RADAR Research Archive and Digital Asset Repository Copyright © and Moral Rights for this thesis are retained by the author and/or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder(s). The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holders. Note if anything has been removed from thesis. Map on p233 When referring to this work, the full bibliographic details must be given as follows: Hogan, J. E. (2012) Taxonomy, Systematics and Biogeography of the Scaritinae (Insecta, Coleoptera, Carabidae). PhD Thesis. Oxford Brookes University. WWW.BROOKES.AC.UK/GO/RADAR Taxonomy, Systematics and Biogeography of the Scaritinae (Insecta, Coleoptera, Carabidae) James Edward Hogan Thesis submitted in partial fulfilment of the requirements of the award of Doctor of Philosophy Oxford Brookes University December 2012 Abstract Scaritinae are a subfamily of ground beetles (Carabidae), containing about 1900 species and 125 genera. They share a distinctive body shape linked to a burrowing lifestyle. The diversity of Scaritinae is concentrated in the tropics and warmer regions of the southern hemisphere, particularly Southern Africa, Madagascar and Australia. The evolutionary history (phylogeny) of scaritines is unknown, leading to conflicting classification schemes and uncertainty over the definition of genera, especially in one sub- group of scaritines, the tribe Scaritini. In particular, it is unclear whether Scaritinae are descended from a common ancestor (monophyletic) or whether they are an artificial group defined by convergent adaptations to burrowing. Phylogenetic relationships of the Scaritinae were investigated in detail for the first time using morphological and molecular data. Analysis of morphological characters resulted in multiple equally parsimonious trees. Bayesian analysis supported a monophyletic Scaritinae and within Scaritini, a basal position of subtribes Carenina and Pasimachina. Relationships of subtribe Scaritina were impossible to reconstruct due to a complex pattern of convergent evolution and character reversals. 18S rRNA gene sequences were aligned using ClustalX and by incorporating secondary structure information using MAFFT. Consistent results were obtained by Bayesian analysis of the MAFFT alignments, supporting the clades Scaritinae and Scaritini, Carenina and Scaritina. The Australian scaritines (Carenina) were found to be sister to all remaining Scaritini. An historical biogeographic reconstruction of the Scaritini was undertaken by incorporating evidence from extant distributions, fossils and the phylogenetic data. It is likely that evolution of the basal lineages of Scaritini occurred before the fragmentation of Gondwana and that the present-day distributions of the later radiation of Scaritina are due to dispersal. As with most groups of Carabidae, the lack of fossil evidence and molecular clock dating precludes any firm biogeographical conclusions. Acknowledgements It is no exaggeration to say this work would have been impossible without the help and tolerance of my family Rae, Maeve and Eddie. Steve Simpson, George McGavin and my supervisor Tim Shreeve have encouraged me from the very beginning. David Maddison and George Ball offered sound advice during the early stages and Petr Bulirsch shared his great knowledge of scaritine taxonomy. Special thanks must go to Darren Mann for help and advice on probably every aspect of this project and for gathering rare beetles from around the world. I also must thank my colleagues Zoë Simmons, Amoret Spooner and Katherine Child who were very supportive during the final stages of this work. For help with translation I am indebted to my family, John Hogan (French), Pat Frith (Italian) and Sophie Hayes (German). Alfried Vogler and John Day were very generous in providing facilities for DNA sequencing. Specimens for DNA work were graciously provided by Jose Galián, Mike Caterino, David Pryce, Daegan Inward and Dan Duran. Max Barclay, Christine Taylor and Beulah Garner kindly arranged loans of specimens from the Natural History Museum, London. This thesis is dedicated to Elaine Hogan, who above all others wished to see its completion. Contents 1. Introduction 1 1.1 Introduction 1 1.1.1 Classification of the Scaritinae 4 1.1.2 Evolution of the Carabidae 12 1.1.3 Evolution of the Scaritinae 14 1.1.4 Reconstructing the evolutionary history of scaritines 20 1.1.5 Morphology and scaritine phylogeny 26 1.1.6 Molecular systematics and scaritine phylogeny 29 1.1.7 Biogeography of the Scaritini 32 1.2. Aims 36 2. Phylogeny of the Scaritinae inferred from morphological data 37 2.1 Characters and character states 37 2.2 Methods 39 2.2.1 Taxon sampling 39 2.2.2 Character definition and coding 43 2.2.2.1 Character definition 43 2.2.2.2 Character coding 49 2.2.2.3 Ordering of character states 49 2.2.2.4 Missing and inapplicable data 50 2.2.2.5 Convergent and parallel evolution 51 2.2.2.6 Convergent and parallel evolution in the Scaritini 53 2.2.2.7 Characters associated with flight 55 2.2.3 The morphological characters 61 2.2.3.1 Dorsal surface of the head 62 2.2.3.2 Mouthparts 70 2.2.3.3 Ventral surface of the head 80 2.2.3.4 Thorax 81 2.2.3.5 Legs 86 2.2.3.6 Elytra 90 2.2.3.7 Abdomen 96 2.2.4 Phylogenetic analysis 97 2.2.4.1 Maximum parsimony methods 98 2.2.4.2 Bayesian inference methods 101 2.3 Results 104 2.3.1 Results of the character scoring 104 2.3.2 Results of the parsimony analysis 107 2.3.3 Results of the character ordering 113 2.3.4 Results of the Bayesian analysis 114 2.3.5 Per-character statistics 117 2.3.6 Phylogenetic relationships 119 2.4 Discussion 131 2.4.1 Homoplasy and multiple equally parsimonious trees 131 2.4.2 Genera defined by labile characters 133 2.4.3 Ecological convergence 136 2.5 Conclusions and future directions 140 3. A study of the male genitalia of Scaritini 142 3.1 Introduction 142 3.1.1 Internal structure of the aedeagus 142 3.2 Method 144 3.3 Results 145 3.4 Conclusions 152 4. Phylogeny of the Scaritinae inferred from molecular data 154 4.1 Introduction 154 4.1.1 The small subunit 18S rRNA gene 154 4.1.2 Structure of the 18S rRNA molecule 155 4.1.3 Sequence alignment 157 4.1.3.1 Incorporating secondary structure information 159 4.1.3.2 The problem of ambiguous alignment 163 4.2 Methods 164 4.2.1 Taxon Sampling 164 4.2.2 DNA extraction, amplification and sequencing 168 4.2.2.1 DNA extraction 168 4.2.2.2 DNA Amplification 169 4.2.2.3 DNA Sequencing 170 4.2.2.4 DNA sequence editing 170 4.2.3 Analysis methods 170 4.2.3.1 The ‘multiple analysis’ method 170 4.2.3.2 Multiple sequence alignment 171 4.2.3.3 Data partitioning 173 4.2.3.4 Phylogenetic analysis 175 4.2.3.5 Phylogenetic analysis with PAUP* 175 4.2.3.6 Phylogenetic analysis with MrBayes 176 4.2.3.7 Gap coding 177 4.2.3.8 Construction of the combined consensus trees |178 4.3 Results 180 4.3.1 The sequence data 180 4.3.2 The alignments and parameters 180 4.3.3 The data partitions 188 4.3.3.1 Phylogenetic signal of the length-conserved regions 188 4.3.3.2 Phylogenetic signal of the length-variable regions 194 4.3.4 Phylogeny inferred from the full length 18S sequence 200 4.3.5 Reversible jump MCMC and substitution models 212 4.3.6 Phylogenetic relationships 212 4.3.6.1 The mid-grade Carabidae outgroups 212 4.3.6.2 Scaritine relationships 214 4.4 Discussion 219 4.4.1 The data partitions 219 4.4.2 Alignment methods 220 4.4.3 Phylogenetic methods 221 4.4.4 Relationships of the Scaritinae 222 4.5 Conclusions and future directions 224 5. Biogeography of the Scaritini 226 5.1 The present distribution of Scaritini 226 5.2 The fossil record of Carabidae and Scaritinae 230 5.3 Vicariance and the distribution of Scaritini 232 5.4 Biogeography of the basal subtribes of Scaritini: Carenina and Pasimachina 235 5.5 Dispersal and the distribution of Scaritina 239 5.6 Biogeography and taxonomy 243 5.7 Conclusions and future directions 244 6. Conclusions and directions for further work 246 6.1 Morphological versus molecular data 246 6.2 Evolution of the mid-grade Carabidae and Scaritinae 250 6.3 Classification of the Scaritinae 252 6.4 Biogeography 253 6.5 Concluding remarks 254 References 255 Appendix 288 Chapter 1 Introduction 1.1 Introduction. The family Carabidae, commonly known as ground beetles, is one of the larger families of Coleoptera, comprising about 35,000 species (Lorenz, 2005). The focus of this research is on the Scaritinae, a subfamily of the Carabidae comprising about 1850 species and 125 genera (Lorenz, 2005). Scaritinae are specialised for burrowing and are easily distinguished from other ground beetles both by their distinctive body shape and by their front legs modified for digging (figure 1.1). Scaritines occur in a wide variety of habitats, from lowland tropical forest to semi-desert and from ocean beaches to the tops of mountains. They are present on all continents except Antarctica and are most numerous in the tropics and warmer regions of the Southern Hemisphere. Some areas, such as Madagascar and Australia, have a large and diverse endemic fauna.