UNIVERSITY OF CALIFORNIA, SAN DIEGO Deep-Diving Cetaceans of the Gulf of Mexico: Acoustic Ecology and Response to Natural and Anthropogenic Forces Including the Deepwater Horizon Oil Spill Adissertationsubmittedinpartialsatisfactionofthe requirements for the degree Doctor of Philosophy in Oceanography by Karlina Paul Merkens Committee in charge: John Hildebrand, Chair Jay Barlow Phil Hastings William Hodgkiss James Neih 2013 Copyright Karlina Paul Merkens, 2013 All rights reserved. The dissertation of Karlina Paul Merkens is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2013 iii DEDICATION To Lillian Irene, my inspiration, motivation, and the apple of my eye. And to Michael, today, tomorrow, and forever. iv EPIGRAPH I must go down to the seas again, to the lonely sea and the sky, And all I ask is a tall ship and a star to steer her by, And the wheel’s kick and the wind’s song and the white sail’s shaking, And a grey mist on the sea’s face, and a grey dawn breaking. I must go down to the seas again, for the call of the running tide Is a wild call and a clear call that may not be denied; And all I ask is a windy day with the white clouds flying, And the flung spray and the blown spume, and the sea-gulls crying. I must go down to the seas again, to the vagrant gypsy life, To the gull’s way and the whale’s way, where the wind’s like a whetted knife; And all I ask is a merry yarn from a laughing fellow-rover, And quiet sleep and a sweet dream when the long trick’s over. —SeaFever,JohnMasefield v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph ..................................... v TableofContents................................. vi List of Figures . ix List of Tables . xi Acknowledgements ................................ xii VitaandPublications .............................. xv Abstract of the Dissertation . xvii Chapter1 Introduction ........................... 1 1.1 Cetaceans .......................... 1 1.2 Deep-DivingCetaceans . 2 1.3 TheGulfofMexico ..................... 6 1.4 The Deepwater Horizon Oil Spill . 8 1.5 Data Collection and Analysis Overview . 10 1.6 Summary .......................... 10 Chapter2 DataAcquisitionandProcessing . 13 2.1 Acoustic Data . 13 2.1.1 Instrumentation and Sites . 13 2.1.2 Analysis of Recordings . 17 2.2 EnvironmentalData . 20 2.2.1 DataFromHARPs . 20 2.2.2 Data from Satellites and Other Sources . 23 2.3 DataExploration ...................... 28 2.4 Trend Analysis . 33 2.4.1 Seasonal and Oil-spill related trends . 33 2.4.2 Diel patterns . 34 2.5 HabitatModeling ...................... 35 2.5.1 Generalized Additive Models (GAMs) . 35 2.5.2 Zero-inflated Negative Binomial (ZINB) GeneralizedLinearModels . 37 2.6 Summary .......................... 39 vi Chapter 3 Sperm whale ecology and habitat modeling . 40 3.1 Abstract . 40 3.2 Introduction to Sperm Whales . 41 3.2.1 General Biology and Distribution . 41 3.2.2 Social Structure and Behavior . 41 3.2.3 Temporal Patterns . 43 3.2.4 HabitatPreferences . 44 3.2.5 Acoustics . 45 3.3 Sperm-WhaleSpecificMethods . 45 3.4 Results of Exploratory Analysis . 45 3.5 Results and Discussion of Trend Analysis . 48 3.5.1 Diel patterns . 48 3.5.2 Seasonal trends . 51 3.5.3 Oil-spill related trends . 54 3.6 Results and Discussion of GAMs and ZINB models . 58 3.6.1 Sperm whales at Mississippi Canyon . 59 3.6.2 SpermwhalesatGreenCanyon . 63 3.6.3 SpermwhalesatDryTortugas. 67 3.7 Summary .......................... 71 Chapter 4 Beaked whale ecology and habitat modeling . 74 4.1 Abstract . 74 4.2 Introduction . 75 4.2.1 General Biology, Behavior, Social Structure and Distribution . 75 4.2.2 Temporal Patterns . 78 4.2.3 HabitatPreferences . 78 4.2.4 Acoustics . 79 4.3 BeakedWhaleSpecificMethods . 79 4.4 Results of Exploratory Analysis . 81 4.5 Results and Discussion of Trend Analysis . 86 4.5.1 Diel patterns . 86 4.5.2 Seasonal trends . 92 4.5.3 Oil-spill related trends . 97 4.6 Results and Discussion of GAMs and ZINB models . 103 4.6.1 Cuvier’sBeakedWhales . 103 4.6.2 Gervais’beakedwhales . 112 4.7 Summary .......................... 119 Chapter 5 Kogia spp. ecology and habitat modeling . 122 5.1 Abstract . 122 5.2 Introduction to Kogia spp. 123 5.2.1 General Biology . 123 vii 5.2.2 Distribution, Habitat Preferences, Behavior and TemporalPatterns . 124 5.2.3 Acoustics . 126 5.3 Kogia SpecificMethods. 127 5.4 Results of Exploratory Analysis . 128 5.5 Results of Trend Analysis . 130 5.5.1 Diel patterns . 130 5.5.2 Seasonal trends . 132 5.5.3 Oil-spill related trends . 135 5.6 Results and Discussion of ZINB models . 137 5.6.1 Kogia spp. atMississippiCanyon . 138 5.6.2 Kogia spp. atGreenCanyon. 140 5.6.3 Kogia spp. at Dry Tortugas . 142 5.7 Summary .......................... 144 Bibliography . 146 viii LIST OF FIGURES Figure 1.1: Gulf of Mexico Bathymetry and Circulation . 7 Figure 1.2: Extent of Cumulative Surface Oil from Deepwater Horizon Oil Spill . 9 Figure 1.3: Gulf of Mexico Deep Water HARP locations . 11 Figure 2.1: HARP schematic . 14 Figure 2.2: HARP Reording Effort....................... 16 Figure 2.3: Long Term Spectral Average example . 18 Figure2.4: AISExample ............................ 21 Figure 2.5: Example of vessel detections in HARP data. 22 Figure2.6: Timeseriesofnumberofboatsperday. 22 Figure2.7: Timeseriesofnoiseat40Hz . 23 Figure 2.8: Example spectrograms with and without air guns . 24 Figure 2.9: Single Image Edge Detection example . 27 Figure 2.10: Example Histograms and QQ plots . 29 Figure 2.11: Example Cleveland Dot Plots of Transformed Data . 31 Figure2.12:ExamplePairsPlot. 32 Figure 2.13: Example tweedie profile plot . 36 Figure 3.1: Sperm whale distribution . 42 Figure3.2: Timeseriesofspermwhaledetections . 47 Figure3.3: Dielpatternsofspermwhales . 50 Figure 3.4: Box plot of seasonal sperm whale detections . 53 Figure 3.5: Box plot of sperm whale detections in summer 2010 and 2011 . 55 Figure 3.6: Example plots of slopes of sperm whale detections before and after breakpoints . 57 Figure3.7: Modeledpartialfits forsperm whalesatMC. 60 Figure 3.8: Modeled partial fits for sperm whales at GC . 64 Figure 3.9: Modeledpartial fits forsperm whales atDT . 68 Figure 3.10: Sea Surface Height Anomaly June 2011 . 70 Figure 4.1: Global distribution of beaked whale species . 77 Figure 4.2: Time series of Cuvier’s beaked whale detections . 82 Figure 4.3: Time series of Gervais’ beaked whale detections . 83 Figure4.4: TimeseriesofBWGdetections . 84 Figure 4.5: Diel patterns of Cuvier’s beaked whales . 88 Figure4.6: DielpatternsofGervais’beakedwhales . 89 Figure4.7: Dielpatternsofbeakedwhales . 90 Figure 4.8: Box plot of seasonal Cuvier’s beaked whale detections . 93 Figure 4.9: Box plot of seasonal Gervais’ beaked whale detections . 94 ix Figure 4.10: Box plots of Cuvier’s beaked whale detections in summers 2010 and 2011 . 98 Figure 4.11: Box plots of Gervais’ beaked whale detections in summers 2010 and 2011 . 99 Figure 4.12: Box plots of BWG detections in summers 2010 and 2011 . 100 Figure 4.13: Modeled partial fits for Cuvier’s beaked whales at MC . 105 Figure 4.14: Modeled partial fits for Cuvier’s beaked whales at GC . 108 Figure 4.15: Modeled partial fits for Cuvier’s beaked whales at DT . 110 Figure 4.16: Modeled partial fits for Gervais’ beaked whales at MC . 113 Figure 4.17: Modeled partial fits for Gervais’ beaked whales at GC . 116 Figure 4.18: Modeled partial fits for Gervais’ beaked whales at DT . 118 Figure 5.1: Global distribution of Kogia spp. 125 Figure 5.2: Time series of Kogia spp detections . 129 Figure 5.3: Diel patterns of Kogia spp. 131 Figure 5.4: Box plot of seasonal Kogia spp. detections . 133 Figure 5.5: Box plots of Kogia spp. detections in summers 2010 and 2011 . 136 Figure 5.6: Modeled partial fits for Kogia spp. at MC . 139 Figure 5.7: Modeled partial fits for Kogia spp. at GC . 141 Figure 5.8: Modeled partial fits for Kogia spp. at DT . 143 x LIST OF TABLES Table2.1: HARPdeploymentsummary . 15 Table2.2: SummaryofSpeciesDetectionsbySite . 20 Table3.1: Zero-inflationofspermwhaledataset . 46 Table3.2: Dielpatternsofspermwhales . 49 Table 3.3: Trends in sperm whale detections before and after oil-spill- related breakpoints . 56 Table 3.4: Selected habitat models for sperm whales . 58 Table4.1: Zero-inflationofbeakedwhaledataset . 85 Table 4.2: Diel patterns of Cuvier’s beaked whales . 87 Table4.3: DielpatternsofGervais’beakedwhales . 87 Table4.4: DielpatternsofBWG. 87 Table 4.5: Trends in Cuvier’s beaked whale detections before and after oil- spill-related breakpoints . 101 Table 4.6: Trends in Gervais’ beaked whale detections before and after oil- spill-related breakpoints . 101 Table 4.7: Selected habitat models for Cuvier’s beaked whales . 104 Table 4.8: Selected habitat Models for Gervais’ beaked whales . 112 Table 5.1: Zero-inflation of Kogia spp. data set . 128 Table 5.2: Diel patterns of Kogia spp. 132 Table 5.3: Trends in Kogia spp. detections before and after oil-spill-related breakpoints . 135 Table 5.4: Selected habitat models for Kogia spp. 137 xi ACKNOWLEDGEMENTS Iwouldliketothankmyadvisor,JohnHildebrand,for6+yearsof assistance and guidance, and for providing numerous opportunities to spend time at sea and unlimited access to an truly remarkable quantity of archived data. I would also like to thank my committee, Jay Barlow, Phil Hastings, Bill Hodgkiss and James Nieh, for helping with this project from the beginning to the end. The staffin the SIO grad office deserve a huge thanks for their emotional and administrative assistance from well before I was accepted as a student. Their continual support of the grad students at SIO is absolutely essential and a major component of what makes Scripps such an amazing place.