Pagel’s correlation output on the evolutionary covariation in diet types across different biogeographic regions. Results are presented as P values with the differences in log likelihoods (LnL) occurring within brackets. For each pairwise comparison the degrees of freedom are 4. …………..……………………………………………………………………38 Table 7. Results of Pagel’s correlation on the association in the rates of lifestyle and diet evolution. Data are shown as P values and differences in log likelihoods (LnL) are bracketed. For each pairwise comparison the degrees of freedom are 4…………...………...43 Table 8. The scaled likelihoods of different lifestyle categories at the root node of the Elapid phylogeny.……………………………………………………………………………...…….43 Appendix 3. Diet classes recorded as presence-absence data (1 & 0 respectively)