Thesis (Ph. D.) -- Lincoln University, 2008. / Also available via the World Wide Web.

Incidental mortality in fisheries, especially gillnets, is one of the most important causes of decline of many species of cetaceans around the globe. Local populations of franciscana, Pontoporia blainvillei, and Hector�s dolphins, Cephalorhynchus hectori, have been subject to high levels of mortality in gillnets for several decades. This is due to a combination of extensive overlap in distribution of these coastal dolphins and large numbers of fishing nets. Stage-specific population dynamic models (without environmental stochasticity) suggest that both species have a low potential for population growth of approximately 0.2% (95% CI: -3.7% to 4.2%) to 3.4% (95% CI: 1.6% to 6.4%) for franciscana and 0.85% (95% CI: -1.0% to 2.6%) for Hector�s dolphins. Although the two species have similar population growth rates, they result from different life history strategies. Franciscana has a relatively low adult survival rate (0.86; SD = 0.016) which is compensated by a relatively high reproductive potential. The latter is a combination of early reproduction and high fecundity. Hector�s dolphin has a low reproductive potential, which is a combination of late reproduction and low fecundity, which is probably compensated by a relatively high adult survival rate (0.92; SD = 0.02) Apparent differences in growth rate among franciscana populations are possibly due to a combination of varying population-specific reproductive potential and, in some populations, inaccuracy in parameter estimates. Inaccuracy in estimating natural survival rates is also a cause for the low growth rate of Hector�s dolphins. The estimated low population growth rates of these species are insufficient to compensate for current levels of fishing-related mortality in some local populations, especially when environmental and/or demographic stochasticity is considered. Under these circumstances Banks Peninsula population would have a negative mean population growth rate of 0.54% (95% CI: -2.2% to 0.9%) and would decrease below its initial size in approximately 74% of the simulations. Stochasticity alone would decrease considerably the probability of the Banks Peninsula population to grow and recover from past and current high bycatch levels. Effects of stochasticity were also high for one of the franciscana stocks (i.e. stock from Franciscana Management Area II). In other areas (e.g. West Coast of the South Island; franciscana stock from FMA I) fishing effort and bycatch mortality rate seem not to be impeding population growth. Even in a stochastic environment and under current levels of fishing effort, the West Coast population and the franciscana stock from FMA I would grow at a positive rate of 0.32% (95% CI: -1.2% to 1.8%) and 3.1% (95% CI: 2.2 to 7.2%), respectively. Parameter uncertainty does not change the conclusion that immediate and extreme limitations on fishing practice and effort are necessary to increase the chances of recovery for some local populations/stocks. Fishing effort in New Zealand is regulated by a quota system. The quota system, the low number of fishing boats and the relatively low overlap between fishing nets and dolphins are probably the reasons for the positive population growth of Hector�s dolphins from the West Coast of the South Island. On the other hand, not even the Marine Mammal Sanctuary is sufficient to avoid negative mean population growth rate of Hector�s dolphins under current levels of fishing effort off Banks Peninsula. In Brazil, Uruguay and Argentina, where franciscana occurs, gillnet fisheries are not regulated. In some areas, faced with a declining fish stocks, fishermen have increased fishing effort to compensate for reduced catches, and the bycatch of franciscana has increased as a consequence. Strategies aiming at the conservation of these two species are likely to benefit other components of the ecosystem. Especially in the case of franciscana, reducing fishing effort is likely to promote the recovery of depleted fish stocks.

Incidental mortality in fisheries, especially gillnets, is one of the most important causes of decline of many species of cetaceans around the globe. Local populations of franciscana, Pontoporia blainvillei, and Hector�s dolphins, Cephalorhynchus hectori, have been subject to high levels of mortality in gillnets for several decades. This is due to a combination of extensive overlap in distribution of these coastal dolphins and large numbers of fishing nets. Stage-specific population dynamic models (without environmental stochasticity) suggest that both species have a low potential for population growth of approximately 0.2% (95% CI: -3.7% to 4.2%) to 3.4% (95% CI: 1.6% to 6.4%) for franciscana and 0.85% (95% CI: -1.0% to 2.6%) for Hector�s dolphins. Although the two species have similar population growth rates, they result from different life history strategies. Franciscana has a relatively low adult survival rate (0.86; SD = 0.016) which is compensated by a relatively high reproductive potential. The latter is a combination of early reproduction and high fecundity. Hector�s dolphin has a low reproductive potential, which is a combination of late reproduction and low fecundity, which is probably compensated by a relatively high adult survival rate (0.92; SD = 0.02) Apparent differences in growth rate among franciscana populations are possibly due to a combination of varying population-specific reproductive potential and, in some populations, inaccuracy in parameter estimates. Inaccuracy in estimating natural survival rates is also a cause for the low growth rate of Hector�s dolphins. The estimated low population growth rates of these species are insufficient to compensate for current levels of fishing-related mortality in some local populations, especially when environmental and/or demographic stochasticity is considered. Under these circumstances Banks Peninsula population would have a negative mean population growth rate of 0.54% (95% CI: -2.2% to 0.9%) and would decrease below its initial size in approximately 74% of the simulations. Stochasticity alone would decrease considerably the probability of the Banks Peninsula population to grow and recover from past and current high bycatch levels. Effects of stochasticity were also high for one of the franciscana stocks (i.e. stock from Franciscana Management Area II). In other areas (e.g. West Coast of the South Island; franciscana stock from FMA I) fishing effort and bycatch mortality rate seem not to be impeding population growth. Even in a stochastic environment and under current levels of fishing effort, the West Coast population and the franciscana stock from FMA I would grow at a positive rate of 0.32% (95% CI: -1.2% to 1.8%) and 3.1% (95% CI: 2.2 to 7.2%), respectively. Parameter uncertainty does not change the conclusion that immediate and extreme limitations on fishing practice and effort are necessary to increase the chances of recovery for some local populations/stocks. Fishing effort in New Zealand is regulated by a quota system. The quota system, the low number of fishing boats and the relatively low overlap between fishing nets and dolphins are probably the reasons for the positive population growth of Hector�s dolphins from the West Coast of the South Island. On the other hand, not even the Marine Mammal Sanctuary is sufficient to avoid negative mean population growth rate of Hector�s dolphins under current levels of fishing effort off Banks Peninsula. In Brazil, Uruguay and Argentina, where franciscana occurs, gillnet fisheries are not regulated. In some areas, faced with a declining fish stocks, fishermen have increased fishing effort to compensate for reduced catches, and the bycatch of franciscana has increased as a consequence. Strategies aiming at the conservation of these two species are likely to benefit other components of the ecosystem. Especially in the case of franciscana, reducing fishing effort is likely to promote the recovery of depleted fish stocks.

Hector�s dolphin (Cephalorhynchus hectori) is an endangered coastal species endemic to New Zealand. Their distribution, like other marine organisms, is intertwined with the dynamics of their local habitats, and at a larger scale, the coastal waters around New Zealand. The main purpose of this thesis was to identify specific habitat requirements of this rare dolphin. Hector�s dolphin distribution around the South Island was quantified along several temporal and spatial scales. Large-scale density analyses of abundance surveys found over half of the South Island�s current population occurred within only three main regions. Two of these strongholds are along the west coast and the third is located around Banks Peninsula on the east coast. Smaller-scale analyses at Banks Peninsula found the majority of the dolphin community was preferentially using core regions within the marine mammal sanctuary. Monthly surveys showed that in summer and autumn statistically more dolphins occurred within inshore regions ([less than or equal to]one kilometre), spread throughout the surveyed coastline. From May through winter, dolphin densities rapidly declined. Remaining dolphins were significantly clumped in more offshore waters of eastern regions. The lowest encounter rates occurred between August and September. Certain 'hotspots' consistently had higher dolphin densities throughout the study period while others were preferred seasonally. To address habitat preferences, surveys simultaneously collected oceanographic samples using a CTD profiler. In general, physical variables of the Peninsula�s eastern and southeastern waters varied less, despite being regularly exposed to upwellings and the varied presence of sub-tropical waters. Semi-sheltered bays and shallow inshore waters were highly variable and more susceptible to spatially discrete influences, such as localised river outflows and exchange events. Several hydrographic features were seasonally predictable due to their dependence on climate. The stratification and location of the two dominant water masses (neritic and sub-tropical) accounted for over half of the temporal and spatial variability observed in oceanographic data. Possible relationships between oceanographic features and aggregations of dolphins within Banks Peninsula were examined using global regression and a spatial technique known as geographical weighted regression (GWR). GWR models out-performed corresponding global models, despite differences in degrees of freedom and increased model complexity. GWR results found relationships varied over localised scales that were concealed by global methods. Monthly GWR models suggested the seasonal presence and strength of local oceanographic fronts influenced dolphin distribution. Dolphin aggregations coincided with the steepest gradients between water masses along eastern regions of the Peninsula, and strong exchange events along the edges of the study area. The continued survival of this endangered species is contingent on its protection. Long-term monitoring programmes are needed for the three main strongholds identified in this study. The occurrence of Hector�s dolphin 'hotspots' along frontal zones within Banks Peninsula also suggests alternative and increased protection strategies are needed for this sanctuary to be effective. In light of this thesis� findings and based on marine protection research, future sanctuaries need to consider why Hector�s dolphins are preferentially using particular regions and how their association with certain oceanographic features can help make informed decisions on more appropriate protected areas.

Hector�s dolphin (Cephalorhynchus hectori) is an endangered coastal species endemic to New Zealand. Their distribution, like other marine organisms, is intertwined with the dynamics of their local habitats, and at a larger scale, the coastal waters around New Zealand. The main purpose of this thesis was to identify specific habitat requirements of this rare dolphin. Hector�s dolphin distribution around the South Island was quantified along several temporal and spatial scales. Large-scale density analyses of abundance surveys found over half of the South Island�s current population occurred within only three main regions. Two of these strongholds are along the west coast and the third is located around Banks Peninsula on the east coast. Smaller-scale analyses at Banks Peninsula found the majority of the dolphin community was preferentially using core regions within the marine mammal sanctuary. Monthly surveys showed that in summer and autumn statistically more dolphins occurred within inshore regions ([less than or equal to]one kilometre), spread throughout the surveyed coastline. From May through winter, dolphin densities rapidly declined. Remaining dolphins were significantly clumped in more offshore waters of eastern regions. The lowest encounter rates occurred between August and September. Certain 'hotspots' consistently had higher dolphin densities throughout the study period while others were preferred seasonally. To address habitat preferences, surveys simultaneously collected oceanographic samples using a CTD profiler. In general, physical variables of the Peninsula�s eastern and southeastern waters varied less, despite being regularly exposed to upwellings and the varied presence of sub-tropical waters. Semi-sheltered bays and shallow inshore waters were highly variable and more susceptible to spatially discrete influences, such as localised river outflows and exchange events. Several hydrographic features were seasonally predictable due to their dependence on climate. The stratification and location of the two dominant water masses (neritic and sub-tropical) accounted for over half of the temporal and spatial variability observed in oceanographic data. Possible relationships between oceanographic features and aggregations of dolphins within Banks Peninsula were examined using global regression and a spatial technique known as geographical weighted regression (GWR). GWR models out-performed corresponding global models, despite differences in degrees of freedom and increased model complexity. GWR results found relationships varied over localised scales that were concealed by global methods. Monthly GWR models suggested the seasonal presence and strength of local oceanographic fronts influenced dolphin distribution. Dolphin aggregations coincided with the steepest gradients between water masses along eastern regions of the Peninsula, and strong exchange events along the edges of the study area. The continued survival of this endangered species is contingent on its protection. Long-term monitoring programmes are needed for the three main strongholds identified in this study. The occurrence of Hector�s dolphin 'hotspots' along frontal zones within Banks Peninsula also suggests alternative and increased protection strategies are needed for this sanctuary to be effective. In light of this thesis� findings and based on marine protection research, future sanctuaries need to consider why Hector�s dolphins are preferentially using particular regions and how their association with certain oceanographic features can help make informed decisions on more appropriate protected areas.

The efficacy of a Marine Protected Area (MPA) is contingent on it having a design appropriate for the species it is intended to protect. Hector�s dolphin (Cephalorhynchus hectori), a coastal delphinid endemic to New Zealand, is endangered due to bycatch in gillnets. Analyses of survival rate and population viability suggest that the Banks Peninsula population is most likely still declining despite the presence of the Banks Peninsula Marine Mammal Sanctuary (BPMMS), where gillnetting is regulated. More data on distribution and movements of dolphins are therefore required to improve the design of the BPMMS. On aerial surveys of Hector�s dolphin distribution at Banks Peninsula over three years, sightings were made up to 19 n.mi. offshore. On average, 19% of dolphins were sighted outside the BPMMS�s 4 n.mi. offshore boundary in summer, compared to 56% in winter. On similar surveys of the South Island�s west coast, all dolphins were sighted within 6 n.mi. of the coast and there was no seasonal change in distribution. At each location, Mantel tests indicated that distance offshore had the strongest and most consistent effect on distribution. However, a logistic regression model using the combined datasets suggested that distribution was most strongly defined by water depth, with all sightings made inside the 90 m isobath. Boat surveys were carried out at Banks Peninsula (2002 to 2006) to continue the long-term photo-ID project. Using the 22 year dataset, alongshore home-range of the 20 most frequently sighted dolphins was estimated by univariate kernel methods. Mean alongshore range was 49.69 km (SE = 5.29), 60% larger than the previous estimate. Fifteen percent of these individuals had ranges extending beyond the northern boundary of the BPMMS. An acoustic data logger, the T-POD, was trialled for passive acoustic monitoring of Hector�s dolphins. Simultaneous T-POD/theodolite surveys revealed that T-PODs reliably detected dolphins within 200m. No detections were made beyond 500m. To monitor inshore habitat use, T-PODs were deployed in three locations at Banks Peninsula (n = 431 days). A GLM analysis of Detection Positive Minutes (DPM) per day indicated that season had the largest effect on detection rate, with over twice as many DPMs per day in summer (x̄ = 99.8) as winter (x̄ = 47.6). The new findings on Hector�s dolphin distribution and ranging can be used to improve the design of the BPMMS. It is recommended that the offshore boundary of the BPMMS is extended to 20 n.mi. (37 km), the northern boundary is moved 12 km north and recreational gillnetting is prohibited year round. In areas where distribution of Hector�s dolphin has not been studied, the offshore boundary of MPAs should enclose the 100 m isobath.

The efficacy of a Marine Protected Area (MPA) is contingent on it having a design appropriate for the species it is intended to protect. Hector�s dolphin (Cephalorhynchus hectori), a coastal delphinid endemic to New Zealand, is endangered due to bycatch in gillnets. Analyses of survival rate and population viability suggest that the Banks Peninsula population is most likely still declining despite the presence of the Banks Peninsula Marine Mammal Sanctuary (BPMMS), where gillnetting is regulated. More data on distribution and movements of dolphins are therefore required to improve the design of the BPMMS. On aerial surveys of Hector�s dolphin distribution at Banks Peninsula over three years, sightings were made up to 19 n.mi. offshore. On average, 19% of dolphins were sighted outside the BPMMS�s 4 n.mi. offshore boundary in summer, compared to 56% in winter. On similar surveys of the South Island�s west coast, all dolphins were sighted within 6 n.mi. of the coast and there was no seasonal change in distribution. At each location, Mantel tests indicated that distance offshore had the strongest and most consistent effect on distribution. However, a logistic regression model using the combined datasets suggested that distribution was most strongly defined by water depth, with all sightings made inside the 90 m isobath. Boat surveys were carried out at Banks Peninsula (2002 to 2006) to continue the long-term photo-ID project. Using the 22 year dataset, alongshore home-range of the 20 most frequently sighted dolphins was estimated by univariate kernel methods. Mean alongshore range was 49.69 km (SE = 5.29), 60% larger than the previous estimate. Fifteen percent of these individuals had ranges extending beyond the northern boundary of the BPMMS. An acoustic data logger, the T-POD, was trialled for passive acoustic monitoring of Hector�s dolphins. Simultaneous T-POD/theodolite surveys revealed that T-PODs reliably detected dolphins within 200m. No detections were made beyond 500m. To monitor inshore habitat use, T-PODs were deployed in three locations at Banks Peninsula (n = 431 days). A GLM analysis of Detection Positive Minutes (DPM) per day indicated that season had the largest effect on detection rate, with over twice as many DPMs per day in summer (x̄ = 99.8) as winter (x̄ = 47.6). The new findings on Hector�s dolphin distribution and ranging can be used to improve the design of the BPMMS. It is recommended that the offshore boundary of the BPMMS is extended to 20 n.mi. (37 km), the northern boundary is moved 12 km north and recreational gillnetting is prohibited year round. In areas where distribution of Hector�s dolphin has not been studied, the offshore boundary of MPAs should enclose the 100 m isobath.

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.