Kahawai Phylogeny and Phylogenetics A genetic investigation into commercial and recreational fisheries management and practice By Brenton Hodgson A thesis submitted to the Victoria University of Wellington in partial fulfilment of the requirements for the degree of Masters of Science in Marine Biology School of Biological Sciences Victoria University of Wellington 2011 Kahawai Phylogeny and Phylogenetics Brenton Hodgson i Abstract Globally, commercially exploited fish species are coming under more and more pressure as the population of humans grow. Protein from the sea has traditionally been available to coastal communities throughout history. In modern times however, traditional artisanal fisheries have been replaced by commercial fishing industries. It is estimated by some authorities that these modern fisheries have led to decreases in pre-exploitation biomass of desirable species of up to 90%. As desirable species decline, secondary species become more valuable and subject to exploitation. An issue with this exploitation is that management decisions of fish stocks are often based on political or commercial concerns rather than sound science focussed on preserving stocks, and ultimately, fishing industries. To investigate phylogenetic and phylogeographic relationships of fish, kahawai (Arripis trutta) was used as a proxy species. A. trutta is one of only four members of the genus Arripis, which in turn is the sole member of the family Arripidae. It was found that a single, highly connected population of A. trutta inhabit New Zealand waters, and approximately 15 migrants per generation make the journey between New Zealand and Australia, genetically linking these populations. A phylogeny of A. trutta was resolved using mitochondrial DNA, and while COX1 data supported the hypothesis that A. trutta forms a monophyletic clade within the Stromateoids (medusa fish, squaretails and drift fish) and the Scombrids (tuna, mackerel and their allies) suggesting a common ancestor, other data collected during the investigation does not support this hypothesis. Kahawai Phylogeny and Phylogenetics Brenton Hodgson ii Acknowledgments A work of this nature is never solely the work of one person. To complete this thesis, I have had input, advice and assistance from people in several countries. Firstly, I must acknowledge my supervisor, Dr Peter Ritchie, at Victoria University of Wellington. Pete provided me with laboratory space, advice, critical evaluation of the work at each of its many stages and a kick in the rear when needed. To Pete, I say thank you. Secondly, I need to acknowledge the assistance of my lab mates and co-students. While too many to name individually, some deserve special mention. These are Joanna Wilson, Surrey Scott, Alex Boast, Monica Gruber, Rosalynn Anderson-Lederer, Sebastian Hernandez, Andrea Varela, Allan Burne, Sebastien Rioux-Paquette, Shauna Baillie, Lisa Bryant and Elizabeth Heeg. Thanks for the good times and the help with sample preparation, lab techniques, data analysis, shoulders to cry on, coffee when needed and all the rest. It is appreciated more than you can know. Thirdly, thank you to the commercial and recreational anglers (many of whom I’ve never met or even known the names of) who supplied me with fish samples throughout the laboratory phase of my thesis, and to the complete strangers on the Randi.org, fishnhunt.co.nz and westernfishing.com.au websites who supplied samples of species not readily available and assistance with Microsoft Excel. Great work guys. Hope to see you on the water some time! Finally, I’d like to thank my family and friends for putting up with me as I worked through this process. You have endured stories of fish caught and lost, sagas of PCRs and sequencing gone wrong and endless tales of why kahawai need to be studied, and why I was doing it. To my friends at the Wellington Improvisation Troupe, my hunting and fishing buddies and especially to my sons Joshua and Jeffery and my partner Alison, thank you. This thesis is dedicated to you all. Kahawai Phylogeny and Phylogenetics Brenton Hodgson iii Table of Contents Abstract ............................................................................................................... ii Acknowledgments .............................................................................................. iii Table of Figures ................................................................................................. vi Chapter 1. Introduction .................................................................................. 1 1.1 The physical ocean environment and factors that impact gene flow ...... 1 1.2 Pelagic Larval Duration (PLD) and fish migration .................................. 2 1.3 Fishery stocks and pressures ................................................................ 4 1.4 The Arripidae family ............................................................................... 6 1.5 An introduction to tarakihi (Nemadactylus macropterus)...................... 13 1.6 Aims of this thesis study ...................................................................... 14 1.7 References .......................................................................................... 15 Chapter 2. Phylogeny of the Arripidae ......................................................... 30 2.1 Abstract ................................................................................................ 30 2.2 Introduction .......................................................................................... 30 2.3 Materials and methods......................................................................... 31 Use of published sequences ...................................................................... 31 Primer generation, DNA extraction, mitochondrial DNA amplification and sequencing ................................................................................................. 32 Phylogeny ................................................................................................... 32 2.4 Results ................................................................................................. 34 Nucleotide composition and average pairwise distances ........................... 34 Sequences resolved ................................................................................... 36 2.5 Summary ............................................................................................. 39 2.6 References .......................................................................................... 41 Chapter 3. Marine Phylogeography and Applying DNA Markers to Arripis trutta and Nemadactylus macropterus .............................................................. 46 3.1 Abstract ................................................................................................ 46 3.2 Introduction .......................................................................................... 46 3.3 Materials and Methods......................................................................... 48 Sample collection ....................................................................................... 48 DNA Extraction, mitochondrial DNA amplification and sequencing ............ 49 Population structure ................................................................................... 50 Kahawai Phylogeny and Phylogenetics Brenton Hodgson iv Effective population size and migration ...................................................... 51 Demographic history and comparison with Nemadactylus macropterus .... 51 3.4 Results ................................................................................................. 52 Nucleotide and haplotype diversity ............................................................. 52 Population divergences .............................................................................. 54 Demographic history (Wellington comparisons) ......................................... 61 3.5 Discussion ........................................................................................... 62 Population metrics and comparisons between A. trutta and N. macropterus ................................................................................................................... 62 3.6 References .......................................................................................... 66 Chapter 4. Discussion .................................................................................. 69 4.1 Summary and conclusions ................................................................... 69 4.2 Implications of this study ...................................................................... 71 4.3 Opportunities for future work in this area ............................................. 73 4.4 References .......................................................................................... 75 Appendix 1. Collection Instructions ................................................................ 78 Appendix 2. Arripis trutta COX1 Variable Nucleotides ................................... 80 Appendix 3. Arripis trutta COX1 Haplotype List ............................................. 81 Appendix 4. 12S Sequence Data ................................................................... 83 Appendix 5. Cyt B Sequence Data ................................................................ 87 Kahawai Phylogeny and Phylogenetics Brenton Hodgson v Table of Figures Figure 1-1: New Zealand, showing major ocean currents (after Carter