Tsang, Yin Ting Anton. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 373-402). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.iv / 論文摘要 --- p.viii / Table of Contents --- p.xi / List of Tables --- p.xvii / List of Figures --- p.xxiii / Chapter Chapter 1 --- Who are “our dolphins and their MPA´ح？ - A general introduction / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.1.1 --- What is a MPA? --- p.1 / Chapter 1.1.2 --- Why MPAs? --- p.2 / Chapter 1.1.3 --- MPAs & Cetaceans --- p.3 / Chapter 1.2 --- MPAs & Marine Conservation in Hong Kong --- p.5 / Chapter 1.3 --- The Mascot of Hong Kong ´ؤ The Chinese White Dolphin --- p.8 / Chapter 1.3.1 --- Cetaceans in Hong Kong --- p.8 / Chapter 1.3.2 --- History of the Indo-Pacific Humpback Dolphins --- p.9 / Chapter 1.3.3 --- Taxonomy of the Indo-Pacific Humpback Dolphins --- p.11 / Chapter 1.3.4 --- General Descriptions of the Indo-Pacific Humpback Dolphins --- p.12 / Chapter 1.3.5 --- Distribution of the Indo-Pacific Humpback Dolphins --- p.13 / Chapter 1.3.6 --- Conservation Status of the Indo-Pacific Humpback Dolphins & Threats that They are Facing --- p.14 / Chapter 1.4 --- The “Dolphin Sanctuary´ح？ - Sha Chau & Lung Kwu Chau Marine Park --- p.15 / Chapter 1.5 --- Significance & Objectives of This Study --- p.18 / Chapter 1.6 --- Study Areas --- p.19 / Chapter 1.7 --- Organization of This Thesis --- p.21 / Chapter Chapter 2 --- "How are our dolphins doing in the MPA? - Abundance, behaviour and habitat use of the Indo-Pacific humpback dolphins within and outside the marine park" / Chapter 2.1 --- Introduction --- p.27 / Chapter 2.2 --- Methodology --- p.30 / Chapter 2.2.1 --- Field Sampling --- p.30 / Chapter 2.2.1.1 --- Dolphin survey --- p.30 / Chapter 2.2.1.2 --- Collection of information on physical parameters --- p.34 / Chapter 2.2.2 --- Data Analysis --- p.35 / Chapter 2.2.2.1 --- Definition of parameters --- p.35 / Chapter a) --- Seasonality --- p.35 / Chapter b) --- Dolphin observation regions and areas --- p.36 / Chapter c) --- Standardization of effort --- p.37 / Chapter 2.2.2.2 --- Statistical analysis --- p.38 / Chapter 2.3 --- Results --- p.41 / Chapter 2.3.1 --- Observability --- p.41 / Chapter 2.3.2 --- Distribution of Dolphin Sightings --- p.42 / Chapter 2.3.3 --- Number of Dolphin Sightings --- p.46 / Chapter 2.3.4 --- Dolphin Sightings at Different Tidal Movements --- p.48 / Chapter 2.3.5 --- Sighting Rate and Density of Dolphin Sightings --- p.49 / Chapter 2.3.6 --- Composition --- p.54 / Chapter 2.3.7 --- Group Size --- p.56 / Chapter 2.3.8 --- Dive Times --- p.59 / Chapter 2.3.9 --- Behaviours --- p.62 / Chapter 2.4 --- Discussion --- p.64 / Chapter 2.4.1 --- Identifying “Hotspots´ح --- p.64 / Chapter 2.4.2 --- Areas other than “Hotspots´ح --- p.71 / Chapter 2.4.3 --- Is SLMP Effective? --- p.72 / Chapter 2.4.4 --- Seasonality of the Indo-Pacific Humpback Dolphins --- p.75 / Chapter 2.5 --- Chapter Summary --- p.77 / Chapter Chapter 3 --- How is our MPA doing to the dolphins? - Factors affecting the abundance and behaviours of the Indo-Pacific humpback dolphins / Chapter 3.1 --- Introduction --- p.129 / Chapter 3.2 --- Methodology --- p.132 / Chapter 3.2.1 --- Field Sampling --- p.132 / Chapter 3.2.1.1 --- Fish survey --- p.132 / Chapter 3.2.1.2 --- Traffic count --- p.133 / Chapter 3.2.2 --- Data Analysis --- p.135 / Chapter 3.2.2.1 --- Definition of parameters --- p.135 / Chapter a) --- Food species --- p.135 / Chapter b) --- Regions and study areas --- p.136 / Chapter c) --- Standardization of effort --- p.137 / Chapter 3.2.2.2 --- Statistical analysis --- p.137 / Chapter 3.3 --- Results --- p.140 / Chapter 3.3.1 --- Abundance & Biomass of Fish --- p.140 / Chapter 3.3.2 --- Diversity & Species Richness of Fish --- p.153 / Chapter 3.3.3 --- Distribution & Density of Vessel Traffic --- p.158 / Chapter 3.3.4 --- Patterns of Vessel Traffic --- p.164 / Chapter 3.3.5 --- "Relationship among Dolphin, Fish & Vessel Traffic" --- p.166 / Chapter 3.3.5.1 --- Fish & dolphin --- p.166 / Chapter 3.3.5.2 --- Traffic & dolphin --- p.167 / Chapter 3.3.5.3 --- "Fish, vessel traffic & dolphin" --- p.173 / Chapter 3.4 --- Discussion --- p.174 / Chapter 3.4.1 --- How Was the Fish Doing to the Dolphins? --- p.174 / Chapter 3.4.2 --- How Was Traffic Doing to the Dolphins? --- p.179 / Chapter 3.4.3 --- Is SLMP Effective? --- p.184 / Chapter 3.4.4 --- Limitations of This Study --- p.187 / Chapter 3.5 --- Chapter Summary --- p.189 / Chapter Chapter 4 --- An example to follow or a lesson to learn? - The effectiveness of Sha Chau & Lung Kwu Chau Marine Park in conserving the Indo-Pacific humpback dolphins / Chapter 4.1 --- Introduction --- p.275 / Chapter 4.2 --- Methodology --- p.279 / Chapter 4.2.1 --- Source of Data --- p.279 / Chapter 4.2.1.1 --- Dolphin survey --- p.279 / Chapter 4.2.1.2 --- Fish survey --- p.280 / Chapter 4.2.2 --- Data Analysis --- p.281 / Chapter 4.2.2.1 --- Definition of parameters --- p.281 / Chapter a) --- Years --- p.281 / Chapter b) --- Standardization of effort --- p.282 / Chapter 4.2.2.2 --- Statistical analysis --- p.283 / Chapter 4.3 --- Results --- p.284 / Chapter 4.3.1 --- Comparison of Dolphin Survey Results --- p.284 / Chapter 4.3.1.1 --- Abundance --- p.284 / Chapter 4.3.1.2 --- Group size --- p.286 / Chapter 4.3.1.3 --- Behaviours --- p.287 / Chapter 4.3.2 --- Comparison of Fish Survey Results --- p.289 / Chapter 4.3.2.1 --- Fish abundance & biomass --- p.289 / Chapter 4.3.2.2 --- Fish species & diversity --- p.294 / Chapter 4.3.3 --- Trends of Dolphin & Fish --- p.297 / Chapter 4.3.3.1 --- Dolphin trends --- p.297 / Chapter 4.3.3.2 --- Fish trends --- p.299 / Chapter 4.3.3.3 --- Correlations between dolphin & fish trends --- p.301 / Chapter 4.4 --- Discussion --- p.302 / Chapter 4.4.1 --- How Were the Dolphins & Fish doing Throughout These Years? --- p.302 / Chapter 4.4.2 --- Further Implications on Cetacean Conservation in Hong Kong --- p.306 / Chapter 4.4.3 --- Is SLMP Effective? --- p.309 / Chapter 4.4.4 --- Limitations of This Study --- p.315 / Chapter 4.5 --- Chapter Summary --- p.316 / Chapter Chapter 5 --- "How shall our dolphin MPA be doing? - Summary, conclusions & further recommendations" / Chapter 5.1 --- Summary & Conclusions --- p.358 / Chapter 5.2 --- Further Recommendations --- p.364 / Chapter 5.2.1 --- Larger MPA for the CWD in the Pearl River Estuary --- p.364 / Chapter 5.2.2 --- Fishing Management --- p.366 / Chapter 5.2.3 --- Traffic Management --- p.367 / Chapter 5.2.4 --- Developmental Management --- p.368 / Chapter 5.3 --- PLEASE ACT FAST!! --- p.369 / List of References --- p.373

This thesis presents investigations of diversity at three genes (class I, DQA and DQB) of the Major Histocompatibility Complex (MHC) in cetaceans. The MHC genes encode for proteins that are crucial for initiating an immune response by binding invading pathogens in vertebrates. It has been acknowledged that a high diversity at these genes results in the ability to recognise a wider range of pathogens, therefore functional diversity is important for the survival of a species. Furthermore this diversity has been created under the influence of selection, which can reveal interesting contrasts with neutral markers about the history of selection of populations and species. The diversity at two genes (DQA and DQB) in natural populations of two contrasting species of cetaceans has been investigated in more detail. The species selected included both sub-species of Hector’s dolphin, the Hector’s dolphin (Cephalorhynchus hectori hectori) and the Maui’s dolphin (Cephalorhynchus hectori maui), as well as the long-finned pilot whale (Globicephala melas). These species were chosen, because both Hector’s dolphin sub-species contrast with the pilot whale species in regards to their population size, abundance, population structure and life history. For example both sub-species of Hector’s dolphin have small population sizes and only inhabit coastal areas around New Zealand, whereas the pilot whale is an abundant, pelagic dolphin species. In Chapter 2 the expression of class II MHC genes (DQA and DQB) was demonstrated for the first time for a cetacean species, the Hector’s dolphin. Using available information from the bottlenose dolphin (Tursiops truncatus), I also designed primers to investigate class I MHC. Fragments of MHC genes were amplified from cDNA, which was derived from blood samples of two Hector’s dolphins. These dolphins were the subject of a temporary live capture, presenting a unique opportunity for blood collection. No evidence was found for duplication of both MHC class II loci, but cloning suggested a minimum of three copies of class I genes within the genomic DNA. However, the expression of all class I genes was uncertain, since only one allele could be isolated from cDNA. Functionality for all three genes (class I, DQA and DQB) was supported by the evidence for balancing selection having operated on these genes, indicated by a higher ratio of non-synonymous to synonymous substitutions. In Chapter 3, a combination of single-strand conformation polymorphism (SSCP) and direct sequencing was used to describe DQA and DQB diversity in the Hector’s and Maui’s dolphin. Genetic samples for the Hector’s dolphin were available from previously collected stranding and biopsy samples (n = 233), representing three populations from the South Coast of New Zealand and the sub-species on the West Coast of the North Island of New Zealand. For the Hector’s dolphin of the South Island, a surprisingly large number of alleles at both loci (DQA = 4, DQB = 6) were found, considering their small population size and compared to other cetacean populations with larger population sizes. The Maui’s dolphin has been classified as critically endangered with less than 100 dolphins, but showed a relatively high nucleotide diversity for DQB ( = 4.5%). This diversity was based on only three alleles that have been retained in the sub-species, representing the most divergent of all six alleles. All populations showed strong geographic differentiation at both loci (DQA: FST=0.252; DQB: FST=0.333), with the greatest differentiation between the South Island population and the North Island Maui’s dolphin. Comparison to mitochondrial and microsatellite diversity suggested influence of stochastic genetic drift, although the pressure of balancing selection acting on DQB over an evolutionary time period was also evident by a higher ratio of non-synonymous to synonymous substitutions (dN/dS=5.9) and by a pattern of trans-specific allele sharing within the family of Delphinidae. In Chapter 4 similar methods were used to describe DQA and DQB in pilot whales using genetic samples from the long-finned pilot whale that were available from five mass-strandings from around New Zealand (n = 237). A larger number of alleles than for the Hector’s dolphin were found at both loci (DQA= 8; DQB= 8), although their large population size and pelagic abundance raises the expectation of an even greater number of alleles. The overall differentiation between mass-strandings was low, but significant for both loci (DQA: FST =0.012, DQB: FST =0.014). The differentiation of all strandings was greatest for the Golden Bay mass-stranding at DQA, but deviation from Hardy-Weinberg equilibrium at DQB suggested either sub-structure within mass-strandings (Wahlund effect) or the presence of null alleles. As for the Hector’s dolphin and other mammalian species, the influence of balancing selection acting on DQB over a long evolutionary time period was evident by a higher ratio non-synonymous to synonymous substitutions (dN/dS=9.3) and by a pattern of trans-specific allele sharing within the family of Delphinidae. Overall, diversity is surprisingly similar between these two cetacean species despite different life history characteristic, but low compared to domesticated ungulate species, such as the cow. If low MHC diversity is a general feature of cetaceans, due to the marine environment as suggested previously or rather a side effect of short-term demographic forces remains speculative. A standardised nomenclature for the increasing number of MHC alleles from cetacean is proposed in this thesis to assist with future development of this research.

Populations of the humpback dolphin in Natal, South Africa, are subject to increasing pressures including capture in the shark nets and habitat degradation, and concern has been raised about the status of the population. A minimum of 95 humpback dolphins were caught in the shark nets during the period from 1980 to 1992. Capture and sighting records of the Natal Sharks Board revealed a relatively high occurrence of humpback dolphins at Richards Bay. Elsewhere, in southern Natal, the infrequent sightings and captures were attributed to a seasonal occurrence of dolphins, possibly due to temporary movements away from resident areas. Sighting rates reported by the Natal Sharks Board has decreased by 55%from 1984-86 to 1990-92 and may reflect a decrease in the population. In a photo-identification study, searches took place in ten search areas in Natal. The sighting rates in the different areas revealed a relatively high density of humpback dolphins occurring in north central Natal, from the Tugela River to the St. Lucia estuary (including Richards Bay). This distribution correlated significantly with the turbidity of the water and the width of the inshore continental shelf, and was inversely related to the density of bottlenose dolphins. Within the northern Tugela Bank region, higher densities of dolphins were found surrounding the five river mouths and estuaries. The Natal population was estimated to be between 161 to 166 animals (95% confidence limits 134 to 229). The annual mortality due to shark net captures approximates 4,5%of the population. Various evidence, including a high mortality rate and a decrease in the annual sighting per unit effort reported by the Natal Sharks Board suggest that the humpback dolphin population in Natal is vulnerable and may be decreasing in size. A proposal is made to reduce the capture rate by relocating shark nets away from the Richards Bay harbour. / Thesis (M.Sc.)-University of Natal, 1994.

This thesis presents investigations of diversity at three genes (class I, DQA and DQB) of the Major Histocompatibility Complex (MHC) in cetaceans. The MHC genes encode for proteins that are crucial for initiating an immune response by binding invading pathogens in vertebrates. It has been acknowledged that a high diversity at these genes results in the ability to recognise a wider range of pathogens, therefore functional diversity is important for the survival of a species. Furthermore this diversity has been created under the influence of selection, which can reveal interesting contrasts with neutral markers about the history of selection of populations and species. The diversity at two genes (DQA and DQB) in natural populations of two contrasting species of cetaceans has been investigated in more detail. The species selected included both sub-species of Hector’s dolphin, the Hector’s dolphin (Cephalorhynchus hectori hectori) and the Maui’s dolphin (Cephalorhynchus hectori maui), as well as the long-finned pilot whale (Globicephala melas). These species were chosen, because both Hector’s dolphin sub-species contrast with the pilot whale species in regards to their population size, abundance, population structure and life history. For example both sub-species of Hector’s dolphin have small population sizes and only inhabit coastal areas around New Zealand, whereas the pilot whale is an abundant, pelagic dolphin species. In Chapter 2 the expression of class II MHC genes (DQA and DQB) was demonstrated for the first time for a cetacean species, the Hector’s dolphin. Using available information from the bottlenose dolphin (Tursiops truncatus), I also designed primers to investigate class I MHC. Fragments of MHC genes were amplified from cDNA, which was derived from blood samples of two Hector’s dolphins. These dolphins were the subject of a temporary live capture, presenting a unique opportunity for blood collection. No evidence was found for duplication of both MHC class II loci, but cloning suggested a minimum of three copies of class I genes within the genomic DNA. However, the expression of all class I genes was uncertain, since only one allele could be isolated from cDNA. Functionality for all three genes (class I, DQA and DQB) was supported by the evidence for balancing selection having operated on these genes, indicated by a higher ratio of non-synonymous to synonymous substitutions. In Chapter 3, a combination of single-strand conformation polymorphism (SSCP) and direct sequencing was used to describe DQA and DQB diversity in the Hector’s and Maui’s dolphin. Genetic samples for the Hector’s dolphin were available from previously collected stranding and biopsy samples (n = 233), representing three populations from the South Coast of New Zealand and the sub-species on the West Coast of the North Island of New Zealand. For the Hector’s dolphin of the South Island, a surprisingly large number of alleles at both loci (DQA = 4, DQB = 6) were found, considering their small population size and compared to other cetacean populations with larger population sizes. The Maui’s dolphin has been classified as critically endangered with less than 100 dolphins, but showed a relatively high nucleotide diversity for DQB ( = 4.5%). This diversity was based on only three alleles that have been retained in the sub-species, representing the most divergent of all six alleles. All populations showed strong geographic differentiation at both loci (DQA: FST=0.252; DQB: FST=0.333), with the greatest differentiation between the South Island population and the North Island Maui’s dolphin. Comparison to mitochondrial and microsatellite diversity suggested influence of stochastic genetic drift, although the pressure of balancing selection acting on DQB over an evolutionary time period was also evident by a higher ratio of non-synonymous to synonymous substitutions (dN/dS=5.9) and by a pattern of trans-specific allele sharing within the family of Delphinidae. In Chapter 4 similar methods were used to describe DQA and DQB in pilot whales using genetic samples from the long-finned pilot whale that were available from five mass-strandings from around New Zealand (n = 237). A larger number of alleles than for the Hector’s dolphin were found at both loci (DQA= 8; DQB= 8), although their large population size and pelagic abundance raises the expectation of an even greater number of alleles. The overall differentiation between mass-strandings was low, but significant for both loci (DQA: FST =0.012, DQB: FST =0.014). The differentiation of all strandings was greatest for the Golden Bay mass-stranding at DQA, but deviation from Hardy-Weinberg equilibrium at DQB suggested either sub-structure within mass-strandings (Wahlund effect) or the presence of null alleles. As for the Hector’s dolphin and other mammalian species, the influence of balancing selection acting on DQB over a long evolutionary time period was evident by a higher ratio non-synonymous to synonymous substitutions (dN/dS=9.3) and by a pattern of trans-specific allele sharing within the family of Delphinidae. Overall, diversity is surprisingly similar between these two cetacean species despite different life history characteristic, but low compared to domesticated ungulate species, such as the cow. If low MHC diversity is a general feature of cetaceans, due to the marine environment as suggested previously or rather a side effect of short-term demographic forces remains speculative. A standardised nomenclature for the increasing number of MHC alleles from cetacean is proposed in this thesis to assist with future development of this research.

This thesis presents investigations of diversity at three genes (class I, DQA and DQB) of the Major Histocompatibility Complex (MHC) in cetaceans. The MHC genes encode for proteins that are crucial for initiating an immune response by binding invading pathogens in vertebrates. It has been acknowledged that a high diversity at these genes results in the ability to recognise a wider range of pathogens, therefore functional diversity is important for the survival of a species. Furthermore this diversity has been created under the influence of selection, which can reveal interesting contrasts with neutral markers about the history of selection of populations and species. The diversity at two genes (DQA and DQB) in natural populations of two contrasting species of cetaceans has been investigated in more detail. The species selected included both sub-species of Hector’s dolphin, the Hector’s dolphin (Cephalorhynchus hectori hectori) and the Maui’s dolphin (Cephalorhynchus hectori maui), as well as the long-finned pilot whale (Globicephala melas). These species were chosen, because both Hector’s dolphin sub-species contrast with the pilot whale species in regards to their population size, abundance, population structure and life history. For example both sub-species of Hector’s dolphin have small population sizes and only inhabit coastal areas around New Zealand, whereas the pilot whale is an abundant, pelagic dolphin species. In Chapter 2 the expression of class II MHC genes (DQA and DQB) was demonstrated for the first time for a cetacean species, the Hector’s dolphin. Using available information from the bottlenose dolphin (Tursiops truncatus), I also designed primers to investigate class I MHC. Fragments of MHC genes were amplified from cDNA, which was derived from blood samples of two Hector’s dolphins. These dolphins were the subject of a temporary live capture, presenting a unique opportunity for blood collection. No evidence was found for duplication of both MHC class II loci, but cloning suggested a minimum of three copies of class I genes within the genomic DNA. However, the expression of all class I genes was uncertain, since only one allele could be isolated from cDNA. Functionality for all three genes (class I, DQA and DQB) was supported by the evidence for balancing selection having operated on these genes, indicated by a higher ratio of non-synonymous to synonymous substitutions. In Chapter 3, a combination of single-strand conformation polymorphism (SSCP) and direct sequencing was used to describe DQA and DQB diversity in the Hector’s and Maui’s dolphin. Genetic samples for the Hector’s dolphin were available from previously collected stranding and biopsy samples (n = 233), representing three populations from the South Coast of New Zealand and the sub-species on the West Coast of the North Island of New Zealand. For the Hector’s dolphin of the South Island, a surprisingly large number of alleles at both loci (DQA = 4, DQB = 6) were found, considering their small population size and compared to other cetacean populations with larger population sizes. The Maui’s dolphin has been classified as critically endangered with less than 100 dolphins, but showed a relatively high nucleotide diversity for DQB ( = 4.5%). This diversity was based on only three alleles that have been retained in the sub-species, representing the most divergent of all six alleles. All populations showed strong geographic differentiation at both loci (DQA: FST=0.252; DQB: FST=0.333), with the greatest differentiation between the South Island population and the North Island Maui’s dolphin. Comparison to mitochondrial and microsatellite diversity suggested influence of stochastic genetic drift, although the pressure of balancing selection acting on DQB over an evolutionary time period was also evident by a higher ratio of non-synonymous to synonymous substitutions (dN/dS=5.9) and by a pattern of trans-specific allele sharing within the family of Delphinidae. In Chapter 4 similar methods were used to describe DQA and DQB in pilot whales using genetic samples from the long-finned pilot whale that were available from five mass-strandings from around New Zealand (n = 237). A larger number of alleles than for the Hector’s dolphin were found at both loci (DQA= 8; DQB= 8), although their large population size and pelagic abundance raises the expectation of an even greater number of alleles. The overall differentiation between mass-strandings was low, but significant for both loci (DQA: FST =0.012, DQB: FST =0.014). The differentiation of all strandings was greatest for the Golden Bay mass-stranding at DQA, but deviation from Hardy-Weinberg equilibrium at DQB suggested either sub-structure within mass-strandings (Wahlund effect) or the presence of null alleles. As for the Hector’s dolphin and other mammalian species, the influence of balancing selection acting on DQB over a long evolutionary time period was evident by a higher ratio non-synonymous to synonymous substitutions (dN/dS=9.3) and by a pattern of trans-specific allele sharing within the family of Delphinidae. Overall, diversity is surprisingly similar between these two cetacean species despite different life history characteristic, but low compared to domesticated ungulate species, such as the cow. If low MHC diversity is a general feature of cetaceans, due to the marine environment as suggested previously or rather a side effect of short-term demographic forces remains speculative. A standardised nomenclature for the increasing number of MHC alleles from cetacean is proposed in this thesis to assist with future development of this research.

This thesis presents investigations of diversity at three genes (class I, DQA and DQB) of the Major Histocompatibility Complex (MHC) in cetaceans. The MHC genes encode for proteins that are crucial for initiating an immune response by binding invading pathogens in vertebrates. It has been acknowledged that a high diversity at these genes results in the ability to recognise a wider range of pathogens, therefore functional diversity is important for the survival of a species. Furthermore this diversity has been created under the influence of selection, which can reveal interesting contrasts with neutral markers about the history of selection of populations and species. The diversity at two genes (DQA and DQB) in natural populations of two contrasting species of cetaceans has been investigated in more detail. The species selected included both sub-species of Hector’s dolphin, the Hector’s dolphin (Cephalorhynchus hectori hectori) and the Maui’s dolphin (Cephalorhynchus hectori maui), as well as the long-finned pilot whale (Globicephala melas). These species were chosen, because both Hector’s dolphin sub-species contrast with the pilot whale species in regards to their population size, abundance, population structure and life history. For example both sub-species of Hector’s dolphin have small population sizes and only inhabit coastal areas around New Zealand, whereas the pilot whale is an abundant, pelagic dolphin species. In Chapter 2 the expression of class II MHC genes (DQA and DQB) was demonstrated for the first time for a cetacean species, the Hector’s dolphin. Using available information from the bottlenose dolphin (Tursiops truncatus), I also designed primers to investigate class I MHC. Fragments of MHC genes were amplified from cDNA, which was derived from blood samples of two Hector’s dolphins. These dolphins were the subject of a temporary live capture, presenting a unique opportunity for blood collection. No evidence was found for duplication of both MHC class II loci, but cloning suggested a minimum of three copies of class I genes within the genomic DNA. However, the expression of all class I genes was uncertain, since only one allele could be isolated from cDNA. Functionality for all three genes (class I, DQA and DQB) was supported by the evidence for balancing selection having operated on these genes, indicated by a higher ratio of non-synonymous to synonymous substitutions. In Chapter 3, a combination of single-strand conformation polymorphism (SSCP) and direct sequencing was used to describe DQA and DQB diversity in the Hector’s and Maui’s dolphin. Genetic samples for the Hector’s dolphin were available from previously collected stranding and biopsy samples (n = 233), representing three populations from the South Coast of New Zealand and the sub-species on the West Coast of the North Island of New Zealand. For the Hector’s dolphin of the South Island, a surprisingly large number of alleles at both loci (DQA = 4, DQB = 6) were found, considering their small population size and compared to other cetacean populations with larger population sizes. The Maui’s dolphin has been classified as critically endangered with less than 100 dolphins, but showed a relatively high nucleotide diversity for DQB ( = 4.5%). This diversity was based on only three alleles that have been retained in the sub-species, representing the most divergent of all six alleles. All populations showed strong geographic differentiation at both loci (DQA: FST=0.252; DQB: FST=0.333), with the greatest differentiation between the South Island population and the North Island Maui’s dolphin. Comparison to mitochondrial and microsatellite diversity suggested influence of stochastic genetic drift, although the pressure of balancing selection acting on DQB over an evolutionary time period was also evident by a higher ratio of non-synonymous to synonymous substitutions (dN/dS=5.9) and by a pattern of trans-specific allele sharing within the family of Delphinidae. In Chapter 4 similar methods were used to describe DQA and DQB in pilot whales using genetic samples from the long-finned pilot whale that were available from five mass-strandings from around New Zealand (n = 237). A larger number of alleles than for the Hector’s dolphin were found at both loci (DQA= 8; DQB= 8), although their large population size and pelagic abundance raises the expectation of an even greater number of alleles. The overall differentiation between mass-strandings was low, but significant for both loci (DQA: FST =0.012, DQB: FST =0.014). The differentiation of all strandings was greatest for the Golden Bay mass-stranding at DQA, but deviation from Hardy-Weinberg equilibrium at DQB suggested either sub-structure within mass-strandings (Wahlund effect) or the presence of null alleles. As for the Hector’s dolphin and other mammalian species, the influence of balancing selection acting on DQB over a long evolutionary time period was evident by a higher ratio non-synonymous to synonymous substitutions (dN/dS=9.3) and by a pattern of trans-specific allele sharing within the family of Delphinidae. Overall, diversity is surprisingly similar between these two cetacean species despite different life history characteristic, but low compared to domesticated ungulate species, such as the cow. If low MHC diversity is a general feature of cetaceans, due to the marine environment as suggested previously or rather a side effect of short-term demographic forces remains speculative. A standardised nomenclature for the increasing number of MHC alleles from cetacean is proposed in this thesis to assist with future development of this research.

Whale-watching provides economic opportunities worldwide and particularly proliferates in developing countries, such as the Philippines. The sustainability of whale-watching is increasingly debated as these activities also negatively impact cetaceans through changes in behavior, communication, habitat use, morbidity, mortality, and life-history parameters. This study evaluated the total annual cost, revenue, and profit of whale-watching operators in Bais, Philippines, and predicted the changes in the population for spinner dolphin Stenella longirostris with varying levels of whale-watching effort. Total revenue was 3,805,077 PHP ($92,478 USD) while total cost was 5,649,094 PHP ($137,294 USD) with a discount rate of ten percent. The total annual profit of whale-watching in Bais was – 1,844,017 PHP (– $44,817 USD). On average, each operator in Bais lost 160,350 PHP ($3,897 USD) per year from whale-watching. Through time, the spinner dolphin population decreased as it was exposed to more vessels, causing effort to increase, and thus decreased profit for operators. Under current whale-watching effort, the spinner dolphin population was predicted to decrease by 94 percent in 25 years. If Bais reduced effort in their operations to only three vessels whale-watching per day, the spinner dolphin population increased to 80 percent of its initial population size. This was the first study to predict the spinner dolphin population and estimate the total annual profit from whale-watching in Bais, Philippines. It provided data to locals for efficient, profitable, and sustainable decisions in whale-watching operations.

The ecology and population biology of bottlenose and humpback dolphins inhabiting the Maputo Bay, Southern Mozambique were studied through boat based photoidentification surveys and behavioural methods between December 1995 and December 1997. Data from preliminary surveys carried out in 1992 are also included. Bottlenose dolphins occurred throughout the year in Maputo Bay, but were sighted infrequently (36% of surveys). Their occurrence and group size were significantly larger during winter. Group size of bottlenose dolphins not differ significantly between months, daylight hours, semi-lunar tidal cycles and depth. Most identifiable bottlenose dolphin individuals had low site fidelity, but nursing females had relatively high site fidelity, implying that Maputo Bay is a nursing area. The group dynamics of bottlenose dolphins suggests a fluid (fission-fusion) social organisation. Age and sex appears to influence the degree of association between individuals. An influx of bottlenose dolphins occurred during winter and influenced group size and occurrence. Bottlenose dolphins occurred in restricted areas of the Bay, preferring the north eastern area (the pass between the Bay and the Ocean), and along the 3 km strip from the east coast of Inhaca Island. Their distribution here did not vary with depth, although they did not occur in intertidal areas. Feeding dominated both frequency and proportion of time of bottlenose dolphin behaviour. Social behaviour accounted for a small proportion of time (10%) and was greater in open unsheltered areas. Neither season, nor depth, nor daylight, nor tides influenced the proportion of time allocated to the types of behaviours. Non directional movement occurred on most of the sightings of bottlenose dolphins, but smaller groups of dolphins moved inshore at high tide late in the afternoon. Few bottlenose dolphin births were observed and the numbers of animals born varied between years. Recruitment rates at six months and one year were low and mortality rates of calves appeared high, but were probably inaccurate because the fate of mother-calf pairs that left the area could not be established. Population estimates of the bottlenose dolphins varied between 170 and 526 individuals. The precision of these estimates was poor, because of high proportion of transient individuals which almost certainly violated some model assumptions. Humpback dolphins occurred throughout the year in Maputo Bay, but were sighted infrequently (21% of surveys). The occurrence and group size of humpback dolphins were not influenced by season, months, daylight, semi-lunar tidal cycles and depth. Groups of humpback dolphins in Maputo Bay were the largest observed along the east coast of Southern Africa. Most identified humpback dolphin individuals showed low site fidelity, but a relatively high proportion of individuals (including nursing females) had high site fidelity. Humpback dolphin groups had a fluid (fission- fusion) social organisation, but there was a large proportion of stable associations between resident individuals. Age and sex appears to influence the degree of association between individuals. An influx of humpback dolphin individuals occurred during summer but did not change group size or occurrence, suggesting the occurrence of an outflux of other individuals. Humpback dolphins in the Bay ranged between the deep north eastern Maputo Bay to the southern intertidal areas. Most sightings occurred within 1 km from shore along the eastern coast of Inhaca Island, at variable depth. Humpback dolphins spent more time feeding (57%) and travelling (30%) than socializing and resting, because of their movements between extensive intertidal areas and deep channels. Social behaviour contributed a small proportion of time (10%), but increased when humpback dolphins moved towards and within shallow sheltered areas. Neither season, nor depth, nor daylight, nor tides influenced the proportion of time allocated to the types of behaviours of this species. Non directional movement occurred on most of the sightings of humpback dolphins, thought this was significantly influenced by diurnal tides. Few humpback dolphin births were observed and their numbers varied between years. Recruitment rates at six months and one year were low and mortality rates appeared high, but were probably inaccurate because the fate of mother-calf pairs that left the area could not be established. Population estimates of humpback dolphins varied between 105 and 308 individuals, but their precision was poor, because of a high proportion of transient individuals which almost certainly violated some model assumptions. Maputo Bay is a feeding, breeding and nursing area for bottlenose and humpback dolphins. These species are threatened by intense fishing activity, habitat degradation, coastal development and disturbance by powerboats and other activities (tourism, port) carried out in and around Maputo Bay. Their low estimated growth rates imply the implementation of precautionary conservation measures. The actual distribution of these species may reflect the deterioration of the habitats in the western part of the Bay. A coastal zone management plan to address environmental problems affecting the dolphin species need to be formulated and implemented. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.

The ranging behaviour, habitat preferences, genetic structure, and demographic parameters of bottlenose dolphins living in the Azores were studied using data collected from 1999 to 2004. Only 44 dolphins out of 966 identified were frequently sighted within and between years and showed strong site fidelity. The remaining individuals were either temporary migrants from within or outside the archipelago, or transients. Estimates of home range size were three times larger than previously reported for this species, possibly as a result of the lower availability of food resources. Mitochondrial DNA sequences showed very high gene and nucleotide diversity. There was no evidence of population structuring within the Azores. The Azorean population was not differentiated from the pelagic population of the Northwest Atlantic, suggesting the "unproductive" waters of the Atlantic do not constitute a barrier to dispersal. Population size, survival and temporary emigration rates were estimated using open-population models and Pollock's robust design. A few hundreds of dolphins occur in the area on a given year, though the majority should use it temporarily, as suggested by the high emigration rates. Bottlenose dolphins preferentially used shallow areas with high bottom relief. Temporal and spatial persistence of dolphin-habitat associations documented in this study further supports the idea of a close relationship between certain bathymetric features and important hydrographic processes and suggests the occurrence of prey aggregations over these areas may be, to some extent, predictable. Several results of this study suggest there are no reasons for concern about the status of this population. Yet, the resident group may be negatively affected by increasing pressure from the whale watching activity. Although the proposed Marine Park constitutes important habitat for resident dolphins, at present, the area is clearly insufficient to satisfy their spatial requirements and its conservation value may be limited.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references. / Odontocetes are assumed to use echolocation for navigation and foraging, but neither of these uses of biosonar has been conclusively demonstrated in free-ranging animals. Many bats are known to use echolocation throughout foraging sequences, changing the structure and timing of clicks as they progress towards prey capture. For odontocetes, however, we do not know enough about their foraging behavior to describe such sequences. To conduct detailed behavioral observations of any subject animal, the observer must be able to maintain continuous visual contact with the subject for a period commensurate with the duration of the behavior(s) of interest. Behavioral studies of cetaceans, which spend approximately 95% of their time below the water's surface, have been limited to sampling surface behavior except in special circumstances, e.g. clear-water environments, or with the use of technological tools. I addressed this limitation through development of an observation platform consisting of a remote controlled video camera suspended from a tethered airship with boat-based monitoring, adjustment, and recording of video. The system was used successfully to conduct continuous behavioral observations of bottlenose dolphins in the Sarasota Bay, FL area. This system allowed me to describe previously unreported foraging behaviors and elucidate functions for behaviors already defined but poorly understood. Dolphin foraging was modeled as a stage-structured sequence of behaviors, with the goal-directed feeding event occurring at the end of a series of search, encounter, and pursuit behaviors. The behaviors preceding a feeding event do not occur in a deterministic sequence, but are adaptive and plastic. A single-step transition analysis beginning with prey capture and receding in time has identified significant links between observed behaviors and demonstrated the stage-structured nature of dolphin foraging. Factors affecting the occurrence of specific behaviors and behavioral transitions include mesoscale habitat variation and individual preferences. The role of sound in foraging, especially echolocation, is less well understood than the behavioral component. Recent studies have explored the use of echolocation in captive odontocete foraging and presumed feeding in wild animals, but simultaneous, detailed behavioral and acoustic observations have eluded researchers. The current study used two methods to obtain acoustic data. The overhead video system includes two towed hydrophones used to record 'ambient' sounds of dolphin foraging. The recordings are of the 'ambient' sounds because the source of the sounds, i.e. animal, could not be localized. Many focal follows, however, were conducted with single animals, and from these records the timing of echolocation and other sounds relative to the foraging sequence could be examined. The 'ambient' recordings revealed that single animals are much more vocal than animals in groups, both overall and during foraging. When not foraging, single animals vocalized at a rate similar to the per animal rate in groups of>=2 animals. For single foraging animals, the use of different sound types varies significantly by the habitat in which the animal is foraging. These patterns of use coupled with the characteristics of the different sound types suggest specific functions for each. The presence of multiple animals in a foraging group apparently reduces the need to vocalize, and potential reasons for this pattern are discussed. In addition, the increased vocal activity of single foraging animals lends support to specific hypotheses of sound use in bottlenose dolphins and odontocetes in general. The second acoustic data collection method records sounds known to be from a specific animal. An acoustic recording tag was developed that records all sounds produced by an animal including every echolocation click. The tag also includes an acoustic sampling interval controller and a sensor suite that measures pitch, roll, heading, and surfacing events. While no foraging events occurred while an animal was wearing an acoustic data logger, the rates of echolocation and whistling during different activities, e.g. traveling, were measured. / by Douglas Paul Nowacek. / Ph.D.