Population structure in harbour porpoises (Phocoena phocoena) of British Columbia and widespread hybridization in cetaceans by Carla Anne Crossman BSc, Queen’s University, 2010 A THESIS SUBMITTED IN PARTIAL FUFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in The Faculty of Graduate Studies (Zoology) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2012 © Carla Anne Crossman, 2012 i Abstract Harbour porpoises (Phocoena phocoena) are one of the most abundant small cetaceans in the world and, while they are extensively studied across most of their range, little is known about their biology in British Columbia, Canada. Recent management plans have identified a need to better understand the population structure of harbour porpoises in this region. I investigated the genetic population structure of harbour porpoises in British Columbia using mitochondrial DNA (mtDNA) and eight microsatellite loci. My findings are consistent with a single population of harbour porpoises inhabiting the coastline between Haida G’waii and the southern Juan de Fuca Strait. I also confirmed that hybridization between harbour porpoises and Dall’s porpoises (Phocoenoides dalli) has occurred over a larger geographic region than previously known and I present evidence that the resultant hybrids are reproductively viable and have the potential to successfully backcross with both parental species. Building on these findings, I examined patterns of hybridization across the order Cetacea. I found that species pairs that share a greater number of ecological, morphological, and behavioural traits have a higher propensity to hybridize than species pairs that do not. This trend is largely driven by behavioural and morphological traits such as vocalization frequency and body size. My study aids in understanding harbour porpoise population structure in British Columbia, and highlights the occurrence of widespread cetacean hybridization. ii Preface This work did not require ethics review as the tissue samples were donated by the Animal Heath Centre, Fisheries and Oceans Canada, Simon Fraser University, Vancouver Aquarium Marine Science Centre and the Whale Museum. The tissue samples were not collected for my explicit use in research and were collected from animals that died naturally. iii Table of Contents Abstract.......................................................................................................................................... ii Preface ........................................................................................................................................... iii Table of Contents ........................................................................................................................ iv List of Tables ................................................................................................................................ vi List of Figures ............................................................................................................................. vii List of Equations ........................................................................................................................ viii Acknowledgements .................................................................................................................... ix 1 Introduction ........................................................................................................................... 1 1.1 Conservation genetics ................................................................................................... 1 1.2 Cetacean conservation .................................................................................................. 3 1.3 The harbour porpoise ................................................................................................... 4 1.4 Hybridization ............................................................................................................... 10 1.5 Opportunistic data ...................................................................................................... 10 1.6 Research objectives ...................................................................................................... 11 2 Population Structure and Intergeneric Hybridization .................................................. 13 2.1 Introduction ................................................................................................................. 13 2.1.1 The use of molecular markers for studies of population structure .............. 13 2.1.2 Harbour porpoise population structure ........................................................... 14 2.1.3 Porpoise hybridization ........................................................................................ 16 2.2 Methods ........................................................................................................................ 17 2.2.1 Samples .................................................................................................................. 17 2.2.2 DNA extraction .................................................................................................... 17 2.2.3 Mitochondrial DNA ............................................................................................. 18 2.2.4 Microsatellites ....................................................................................................... 19 2.2.5 Identifying hybrids .............................................................................................. 19 2.2.6 Population structure – mtDNA .......................................................................... 20 2.2.7 Population structure – microsatellites .............................................................. 21 2.3 Results ........................................................................................................................... 23 2.3.1 Identifying hybrids .............................................................................................. 23 2.3.2 mtDNA .................................................................................................................. 27 iv 2.3.3 Microsatellites ....................................................................................................... 30 2.4 Discussion ..................................................................................................................... 34 2.4.1 Hybridization ....................................................................................................... 39 2.4.2 Contributions ........................................................................................................ 40 3 An Analysis of Cetacean Hybridization .......................................................................... 42 3.1 Introduction ................................................................................................................. 42 3.1.1 Research objectives .............................................................................................. 46 3.2 Methods ........................................................................................................................ 46 3.2.1 Data collection ...................................................................................................... 46 3.2.2 Similarity index .................................................................................................... 46 3.2.3 Hybridization and similarity index ................................................................... 49 3.3 Results ........................................................................................................................... 51 3.3.1 Un-weighted analysis .......................................................................................... 51 3.3.2 Weighted analysis ................................................................................................ 56 3.4 Discussion ..................................................................................................................... 60 3.4.1 Species barriers ..................................................................................................... 61 3.4.2 Potential benefits of interspecific mating ......................................................... 62 3.4.3 Conclusions ........................................................................................................... 63 4 Conclusions ......................................................................................................................... 64 4.1 Summary of findings .................................................................................................. 64 4.2 Studies using samples of bycatch and strandings .................................................. 64 4.3 Future directions ......................................................................................................... 65 References ................................................................................................................................... 68 Appendices ................................................................................................................................. 85 A.1 Appendix S1 – Chapter 2 ............................................................................................... 85 A.2 Appendix S2 – Chapter 3 ............................................................................................... 98 v List of Tables Table 2.1 Prior probability and delta K from