ECOLOGICAL AND EVOLUTIONARY DIVERSIFICATION IN SEED BEETLES (COLEOPTERA: BRUCHINAE) A thesis presented by Geoffrey Easton Morse to The Department of Organismic and Evolutionary Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biology Harvard University Cambridge, Massachusetts May, 2003 © 2003 Geoffrey Easton Morse All rights reserved. Thesis advisor: Prof. Brian D. Farrell Geoffrey Easton Morse Ecological and Evolutionary Diversification in Seed Beetles (Coleoptera: Bruchinae) The diversification of phytophagous insects is seen as one of the most fascinating phenomena in the history of life. The goal of this thesis is to investigate the mode and tempo of diversification in one group of these insects, the bruchine beetles (Coleoptera: Chrysomelidae: Bruchinae). These beetles represent the largest diversification of insects that use the embryonic tissue of plants. This thesis integrates multiple levels of analysis in order to provide a thorough picture of diversification, from processes that govern macroevolution across 80 million years to processes that create divergence within and between populations. The research first uses a phylogenetic framework based on mitochondrial and nuclear loci to examine the link between phyletic and ecological diversification in bruchines. Sister-group comparisons and ancestral state reconstructions indicate that these beetles have diversified by treating individual plant species as differentiable niches, causing rates of diversification in the insects to closely correspond to those of their host plants. Because this implies a role for specialization in the diversification of bruchines, the research then examines the trajectory of diet breadth evolution based on a phylogenetic reconstruction of the genus Stator using mitochondrial and nuclear sequence data. Analyses of the trajectory of specialization suggest that a trend toward increased specialization is contingent upon the novelty of the host shift, behavior, and community ecology. This relationship between specialization and diversification is iii examined more closely via interspecific phylogeographic and historical demographic analyses of the speciation of the specialist Stator beali from the generalist S. limbatus using mitochondrial sequence data. Phylogeographic analysis suggests a paraphyletic relationship and indicates a local geographic context for speciation, while demographic analysis suggests an important role for selection in a rapid speciation event, although elucidation of the specific mode of speciation is beyond the scope of this thesis. This combination of microevolutionary and macroevolutionary analyses, and biogeographic and ecological information, provide a framework for investigating the processes and patterns of diversification. The insights that are gained from this integrative framework are more than the sum of their individual parts and provide a solid foundation on which to test specific phylogenetic, genetic, and ecological hypotheses. iv Table of Contents List of Figures………………………………………………………..…………..vi List of Tables………………………………………………….………..………..ix Acknowledgments……………………….…………………………..………......xi I. Chapter 1……………………………………………………………………..……1 Adaptive radiation and ecological diversification in the bruchine seed beetles (Coleoptera: Chrysomelidae: Bruchinae) II. Chapter 2………………………………………………………………………..127 The evolution of specialization in the genus Stator Bridwell (Coleoptera: Chrysomelidae: Bruchinae) III. Chapter 3…………………………………………………………………….….245 Interspecific phylogeography of a paraphyletic species pair: The geographic context of speciation and specialization IV. Chapter 4…………………………………………………………………….….286 Patterns of population differentiation and demographic history in a sister-species pair of seed beetles (Coleoptera: Stator): Implications for Speciation and Specialization V. Literature Cited…………………………………………………………………342 v List of Figures Chapter 1 Figure 1.1 Borowiec’s hypothesis of bruchid relationships 10 Figure 1.2 Saturation analysis, corrected vs. uncorrected distances 71 Figure 1.3 Saturation analysis, ti/tv ratio vs. transversions 72 Figure 1.4 Strict consensus of parsimony analysis 76 Figure 1.5 Burn-in generations for Bayesian analysis 79 Figure 1.6 Consensus Bayesian phylogeny 80 Figure 1.7 Consensus Bayesian phylogram 82 Figure 1.8 Sister groups on parsimony tree 84 Figure 1.9 Sister groups on Bayesian tree 88 Figure 1.10 Host plant clade on parsimony tree 92 Figure 1.11 Host plant clade on Bayesian tree 94 Figure 1.12 Maximum-likelihood reconstruction of host clade, Acanthoscelidini 97 clade 1 Figure 1.13 Maximum-likelihood reconstruction of host clade, Acanthoscelidini 98 clade 2 Figure 1.14 Maximum-likelihood reconstruction of host clade, Basal grade of 99 Bruchidae Figure 1.15 Maximum-likelihood reconstruction of host growth form 100 Figure 1.16 Host species recorded per bruchid host species 116 Chapter 2 Figure 2.1 ‘Grafen’ supertree of Stator host plants 149 Figure 2.2 ‘Minimal evolution’ supertree of Stator host plants 150 Figure 2.3 Supertree of Stator host plant lineages 176 Figure 2.4 Saturation analysis, corrected vs. uncorrected distances 183 Figure 2.5 Saturation analysis, ti/tv ratio vs. transversions 183 Figure 2.6 Strict consensus of parsimony analysis 186 Figure 2.7 Burn-in generations for Bayesian analysis 188 Figure 2.8 Consensus Bayesian phylogeny 189 vi Chapter 2 (Continued) Figure 2.9 Consensus parsimony phylogram 191 Figure 2.10 Consensus Bayesian phylogram 192 Figure 2.11 Histogram of phylogenetic distance (PD) of host species per Stator 193 species, ‘Grafen’ trees Figure 2.12 Histogram of PD of host species per Stator species, ‘Minimal 193 evolution’ trees Figure 2.13 Histogram of number of host species per Stator species 194 Figure 2.14 Histogram of number of host species per Stator species 194 Figure 2.15 Parsimony reconstruction of generalists and specialists 197 Figure 2.16 Parsimony reconstruction of oviposition guild 198 Figure 2.17 Parsimony reconstruction of host plant genera 199 Figure 2.18 Parsimony reconstruction of host plant hierarchical clade 202 Figure 2.19 Maximum likelihood reconstruction of generalists and specialists 204 Figure 2.20 Maximum likelihood reconstruction of host plant clade 206 Figure 2.21 Maximum likelihood reconstruction of of oviposition guild 207 Figure 2.22 GLS reconstruction of number of host species 208 Figure 2.23 GLS reconstruction of number of host genera 209 Figure 2.24 GLS reconstruction of PD of host species, ‘Grafen’ trees 210 Figure 2.25 GLS reconstruction of PD of host species, ‘Minimal evolution’ trees 211 Chapter 3 Figure 3.1 Distribution of Stator limbatus 256 Figure 3.2 Distribution of Stator beali 257 Figure 3.3 Genitalia of S. limbatus and S. beali 259 Figure 3.4 Stator beali eggs on Ebenopsis ebano 260 Figure 3.5 Stator limbatus eggs on Acacia tenuifolia 260 Figure 3.6 Map of sites sampled for S. limbatus and S. beali 263 Figure 3.7 Agreement topology between maximum-likelihood, Bayesian, and 272 parsimony analyses Figure 3.8 Phylogram from maximum-likelihood analysis 273 Figure 3.9 Phylogeography of monophyletic lineages 275 vii Chapter 4 Figure 4.1 Sampling localities of S. beali and S. limbatus within the 303 Tamaulipan biogeographic province Figure 4.2 Genealogical relationships among Stator beali haplotypes 310 Figure 4.3 Genealogical relationships among Stator limbatus haplotypes in the 311 Mexican xerophytic province Figure 4.4 Frequency and distribution of haplotypes sampled for S. limbatus 315 within the Tamaulipan province Figure 4.5 Frequency and distribution of haplotypes sampled for S. beali 316 Figure 4.6 Plot of FST from pairwise population comparisons versus geographic 317 distance within the Tamaulipan geographic province for Stator limbatus and S. beali Figure 4.7 Mismatch distributions for Stator limbatus and S. beali 324 Figure 4.8 Observed and expected site frequency distributions for S. beali 324 given a coalescent model of rapid population expansion (Wakeley and Hey, 1997) Figure 4.9 Maximum likelihood estimation of θ and population growth rate (g) 325 for S. limbatus Figure 4.10 Maximum likelihood estimation of θ and population growth rates (g) 326 for S. beali Figure 4.11 Deterministic backward extrapolation of female effective population 327 sizes of S. limbatus and S. beali given the maximum-likelihood estimations of θ and g viii List of Tables Chapter 1 Table 1.1 Classification and biogeography of the Bruchidae 6 Table 1.2 Species included in molecular phylogenetic analysis of the 29 Bruchidae Table 1.3 Sequences of primers used in molecular phylogenetic analysis of the 38 Bruchidae Table 1.4 Host growth form summarized by exemplar taxa 48 Table 1.5 Host plant clade summarized by exemplar taxa 53 Table 1.6 Ecological codings for macroevolutionary analyses of ecological 63 associations Table 1.7 Properties of gene subsets 70 Table 1.8 Tests of a priori hypotheses of monophyly 75 Table 1.9 Summary of sister-group diversity comparisons 86 Table 1.10 Results of analyses of phylogenetic constraint 91 Table 1.11 Results of the analysis of the apparency hypothesis 103 Chapter 2 Table 2.1 Host plant relationships of 22 species of Stator with established host 143 plant associations Table 2.2 Geographic distribution of 24 well-established species of Stator 146 Table 2.3 Specimens of Stator included in molecular phylogenetic analysis 156 Table 2.4 Sequences of primers used in this study 161 Table 2.5 Discrete ecological codings for analyses of