Taxonomy is destiny: resolving the systematics of unstable squid families using integrative taxonomy to aid cephalopod conservation Heather Elizabeth Braid A thesis submitted through the Institute for Applied Ecology New Zealand, Auckland University of Technology in fulfilment of the requirements for the degree of Doctor of Philosophy supervised by Dr Kat S. R. Bolstad 2018 Table of Contents List of Tables.................................................................................................................... iii List of Figures ................................................................................................................. iv Abstract ............................................................................................................................. 1 Chapter 1: General introduction ........................................................................................ 4 Chapter 2: Resolving the taxonomic status of Asperoteuthis lui Salcedo-Vargas, 1999 (Cephalopoda, Chiroteuthidae) using integrative taxonomy ............................... 19 Chapter 3: One step closer to understanding the chiroteuthid families in the Pacific Ocean ................................................................................................................... 43 Chapter 4: Molecular phylogenetic analysis of the squid family Histioteuthidae (Mollusca, Cephalopoda) ................................................................................... 67 Chapter 5: Cephalopod biodiversity of the Kermadec Islands: implications for conservation ...................................................................................................... 100 Chapter 6: Overall discussion ....................................................................................... 140 References ..................................................................................................................... 150 Appendix 1—Catalogue of the specimens in the chiroteuthid families clade from the National Museum of Nature and Science, Tokyo (NSMT) collections ........................ 170 Appendix 2—Phylogeny of the Bathyteuthoidea ......................................................... 187 Appendix 3—Phylogeny of the Bolitaeninae ............................................................... 188 Appendix 4—Phylogeny of the Octopodidae ............................................................... 189 Appendix 5—Phylogeny of the enoploteuthid families ................................................ 190 i Attestation of Authorship I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person (except where explicitly defined in the acknowledgements), nor material that, to a substantial extent, has been submitted for the award of any other degree or diploma from a university or institute of higher learning. _________________________________________ Heather E. Braid ii List of Tables Table 1—Taxonomic status of deep-sea oegopsid squids worldwide, and in New Zealand waters ...................................................................................................... 5 Table 2—Specimen information for sequences used in Chapter 2 ................................. 21 Table 3—Measurements for Asperoteuthis lui, and mean indices for A. lui, A. acanthoderma, and A. mangoldae ....................................................................... 29 Table 4—Comparison of characters for Asperoteuthis species ...................................... 30 Table 5—Specimen information for sequences used in Chapter 3 ................................. 46 Table 6—Specimen information for sequences used in Chapter 4 ................................. 70 Table 7—Minimum intergeneric distances (%) for cytochrome c oxidase subunit I (COI) among six genera of the Histioteuthidae .................................................. 83 Table 8—Intrageneric distances for cytochrome c oxidase subunit I (COI) in six genera of the Histioteuthidae .......................................................................................... 83 Table 9—Pairwise intra- and inter-specific evolutionary distances for cytochrome c oxidase subunit I (COI) across 18 and 25 species of the Histioteuthidae ........... 83 Table 10—Morphological characteristics of the six proposed genera in the Histioteuthidae .................................................................................................... 86 Table 11—Collection data for specimens analysed in Chapter 5 ................................. 106 Table 12—Specimen data for individuals analysed in Chapter 5 ................................. 108 Table 13—Checklist of the cephalopod fauna of the Kermadec Islands region ........... 117 iii List of Figures Fig. 1—Map of the New Zealand Exclusive Economic Zone and the Kermadec Islands region................................................................................................................... 10 Fig. 2—A conceptual diagram of the flow of this thesis with the research question and approach for each chapter ................................................................................... 18 Fig. 3—Distribution of Asperoteuthis species ................................................................ 23 Fig. 4—Distribution of Asperoteuthis lui specimens examined in Chapter 2................. 24 Fig. 5 Combined maximum-likelihood phylogeny for specimens identified as Asperoteuthis nesisi, A. lui, and ‘?Mastigoteuthis A’ ......................................... 26 Fig. 6—Asperoteuthis lui locking cartilages and eye photophores ................................. 31 Fig. 7—Asperoteuthis lui arm suckers ............................................................................ 32 Fig. 8—Asperoteuthis lui tentacle club ........................................................................... 33 Fig. 9—Asperoteuthis lui radula, palatine palps, and tentacle suckers ........................... 34 Fig. 10—Asperoteuthis lui beaks .................................................................................... 35 Fig. 11—Asperoteuthis lui, NIWA 93268 ...................................................................... 36 Fig. 12—Map of all specimens in the chiroteuthid families clade held in the National Museum of Nature and Science collections ........................................................ 53 Fig. 13—Map of specimens in the chiroteuthid families clade collected from Japanese waters held in the National Museum of Nature and Science collections ............ 54 Fig. 14—Combined phylogeny of the chiroteuthid families clade ................................. 56 Fig. 15—Morphological features of the chiroteuthid families clade .............................. 57 Fig. 16—Combined phylogeny of the Histioteuthidae ................................................... 81 Fig. 17—Morphological features of the Histioteuthidae ................................................ 82 Fig. 18—Collection localities for Chapter 5 ................................................................. 104 Fig. 19—Examples of the specimens examined in Chapter 5 ...................................... 105 Fig. 20—Information sources for the cephalopod species recorded from the Kermadec Islands region .................................................................................................... 116 Fig. 21—A conceptual diagram of the flow of this thesis with the main conclusions from each chapter .............................................................................................. 141 Fig. 22—Rarefaction curves for the cephalopod biodiversity of the Kermadec Islands region................................................................................................................. 146 iv Co-Authored Work Chapter 3 of this thesis was co-authored with Tsunemi Kubodera and Kathrin S. R. Bolstad. The author of this thesis contributed 80% to this manuscript (designed study, identified samples with morphology, performed genetic analyses, and wrote the manuscript), T. Kubodera contributed 10% (collected tissue samples, reviewed the manuscript) and K. S. R. Bolstad contributed 10% (helped design study, and proofread and reviewed the manuscript). _________________________ Heather E. Braid _________________________ Tsunemi Kubodera _________________________ Kathrin S. R. Bolstad v Foreward The new nomenclature in this thesis is not issued for public and permanent scientific record, or for purposes of zoological nomenclature, and is not published within the meaning of the International Code of Zoological Nomenclature (ICZN). vi Dedication This thesis is for the squids. Acknowledgements Above all, I would like to thank Kat Bolstad—the best Doktorvater I could have hoped for—for her fantastic proofreading skills, endless patience, and constant reassurance; without her, this thesis would never have been completed. Many thanks to my kaupapa whānau in the AUT Lab for Cephalopod Ecology & Systematics (ALCES): Alex Lischka for moral support, listening and understanding throughout this process; Aaron Boyd Evans for going on amazing squid adventures in the world as well as in taxonomy; and Jesse Kelly, for encouraging me to be independent and for being fantastic company during many late nights in the lab. Thanks to past members of ALCES: Steve O’Shea for the most intact Asperoteuthis lui specimen available from New Zealand waters for morphological examination,