Academic literature on the topic 'Hector's dolphin'

Two Hector's Dolphin calves Cephalorhynchus hectori were killed by probable boat collision in 1999, indicating that boat strikes may pose more of a threat to the species than previously thought. When discovered, one dead calf was still tended by its mother. After recovery, both animals were necropsied with trauma from boat strikes as the most likely cause of death. These deaths are discussed in the context of increasing human contact with Hector's Dolphins in Akaroa Harbour, and risks to the dolphins caused by this habituation.

During the past decade, Hector's dolphins, Cephalorhynchus hectori, have suffered an alarming level of mortality due to entanglement in commercial and amateur gill nets. In this paper we study two Leslie matrix population models that incorporate known features of dolphin fertility and mortality, focussing on the information they provide regarding age distributions and maximum population growth rates. The simplest model specifies constant survival rates over many age-classes. The second model uses more realistic curves of age-specific survival rates. The results indicate that Hector's dolphin, like most other small cetaceans, has a low potential for population growth. Growth rates of 1.8–4.9% per year are likely to be the maximum possible for Hector's dolphin populations, and C. hectori (and C. commersonii) populations are likely to be declining under recent levels of net entanglement. Survival rate estimates from free-living populations, subject to natural and net-entanglement mortality, showed decreasing populations. Even with the most optimistic reproductive parameters, survival rates would need to be some 5–10% higher than those observed in populations subject to gill-net entanglement before population growth could occur. The likely consequences of a reduction in entanglement mortality through conservation management are explored using the survivorship curve model. These simulations show that the age structure of the population can have an important effect on changes in the size and growth rate of the population during the recovery phase following a reduction in entanglement mortality.

Most delphinids are very social and spend much time in the presence of conspecifics. The proportion of co-occurrences of any two individuals is usually measured by means of association indices. In this study, the "half-weight index" was used to describe the association patterns in three previously unstudied populations of Hector's dolphin, Cephalorhynchus hectori, around the South Island of New Zealand. For inclusion in this analysis individuals were photoidentified repeatedly over a 2-year study period. Only about 1% of the individual associations of dolphin pairs (dyads) tested were found to be significantly different (p less than or equal to 0.01) from random distributions derived from a new constrained Monte Carlo randomisation. The overall association patterns in the two study populations off Kaikoura ( n = 48 individuals) and Moeraki (n = 24) did not differ significantly from what could be expected by chance (p = 0.07 and 0.09, respectively), whereas those in the Jackson Bay population (n = 38) were significantly different from chance (p < 0.0002). Hector's dolphins appear to have a typical fission-fusion society, with many weak associations within the wider envelope of the local population.

Acoustic surveys can have several advantages over visual methods in surveys of cetaceans, although verification is required that novel techniques are effective. The T-POD is an autonomous acoustic data logger with inbuilt filters that can be set to match the click characteristics of the target species. We tested the performance of the T-POD for detecting Hector's dolphins at Flea Bay, Banks Peninsula, New Zealand. Simultaneous visual surveys were conducted from a hillside overlooking the bay, with distances between the T-POD and dolphins measured using a theodolite. Wideband sound recordings confirmed that T-POD detections were echolocation clicks made by Hector's dolphins. Detection probability and click train detection rate decreased with increasing distance, with no detections made beyond 500 m. By fitting detection functions to the probability of detection versus distance we showed that the T-POD effectively detected all dolphin groups within a radius of 198–239 m, depending on the click train categories utilized. The T-POD shows considerable promise as a tool for passive acoustic surveys of Hector's dolphins, with possible applications in studies of distribution, habitat use and echolocation behaviour.

Data are provided on the reproductive biology and life history of Hector's dolphin, Cephalorhynchus hectori, a species found only in New Zealand waters. Samples were taken from 60 dolphins found beach-cast or killed incidentally in fishing gear. Male and female reproductive tracts were examined macroscopically and histologically, and tooth sections provided an age estimate for each individual. The traditional procedure for preparing dolphin teeth was simplified by using a faster stain and more readily available embedding and sectioning equipment. An important advantage of this method is that it facilitates the cutting of thinner sections, increasing the chances of obtaining a section through the centre of the pulp cavity. Sectioning revealed an open pulp cavity in all the teeth examined. The maximum observed age was 19 years for females and 20 years for males. Females reach a larger body size than males, and are apparently larger than males at any given age. Males appear to reach sexual maturity between 6 and 9 years of age, whereas females give birth to their first calf at 7–9 years of age. Mature males have extremely large testes relative to their body size. The largest male found in this study weighed 41.5 kg, with testes (including epididymides) totalling 1.21 kg.

Vocalisations of free-ranging Hector's dolphins were recorded with wide-band recording equipment. Preliminary analyses of these sounds showed them to be high-frequency clicks centred around 120-125kHz. Digital signal processing methods were used to automatically measure many features of the sounds and, in combination with multivariate statistical methods, to provide a quantitative analysis of the acoustic repertoire of Hector's dolphins. Almost all of the sounds made were narrowband, high-frequency clicks of comparatively simple structure. Hector's dolphins make very few audible sounds, the most common of which is made up of high-frequency clicks emitted at such high repetition rates that the repetition rate is audible as a tonal "cry" or "squeal". Multivariate analyses of the automatically measured data revealed different types of high-frequency clicks according to their frequency and timing characteristics. The sounds are described in detail, as are the techniques used to automate the digital measurement process. To gain an insight into the possible role of these signals as echolocation signals, the ambiguity functions of different types of click are presented. With any simple sonar signal, the structural demands of range measurement and resolution of target velocity are in conflict. These analyses show that Hector's dolphin sonar signals are poorly suited to determining target velocity, but are well suited to resolving target range. Information about target velocity is accessible to the dolphin only from the trend of range measurements during a sequence of clicks. To explore whether click types have different communicative meaning, I analysed whether certain click types were used disproportionately in different behavioural contexts. Hector's dolphin clicks do not appear to be used solely in sonar. Click types with complex spectra were used more often in large groups than in small ones, and double pulses (in the time domain) were used more often in "surface active" groups than in "long-diving" ones, suggesting they have some social significance. High repetition rate sounds ("cries") were much more commonly associated with aerial behaviours than with feeding, and appear to indicate excitement. I conclude that there is a general association between sounds and behaviour, and hypothesise that dolphins may have developed a communication system based on the ability to interpret each other's sonar echoes. Several workers have suggested that gillnet entanglement is essentially an acoustic problem, as the dolphin's sonar apparently fails to detect the nets. The Pegasus Bay/Canterbury Bight gillnet fishery was studied to investigate gillnet entanglement. Over the four years of the study, 230 Hector's dolphins were reported killed in gillnets. Most dolphins (89%) were caught within four miles of the shore, and over the summer months of November to February (91%). The acoustic aspects of this problem were explored in an analysis of proposals to reduce entanglement by modifying gillnets. I show that neither making the nets more reflective to dolphin sonar nor warning of their presence by attaching sound emitters has proved successful, and argue that they are unlikely to be successful because of logical and practical difficulties with the concepts. I conclude that the best management strategy for the reduction of gillnet entanglement is the closure of specific areas to gillnetting.

New Zealand's first Marine Mammal Sanctuary was established around Banks Peninsula in 1988, to protect Hector's dolphins from entanglement in gillnets. Understanding distribution and movements of Hector's dolphins inhabiting Banks Peninsula has important implications for their effective management. The need to assess the effectiveness of restricting gillnetting also underscores the need for ongoing estimates of the size of the Banks Peninsula Hector's dolphin population. I analysed spatial and temporal movements of distinctive Hector's dolphins identified around Banks Peninsula. A substantial number of dolphins I identified in the northern portion of Banks Peninsula have been sighted in the southern portion of Banks Peninsula but none of the individuals I identified have been sighted north or south of the peninsula (Slooten, Dawson, Stone and Yoshinaga, unpub. data). These results suggest that Hector's dolphins resident around Banks Peninsula, are a single interacting population. I assessed the applicability of mark-recapture methods using photo-identification of distinctive individuals to estimate the size of the Banks Peninsula population of Hector's dolphins. The maximum average capture probability for Hector's dolphins around Banks Peninsula during my study was in the range of "poor" data. During my study, small sample size and low recapture rates of identified dolphins was generally the case. These results indicated that numbers of Hector's dolphins around Banks Peninsula cannot be estimated reliably from mark-recapture methods with the data which is currently available. I conducted surveys to estimate the abundance of Hector's dolphins in the northern portion of Banks Peninsula. I also used survey data to examine the temporal and spatial distribution of dolphins in the study area. No more than 123 dolphins were counted on a survey and on approximately 70% of surveys, fewer than 41 were counted. I found no significant difference in number of dolphins counted during November to March, suggesting that conducting surveys during this period is an appropriate sampling strategy for estimating abundance. There was a highly significant association between abundance and location, indicating it is inappropriate to extrapolate abundance estimates from one area to another based on a simple density 1 area relationship. Estimates of abundance for Hector's dolphins in the northern portion of Banks Peninsula for 1990/91 and 1991/92 were in the range of previously reported estimates for Banks Peninsula.

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.

Dolphins are increasingly coming into contact with humans, particularly where tourism is involved. It has been assumed that such contact causes chronic stress on dolphin populations. This study examined relatively naive populations of Hector's dolphins and their interaction with various watercrafts. Dolphins in New Zealand have been observed using theodolites and boat-based observations over the last two decades, particularly on the east side of the South Island at Akaroa, which is situated on the coast line of Banks Peninsula. This research was undertaken using shore-based theodolite tracking to observe boat activity around the coast of Lyttelton and Timaru and their associated Harbours. Observations were made mostly over two periods each of six months duration and included the months October through to March during the years 2000-2001 and 2001-2002. Observations made during a third period in 2005 were also incorporated for some of the analyses. Field investigations using a theodolite included more than 376 hours/site/season and recorded dolphin behaviour both with and without the presence of tour boats. Of primary interest were the tours, which ran regular trips to observe Cephalorhynchus hectori in their natural habitat. Hector's dolphins at both Lyttelton and Timaru were consistently observed with particular boat types and not with other types of water craft. Dolphins at Timaru exhibited a greater range of behaviours than those at Lyttelton. Stress-related behaviours such as an increase in swimming speed to open ocean and grouping behaviour were only observed in the presence of boats. Other potential stress behaviours, such as head slaps and repeated tail slaps, were only performed in the absence of boats. Observations implied that some generic dolphin behaviours, which often indicate stressed individuals may not apply to Hector's dolphins, and therefore question the assumption that all dolphin species behave in similar ways. We suggest that low-level tourist boat activity is not placing undue stress on the population. In addition to theodolite observations, tour boat based observations of Hector's dolphin were undertaken and behaviour at each site recorded for a focal animal. Tour boat-based observations concentrated on determining any preference to bow, stern, portside and starboard sides of the vessel. Dolphins consistently showed a preference in direction of approach and departure from tour vessels with a strong tendancy to the bow of the boat, and least with the stern. These results were similar irrespective of site or vessel. Behaviour data were also collected from tour boat vessels over 48 trips/season/site and the data divided into transitional behaviour groups, which included stress behaviours, association / interaction behaviour and neutral behaviour. Behavioural count and time data were collected to reflect the number of times and duration of behaviour occurrence, particularly in relation to transitional behaviours. Determining the presence of stress in Hector's dolphins varied between the data sets and indicated that time is a necessary factor when attempting to determine whether an individual or a general population is genuinely stressed. Quadrant preference and swimming direction in relation to the Black Cat were observed over six years, and both count and time data were collected with regard to behaviour. The results were consistent with preference in quadrant being expressed towards the bow of the boat and least with the stern. The count data suggested no significant impact on Hector's dolphin behaviour in the presence of the Black Cat over time, where time data indicated there was a transition over the years from neutral behaviour in the second year of tour boat activity, to positive behaviour in the third year of boat-activity and finally avoidance behaviour in the seventh year of tour boat activity at Lyttelton Harbour in response to the presence of the Black Cat.

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.

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.

Hector's dolphins are threatened with local extinction by entanglement in coastal gillnets. This thesis provides data on population biology, social organization and behaviour of Hector's dolphins that help assess human impacts on their populations. To estimate population growth, I integrated anatomical studies which estimated longevity and age at first reproduction, with photographic field studies which estimated reproductive rate and survival rate. Sixty incidentally caught and beach-cast dolphins were aged from the growth layers in their teeth. Maximum age was 19 years for females and 20 for males. Females gave birth to their first calf at 7 to 9 years old, and thereafter had one calf every 2 to 3 years. Population models using these data predicted maximum population growth rates of 1.8 to 4.4% per year. These rates were exceeded by the number of Hector's dolphins recently killed in gillnets in the Pegasus Bay-Canterbury Bight area. Survival rates (including gillnet mortality) estimated using photographic identification, also suggested that this population was unable to cope with recent gillnet entanglement levels. Population models using these survival rates (0.797 to 0.865 after the first year of life), even in combination with the most optimistic reproductive rates, resulted in a decreasing population. The population models were also used to explore the likely consequences of management strategies which reduce entanglement mortality. Population and population growth rate fluctuated markedly for several decades after a significant reduction in entanglement mortality, especially if the age structure of the population was biased towards younger individuals. A study of social organization and behaviour pointed to another potential conservation risk. The social organization of Hector's dolphins was studied using photographic identification. Each individual associated loosely with a relatively large number of others, rather than with a few close associates, and groups frequently joined other groups and exchanged members. Sequence analysis was used to classify Hector's dolphin behaviour into five categories: 'feeding', 'sexual" 'aggressive', 'play' and 'aerial', using behaviour sequence analysis. The number of sexual behaviours per individual was highest in groups of 11-15 dolphins, and tended to increase after groups came together. The fluid association patterns and increase in sexual behaviours after groups come together suggest that Hector's dolphins have a promiscuous mating system in which males search for rather than monopolize females. Such a mating system has the potential to reduce fertilization rates in areas of low abundance.

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 uses molecular genetics as a tool to uncover information about the population structure and genetic variation in Hector’s dolphin (Cephalorhynchus hectori), to track population declines and to assess the evolutionary origins and taxonomic status of this species. A high-resolution genetic analysis of population structure was considered important for the determination of population boundaries and delimitation of conservation management units due to potentially unsustainable fisheries-related mortality. Population structure and dispersal rates were assessed using 281 samples collected from individual Hector’s dolphins of ten population groups representing the known geographic range of this species. Variation among mitochondrial DNA sequences (ΦST = 0.545) and microsatellite allele frequencies at six loci (RST = 0.252) indicated the presence of four genetically isolated regional populations, North Island (n = 29), East Coast South Island (n = 110), West Coast South Island (n = 122) and South Coast South Island (n = 19). Significant levels of genetic differentiation were not detected within local sub-populations of the East Coast and West Coast regional populations. However, the estimated geneflow between these sub-populations fitted a one-dimensional stepping-stone model (r2 = 0.6225) suggesting a vulnerability of local populations to fragmentation. A measure of expected mtDNA diversity (Tajima’s D statistic) suggested decline in eight of the ten populations. Microsatellite heterozygosity was also lower than expected in the East Coast and North Island regions, suggesting either further regional sub-structuring (Wahlund effect), loss of diversity due to population decline or the presence of null alleles. Examination of all Hector’s dolphin museum specimens of known origin (n = 55) enabled comparison of historic (1870 - 1987) genetic diversity to contemporary (1988 – 1999) diversity in two regional populations to assess the possibility that these populations have undergone recent declines. Over the last 20 years the North Island population has been reduced from at least three lineages (h = 0.41) to a single lineage (h = 0, p < 0.05). The diversity of the East Coast, South Island population has declined significantly from h = 0.65 to h = 0.35 (p < 0.05). These results suggest that the low abundance currently observed is due to recent population declines and that the North Island population is threatened with extinction in the near future. Based on a trend analysis of the mtDNA, it can be predicted that the East Coast South Island population may lose all mtDNA diversity within the next 20 years. Alternatively, detection of a one dimensional dispersal pattern may indicate that some populations are at risk of extirpation while others may not be in decline. If this is the case then the East Coast regional population is at risk of fragmentation. On a wider evolutionary scale, Hector’s dolphin is one of four species of the genus Cephalorhynchus, all of which suffer fisheries–related mortality. To describe the origin and radiation of these species, 485 bp of the mitochondrial DNA control region was sequenced from 320 individuals (including previously sequenced 200 Hector’s dolphins) representing nine of the ten species in the sub-family Lissodelphininae. The hypotheses that either Cephalorhynchus is a monophyletic genus or that the four species have arisen separately from pelagic Lissodelphine species and have converged morphologically were tested. The mtDNA phylogeny supported the monophyly of the genus and suggested that the genus Cephalorhynchus originated in the waters of South Africa and, following the West Wind Drift, colonised New Zealand and then South America. Secondary radiations resulting in two genetically isolated populations were found for the Kerguelen Island Commerson’s dolphin and the North Island Hector’s dolphin. A comparison of the genetic differentiation between the Commerson’s dolphins of the Kerguelen Islands (n = 11) and the coast of South America (n = 35), and between the North Island (n = 14) and South Island (n = 185) Hector’s dolphins, was conducted in order to assess the conservation and taxonomic status of these populations. A single fixed substitution in the mtDNA control region was diagnostic for the Kerguelen Island compared to South America (FST = 0.306, ΦST = 0.602) and the North Island compared to the South Island (FST = 0.442, ΦST = 0.495). Population differentiation of four microsatellite alleles (including unique alleles in each of the four populations) between the Kerguelen Island and South American Commerson’s dolphin (FST = 0.036, RST = 0.0493) and between the North and South Island Hector’s dolphins (FST = 0.391, RST = 0.3197) indicated restricted nuclear as well as maternal geneflow. These data, combined with additional evidence of morphological and geographic isolation, indicated that the Kerguelen Island Commerson’s dolphin and the North Island Hector’s dolphin are likely to be reproductively isolated from their alternate con-specific populations. Examination of various species concepts and definitions of conservation units leads to the conclusion that these four populations should each be considered unique at the subspecies level for the purposes of management, protection and evolutionary potential. These results lead to the conclusion that the Hector’s dolphin consists of highly subdivided populations. As a result of this and a low reproductive potential, Hector’s dolphin populations are vulnerable to extirpation through even low levels of human induced mortality. To manage such populations, it is appropriate to consider each of the two islands as separate sub-species. Within the South Island, the populations may be further subdivided into three demographically independent Management Units – the East, West and South Coasts. The South Coast management unit is vulnerable due to its low abundance and isolation and requires further investigation. Population modelling will need to reflect the fact that the local populations within the East and West coast regions share only limited dispersal with immediately adjacent populations and are thus susceptible to fragmentation. These results also show that the population declines of the East Coast South Island and the North Island populations are of recent origin thus implicating fisheries-related mortality as the principal threat to Hector’s dolphin. To prevent further decline or fragmentation of South Island populations more stringent control of inshore gillnet fisheries is required. By contrast, current decline of the North Island population may be a result of inbreeding depression. Given the low abundance and rapid decline of the North Island population, it is imperative to evaluate the potential for inbreeding depression while continuing to mitigate all human-related threats.