An updated model of the krill-predator dynamics of the Antarctic ecosystem

252 Pages·2017·12.69 MB·English

by  Naseera Moosa

University of Cape Town
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Dissertation presented for the degree of Master of Science
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An updated model of thpe krill-predator
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dynamics of the Antarctic ecosystem
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s Supervisor:
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Author: e Prof. Hans-Peter Kunzi
Naseera Moosa v Co-supervisor:
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n Prof. Doug S. Butterworth
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Marine Resource Assessment and Management Group (MARAM)
Department of Mathematics and Applied Mathematics
June 2017
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The copyright of this thesis vests in the author. No
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quotation from it or information derived from it is to be

published without full acknowledgeement of the source.
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The thesis is to be used for private study or non-
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commercial research purposes only.

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Published by the Universit y of Cape Town (UCT) in terms
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of the non-exclusive license granted to UCT by the author.
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Declaration of Authorship
I,NaseeraMoosa,declarethatthisthesistitled,‘Anupdatedmodelofthekrill-predatordynamics
of the Antarctic ecosystem’ and the work presented in it are my own. I confirm that:
(cid:4) This work was done while in candidature for a research degree at the University of Cape
Town.
(cid:4) Where I have consulted the published work of others, this is clearly attributed.
(cid:4) Where I have quoted from the work of others, the source is always given. With the exception
of such quotations, this thesis is entirely my own work.
(cid:4) I have acknowledged all main sources of help.
(cid:4) Where the thesis is based on work done by myself jointly with others, I have made clear
exactly what was done by others and what I have contributed myself.
Signed:
Date: 26/06/2017
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“The future belongs to those who believe in the beauty of their dreams.”
Eleanor Roosevelt
UNIVERSITY OF CAPE TOWN
Abstract
Faculty of Science
Marine Resource Assessment and Management Group (MARAM)
Department of Mathematics and Applied Mathematics
Dissertation presented for the degree of Master of Science in Applied Mathematics
An updated model of the krill-predator dynamics of the Antarctic ecosystem
by Naseera Moosa
The objective of this thesis is to update the Mori-Butterworth (2006) model of the krill-predator
dynamics of the Antarctic ecosystem. Their analysis aimed to determine whether predator-prey
interactionsalonecouldbroadlyexplaintheobservedpopulationtrendsofthespeciesconsideredin
their model. In this thesis, the Antarctic ecosystem is outlined briefly and details are given of the
main krill-eating predators including whales, seals, fish and penguins, together with an historical
record of the human harvesting in the region. The abundances and per capita krill consumption
of the krill-predators are calculated and used to determine the main krill-predators to be used
in the updated model developed. These predators are found to be the blue, fin, humpback and
minkewhalesandcrabeaterandAntarcticfurseals. Thethreemainshipsurveys(IDCR/SOWER,
JARPA and JSV) used to estimate whale abundance, and the abundance estimation method itself
(called distance sampling), are summarised. Updated estimates of abundance and trends are
listed for the main krill-predators. Updated estimates for the biological parameters needed for the
ecosystem model are also reported, and include some differences in approaches to those adopted
for the Mori-Butterworth model. The background to the hypothesis of a krill-surplus during the
mid-20th century is discussed as well as the effects of environmental change in the context of
possible causes of the population changes of the main krill-feeding predators over the last century.
Key features of the results of the updated model are the inclusion of a depensatory effect for
Antarctic fur seals in the krill and predator dynamics, and the imposition of bounds on K (the
a
carrying capacity of krill in Region a, in the absence of its predators); these lead to a better fit
overall. A particular difference in results compared to those from the Mori-Butterworth model
is more oscillatory behaviour in the trajectories for krill and some of its main predators. This
likely results from the different approach to modelling natural mortality for krill and warrants
further investigation. That may in turn resolve a key mismatch in the model which predicts minke
oscillations in the Indo-Pacific region to be out of phase with results from a SCAA assessment of
these whales. A number of other areas for suggested future research are listed. The updated model
presented in this thesis requires further development before it might be considered sufficiently
reliable for providing advice for the regulation and implementation of suitable conservation and
harvesting strategies in the Antarctic.
Acknowledgements
Firstly, I would like to thank the Almighty and the Compassionate, for guiding and helping me in
His small yet infinite ways.
I would like to thank my parents for their continued support and encouragement not only for the
duration of this project but through all the good and bad.
I would like to thank the NRF for their funding support.
To my co-supervisor, Prof. Doug Butterworth. I would like to extend heart-felt thank you to him
for his continued advice and support throughout the duration of this project.
I would like thank Prof. Trevor Branch (University of Washington, USA) for his Excel sheets and
his responses to my many emails regarding blue whales abundance estimates. Thank you also for
the IDCR/SOWER figures.
To Dr. Susan Holloway (MARAM, UCT), Dr. Andrea Ross-Gillespie (MARAM, UCT) and Dr.
Alexandre Zerbini (NOAA) for their assistance with regards to humpback population estimate
trajectories and trend estimates from the IWC models.
I would like to thank Prof. Marthan Bester (Mammal Research Institute, University of Pretoria)
and Dr. Eliezer Gurarie (University of Maryland, USA) for their assistance regarding the updated
crabeater seal abundance estimates from the APIS surveys.
To Prof. Tsutomu Tamura (The Institute of Cetacean Research, Japan), for his assistance with
the krill consumption estimates - thank you for patiently answering my many questions.
To Ms. Cherry Allison from the IWC, for her assistance with the baleen whale catch data.
To Prof. Andre Punt (University of Washington, USA), for his assistance with the minke whale
SCAA population estimate trajectories, and trend and covariance estimates.
I would like to thank Dr. Andrea Ross-Gillespie and Dr. Carryn de Moor (MARAM, UCT) for
their assistance with ADMB. A special thank you to Andrea for her unwavering assistance and
support with R, ADMB and Latex - what could I have done without you!
To Will Robinson, for his assistance with R and ADMB.
I would like to thank Ms. Doro Forck and Ms. Belinda Blackburn from CCAMLR for their
assistance in procuring CCAMLR articles that were not available on their site.
Thank you to the Inter Library Loans team at UCT for their assistance in procuring those “old”
books and journal articles - you were an integral part to this research!
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Contents
Declaration of Authorship i
Abstract iii
Acknowledgements iv
1 Introduction and overview of thesis 1
1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Objective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Other recent associated literature . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4 Thesis outline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4.1 Section 1: Review of the data available for the Antarctic multi-species model
development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4.2 Section 2: Development of a krill-centric Antarctic multi-species model. . . 5
2 The suborder Mysticeti and the families Phocidae and Otariidae in the Antarc-
tic food web 6
2.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 General features of the suborder Mysticeti . . . . . . . . . . . . . . . . . . . . . . . 6
2.3 Mysticeti whale species. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.4 General features of the Phocidae . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.5 Phocidae seal species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.6 General features of the Otariidae . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.7 Otariidae seal species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.8 Other krill-predators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.8.1 Fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.8.2 Penguins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.8.3 Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.9 The Antarctic food web . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.10 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.11 Pictures of the Antarctic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3 Human harvesting in the Antarctic - historical record 21
3.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.2 Harvesting of seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.3 Harvesting of whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.4 Harvesting of krill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
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Contents vi
3.5 Harvesting of fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4 Krill consumption per capita by the main krill-predators 29
4.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.2 Krill consumption by baleen whales. . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.2.1 Diet composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.2.2 Average body weights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4.2.3 Duration of feeding periods in the Antarctic . . . . . . . . . . . . . . . . . . 31
4.2.4 Daily intake of krill. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.2.5 Consumption of krill by baleen whales . . . . . . . . . . . . . . . . . . . . . 34
4.3 Krill consumption by seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.3.1 Diet composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.3.2 Average body weight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.3.3 Duration of the feeding period in the Antarctic . . . . . . . . . . . . . . . . 40
4.3.4 Daily intake of krill. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.3.5 Consumption of krill by seals . . . . . . . . . . . . . . . . . . . . . . . . . . 42
4.4 Krill consumption by fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.5 Krill consumption by penguins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5 Abundance and trend estimation for the main krill-feeding baleen whales in
model 47
5.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.2 Antarctic Ship Surveys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.2.1 IDCR/SOWER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.2.2 JARPA and JARPAII . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
5.2.3 JSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.3 Regions Analysed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.4 Distance Sampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.4.2 The detection function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.4.3 Main assumptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.4.4 Important concepts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.5 Abundance Estimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.5.1 Potential biases associated with the survey estimates . . . . . . . . . . . . . 56
5.6 Abundance and trend estimation for the baleen whales . . . . . . . . . . . . . . . . 60
5.6.1 Blue whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
5.6.2 Minke Whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
5.6.3 Fin Whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
5.6.4 Humpback Whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
5.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
6 Abundance and trend estimation for the main krill-feeding seals in model 80
6.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
6.2 Antarctic fur seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
6.2.1 Abundance estimates and the associated methodology . . . . . . . . . . . . 80
6.2.2 Uncertainties associated with abundance estimates . . . . . . . . . . . . . . 82
6.2.3 Trend estimates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
6.3 Crabeater seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Contents vii
6.3.1 Abundance estimates and their methodology . . . . . . . . . . . . . . . . . 84
6.3.2 Uncertainties associated with abundance estimates . . . . . . . . . . . . . . 87
6.3.3 Trend estimate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
6.4 Leopard seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
6.4.1 Abundance estimate and their methodology . . . . . . . . . . . . . . . . . . 89
6.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
7 Krill, penguins and fish: abundance and trend estimates 97
7.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
7.2 Krill Euphausia superba . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
7.2.1 Acoustic Surveys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
7.2.2 Other Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.2.3 Abundance estimate for krill . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.2.4 Trend estimates for krill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
7.3 Ad´elie penguin Pygoscelis adeliae . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
7.4 Marbled rockcod Notothenia rossii . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
7.5 Mackerel icefish Champsocephalus gunnari . . . . . . . . . . . . . . . . . . . . . . . 104
7.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
8 The selection of input parameter values and bounds on the values of the es-
timable parameters of the model 109
8.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
8.2 Natural annual mortality estimates . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
8.2.1 Whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
8.2.2 Seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
8.3 Maximum annual female birth rate estimates . . . . . . . . . . . . . . . . . . . . . 116
8.3.1 Whales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.3.2 Seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.4 Maximum per capita annual krill consumption estimates . . . . . . . . . . . . . . . 118
8.5 Intrinsic krill growth rate estimates . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
8.6 Input parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
8.7 Minke stomach fullness data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
8.8 Parameter bound ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
8.9 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Appendix A Krill Equations from Butterworth et al. (1994b) 128
9 Hypothesized causes of the population changes of the krill-feeding predators 132
9.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
9.2 Laws’ Krill Surplus hypothesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
9.3 Effects of environmental change . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
9.3.1 Changes in sea-ice habitats . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
9.3.2 Increases in sea-surface temperatures . . . . . . . . . . . . . . . . . . . . . . 136
9.3.3 Changes in circulatory patterns . . . . . . . . . . . . . . . . . . . . . . . . . 137
9.3.4 Ocean acidification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
9.3.5 Changes in UV radiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
9.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
10 A summary of Mori and Butterworth (2006) and their conclusions 143
10.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
10.2 Data and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Contents viii
10.2.1 The species considered and the regional effects incorporated . . . . . . . . . 143
10.2.2 Historical catch record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
10.2.3 Abundance estimates and their relative trends . . . . . . . . . . . . . . . . 144
10.2.4 The population dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
10.3 The model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
10.3.1 Model fitting and parameter estimation . . . . . . . . . . . . . . . . . . . . 147
10.3.2 The likelihood function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
10.4 Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
10.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
11 An updated and refined predator-prey model for exploring Antarctic ecosystem
dynamics 154
11.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
11.2 Data and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
11.2.1 Species considered in the model . . . . . . . . . . . . . . . . . . . . . . . . . 154
11.2.2 Incorporating regional effects . . . . . . . . . . . . . . . . . . . . . . . . . . 154
11.2.3 Historic catch record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
11.2.4 Abundance estimates and their relative trends . . . . . . . . . . . . . . . . 155
11.2.5 Species’ population dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . 155
11.3 The model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
11.3.1 The likelihood function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
11.4 Discussion and Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
11.4.1 Base Case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
11.4.2 Base Case vs the Mori-Butterworth Reference Case . . . . . . . . . . . . . . 166
11.4.3 Base Case vs Sensitivity 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
11.4.4 Base Case vs Sensitivity 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
11.5 Response to the Willis (2014) article . . . . . . . . . . . . . . . . . . . . . . . . . . 169
11.6 Improvements and further sensitivities . . . . . . . . . . . . . . . . . . . . . . . . . 173
11.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Appendix A Catch tables for the krill-predators 198
12 Conclusions and Future Work 205
12.1 Conclusions drawn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
12.2 Improvements and future work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
13 Glossary 209
14 References 216