The population decline of the New Zealand sea lion Phocarctos hookeri: a review of possible causes

The benthic-pelagic continuum: Age class and sex differences in the use of the vertical dimension by a rare pinniped

Sea lions as a group, display strong site fidelity, and varying degrees of vulnerability to environmental change, disease and fisheries interactions. One of the rarest pinnipeds, the New Zealand sea lion (NZSL, Phocarctos hookeri) has a very restricted breeding range. At Campbell Island/Motu Ihupuku, one of the two primary breeding sites, at-sea foraging behaviour is unknown. We hypothesised that NZSL of various sex and age classes would utilise the water column differently due to differing physiological constraints and therefore have different accessibility to prey resources. We tested whether sea lion diving behaviour varied in relation to (i) age and sex class, (ii) time of day and (iii) water depth. We also hypothesised that the proportion of benthic/pelagic diving, and consequently risk of fisheries interaction, would vary in relation to age and sex. Satellite telemetry tags were deployed on 25 NZSL from a range of age/sex classes recording dive depth, duration and location. Adult females and juveniles used inshore, benthic habitats, while sub-adult males also utilised benthic habitats, they predominantly used pelagic habitat at greater distances from the island. Adult females and juveniles exhibited shorter dives than the same age/sex classes at the Auckland Islands, suggesting a lower dive effort for these age/sex classes at Campbell Island/Motu Ihupuku. Adult females dived more frequently than other age/sex classes, likely operating closer to their physiological limits; however, further data for this age class is needed. Sub-adult male use of pelagic prey may increase their exposure to mid-water trawls; however, further research detailing the degree of spatial overlap with fisheries is required. This study highlights the utility of spatially explicit dive data to predict vertical habitat use, niche separation of various age and sex classes of marine predators and attribute potential fisheries interaction risk in relation to predator habitat use.

Diet variation in a critically endangered marine predator revealed with stable isotope analysis

Understanding the foraging ecology of animals gives insights into their trophic relationships and habitat use. We used stable isotope analysis to understand the foraging ecology of a critically endangered marine predator, the Māui dolphin. We analysed carbon and nitrogen isotope ratios of skin samples (n = 101) collected from 1993 to 2021 to investigate temporal changes in diet and niche space. Genetic monitoring associated each sample with a DNA profile which allowed us to assess individual and population level changes in diet. Potential prey and trophic level indicator samples were also collected (n = 166; 15 species) and incorporated in Bayesian mixing models to estimate importance of prey types to Māui dolphin diet. We found isotopic niche space had decreased over time, particularly since the 2008 implementation of a Marine Mammal Sanctuary. We observed a decreasing trend in ∂¹³C and ∂¹⁵N values, but this was not linear and several fluctuations in isotope values occurred over time. The largest variation in isotope values occurred during an El Niño event, suggesting that prey is influenced by climate-driven oceanographic variables. Mixing models indicated relative importance of prey remained constant since 2008. The isotopic variability observed here is not consistent with individual specialization, rather it occurs at the population level.

Developing Immune Profiles of Endangered Australian Sea Lion (Neophoca cinerea) Pups Within the Context of Endemic Hookworm (Uncinaria sanguinis) Infection

As a top predator, the endangered Australian sea lion (Neophoca cinerea) is a sentinel of ecosystem change, where population trends can reflect broader shifts in the marine environment. The population of this endemic pinniped was historically diminished by commercial sealing, and recovery has been slowed by fishery interactions, disease and, potentially, pollutants. Hookworm infects 100% of neonatal pups and has been identified as a contributor to population decline. Here, a multivariable approach using traditional serological and novel molecular tools such as qPCR and ddPCR was used to examine immune phenotypes of developing Australian sea lion pups infected with the endemic hookworm (Uncinaria sanguinis) from two South Australian colonies. Results show changing immunophenotypes throughout the patent period of infection represented by pro-inflammatory cytokines (IL-6), IgG and acute-phase proteins. Although cytokines may prove useful as markers of resistance, in this study, IL-6 is determined to be an early biomarker of inflammation in Australian sea lion pups, excluding the alternative hypothesis. Additionally, immunological differences between animals from high- and low-intensity hookworm seasons, as well as ivermectin-treated animals, indicate hookworm infection modulation of the host immune response, as evidenced by a lower IL-6 mRNA expression in the non-treated groups. This study of the Australian sea lion is an example of an ecoimmunological approach to disease investigation, which can be applied to evaluate the impact of environmental and anthropogenic factors on susceptibility to infectious diseases in free-ranging species

Checklist of marine mammal parasites in New Zealand and Australian waters

Marine mammals are long-lived top predators with vagile lifestyles, which often inhabit remote environments. This is especially relevant in the oceanic waters around New Zealand and Australia where cetaceans and pinnipeds are considered as vulnerable and often endangered due to anthropogenic impacts on their habitat. Parasitism is ubiquitous in wildlife, and prevalence of parasitic infections as well as emerging diseases can be valuable bioindicators of the ecology and health of marine mammals. Collecting information about parasite diversity in marine mammals will provide a crucial baseline for assessing their impact on host and ecosystem ecology. New studies on marine mammals in New Zealand and Australian waters have recently added to our knowledge of parasite prevalence, life cycles and taxonomic relationships in the Australasian region, and justify a first host-parasite checklist encompassing all available data. The present checklist comprises 36 species of marine mammals, and 114 species of parasites (helminths, arthropods and protozoans). Mammal species occurring in New Zealand and Australian waters but not included in the checklist represent gaps in our knowledge. The checklist thus serves both as a guide for what information is lacking, as well as a practical resource for scientists working on the ecology and conservation of marine mammals.

Causes of adult mortality in two populations of New Zealand sea lions (Phocarctos hookeri)

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Infectious disease, including tuberculosis, was the most common cause of death.

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Anthropogenic trauma caused 26% of deaths in mainland sea lions.

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Trauma inflicted by adult male conspecifics caused 24% of deaths.

The New Zealand sea lion is an endangered species endemic to New Zealand. While causes of death are well described for pups of this species, mortality in adults is poorly characterised. This study investigated causes of death in 136 New Zealand sea lions in two different populations: a major breeding site on remote, uninhabited Enderby Island in the sub-Antarctic, and a slowly increasing recolonising population on the inhabited mainland. For animals with at least a partial diagnostic investigation (n = 112), the most frequently diagnosed causes of mortality were infectious disease (41/112; 37%), particularly tuberculosis due to M. pinnipedii (20/112; 18%), and conspecific trauma (27/112; 24%). Anthropogenic trauma was an important cause of death in mainland sea lions (9/33; 26%). Deliberate anthropogenic mortality has previously been identified as the greatest potential threat to population recovery for mainland sea lions, and as human and pinniped populations increase, managing interactions between these species will become increasingly important.

Stable isotope signatures of whisker and blood serum confirm foraging strategies for female New Zealand sea lions (Phocarctos hookeri) derived from telemetry

Recognizing the individual variability of foraging behaviour of marine predators is important for understanding their role in the marine ecosystem and identifying how species may respond to environmental variability or human impacts. This research examines stable isotope signatures (δ13C and δ15N) of blood serum and whiskers from 22 female New Zealand sea lions (Phocarctos hookeri (Gray, 1844)) to determine if the isotopic composition of serum reflects foraging strategy, and whether serum and proximal whisker growth have similar signatures, therefore indicating the isotopic composition of whiskers also reflects the foraging strategy diet at the time of their growth. Female New Zealand sea lions are known to have two distinct foraging strategies (mesopelagic or benthic ecotypes), shown to be habitual within and between years. Females who are known to be mesopelagic foragers have higher overlap and are at greater risk of harmful interactions with fisheries. This research found that the two foraging strategies identified from telemetry are also associated with different δ13C and δ15N isotopic values from blood serum and whiskers. Therefore, stable isotope analysis could be used to determine the proportion of the female population that are likely to be exposed to the detrimental direct and indirect interactions with fisheries.

Marine mammal population decline linked to obscured by-catch

Declines of marine megafauna due to fisheries by-catch are thought to be mitigated by exclusion devices that release nontarget species. However, exclusion devices may instead conceal negative effects associated with by-catch caused by fisheries (i.e., unobserved or discarded by-catch with low postrelease survival or reproduction). We show that the decline of the endangered New Zealand (NZ) sea lion (Phocarctos hookeri) is linked to latent levels of by-catch occurring in sub-Antarctic trawl fisheries. Exclusion devices have been used since 2001 but have not slowed or reversed population decline. However, 35% of the variability in NZ sea lion pup production is explained by latent by-catch, and the population would increase without this factor. Our results indicate that exclusion devices can obscure rather than alleviate fishery impacts on marine megafauna.

Preliminary estimates of the abundance and fidelity of dolphins associating with a demersal trawl fishery

The incidental capture of wildlife in fishing gear presents a global conservation challenge. As a baseline to inform assessments of the impact of bycatch on bottlenose dolphins (Tursiops truncatus) interacting with an Australian trawl fishery, we conducted an aerial survey to estimate dolphin abundance across the fishery. Concurrently, we carried out boat-based dolphin photo-identification to assess short-term fidelity to foraging around trawlers, and used photographic and genetic data to infer longer-term fidelity to the fishery. We estimated abundance at ≈ 2,300 dolphins (95% CI = 1,247–4,214) over the ≈ 25,880-km² fishery. Mark-recapture estimates yielded 226 (SE = 38.5) dolphins associating with one trawler and some individuals photographed up to seven times over 12 capture periods. Moreover, photographic and genetic re-sampling over three years confirmed that some individuals show long-term fidelity to trawler-associated foraging. Our study presents the first abundance estimate for any Australian pelagic dolphin community and documents individuals associating with trawlers over days, months and years. Without trend data or correction factors for dolphin availability, the impact of bycatch on this dolphin population’s conservation status remains unknown. These results should be taken into account by management agencies assessing the impact of fisheries-related mortality on this protected species.

Low Spatial Genetic Differentiation Associated with Rapid Recolonization in the New Zealand Fur Seal Arctocephalus forsteri

Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.

Historical population size of the threatened New Zealand sea lion Phocarctos hookeri

Marine mammal species were exploited worldwide during periods of commercial sealing in the 18th and 19th centuries. For many of these species, an estimate of the pre-exploitation abundance of the species is lacking, as historical catch records are generally scarce and inaccurate. Genetic estimates of long-term effective population size provide a means to estimate the pre-exploitation abundance. Here, we apply genetic methods to estimate the long-term effective population size of the subantarctic lineage of the New Zealand sea lion (NZ sea lion), Phocarctos hookeri . This species is predominantly restricted to the subantarctic islands, south of mainland New Zealand, following commercial sealing in the 19th century. Today, the population consists of ~9,880 animals and population growth is slow. Auckland Island breeding colonies of NZ sea lion are currently impacted by commercial trawl fisheries via regular sea lion deaths as bycatch. In order to estimate sustainable levels of bycatch, an estimate of the population’s carrying capacity ( K ) is required. We apply the genetically estimated long-term effective population size of NZ sea lions as a proxy for the estimated historical carrying capacity of the subantarctic population. The historical abundance of subantarctic NZ sea lions was significantly higher than the target values of K employed by the contemporary management. The current management strategy may allow unsustainable bycatch levels, thereby limiting the recovery of the NZ sea lion population toward historical carrying capacity.

Examining the role of components of Slc11a1 (Nramp1) in the susceptibility of New Zealand sea lions (Phocarctos hookeri) to disease

The New Zealand sea lion (NZSL, Phocarctos hookeri) is a Threatened marine mammal with a restricted distribution and a small, declining, population size. The species is susceptible to bacterial pathogens, having suffered three mass mortality events since 1998. Understanding the genetic factors linked to this susceptibility is important in mitigating population decline. The gene solute carrier family 11 member a1 (Slc11a1) plays an important role in mammalian resistance or susceptibility to a wide range of bacterial pathogens. At present, Slc11a1 has not been characterised in many taxa, and despite its known roles in mediating the effects of infectious disease agents, has not been examined as a candidate gene in susceptibility or resistance in any wild population of conservation concern. Here we examine components of Slc11a1 in NZSLs and identify: i) a polymorphic nucleotide in the promoter region; ii) putative shared transcription factor binding motifs between canids and NZSLs; and iii) a conserved polymorphic microsatellite in the first intron of Slc11a1, which together suggest conservation of Slc11a1 gene structure in otariids. At the promoter polymorphism, we demonstrate a shift away from normal allele frequency distributions and an increased likelihood of death from infectious causes with one allelic variant. While this increased likelihood is not statistically significant, lack of significance is potentially due to the complexity of genetic susceptibility to disease in wild populations. Our preliminary data highlight the potential significance of this gene in disease resistance in wild populations; further exploration of Slc11a1 will aid the understanding of susceptibility to infection in mammalian species of conservation significance.

Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

The effect of MHC polymorphism on individual fitness variation in the wild remains equivocal; however, much evidence suggests that heterozygote advantage is a major determinant. To understand the contribution of MHC polymorphism to individual disease resistance or susceptibility in natural populations, we investigated two MHC class II B loci, DQB and DRB, in the New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened species which is unusually susceptible to death by bacterial infection at an early age; it has suffered three bacterial induced epizootics resulting in high mortality levels of young pups since 1997. The MHC DQB and DRB haplotypes of dead NZSL pups with known cause of death (bacteria, enteritis or trauma) were sequenced and reconstructed, compared to pups that survived beyond 2 months of age, and distinct MHC DRB allele frequency and genotype differences were identified. Two findings were striking: (i) one DRB allele was present only in dead pups, and (ii) one heterozygous DRB genotype, common in live pups, was absent from dead pups. These results are consistent with some functional relationship with these variants and suggest heterozygote advantage is operating at DRB. We found no association between heterozygosity and fitness at 17 microsatellite loci, indicating that general heterozygosity is not responsible for the effect on fitness detected here. This result may be a consequence of recurrent selection by multiple pathogen assault over recent years and highlights the importance of heterozygote advantage at MHC as a potential mechanism for fitness differences in wild populations.

Septicaemia and meningitis caused by infection of New Zealand sea lion pups with a hypermucoviscous strain of Klebsiella pneumoniae

This study describes a syndrome of neonatal septicemia and meningitis in New Zealand sea lions, caused by a strain of Klebsiella pneumoniae that is phenotypically similar to strains causing environmentally-acquired septicemia and neuro-invasive disease in humans. Between late 2006 and early 2010, 123 pups from the Enderby Island breeding colony died of K. pneumoniae infection, with lesions including fibrinous to fibrinosuppurative meningitis, subdural hemorrhage, septic arthritis, herniation and hemorrhage of the cerebellar vermis, lymphadenitis and cellulitis. This infection was responsible for 58% of observed pup mortality over this time period, with most deaths occurring in the latter part of the breeding season (mid February onwards). The results of this study suggest that the pattern of this disease has changed since it was first described in 2002, when most deaths occurred early in the season (early to mid-January), and that it is an important and consistent cause of pup mortality in this population. In addition, a similar disease syndrome and bacterial strain was diagnosed in a single pup in a fragile recolonizing New Zealand sea lion population on mainland New Zealand, and the potential effect on this population is unknown but could have a negative impact on recolonisation at this site.

Long-term survival and reproductive success of New Zealand sea lions (Phocarctos hookeri) treated with ivermectin as pups

Context Hookworms (Uncinaria spp.) are a common parasite of neonatal fur seals and sea lions around the world and may contribute to decreased pup growth and survival. Removal of these parasitic burdens by administration of the anthelmintic ivermectin has been trialled in New Zealand (NZ) sea lion (Phocarctos hookeri) pups at Sandy Bay, Enderby Island, with initial benefits in growth and survival reported. Long-term effects, however, are not known. Aims To determine the impact of ivermectin treatment administered in the first month of life, on long-term survival and fecundity in a sample of NZ sea lion pups. Methods For a sample of treated and control pups born between 2002 and 2004, resighting data to 2012 was assessed with the Cox proportional hazards analysis to evaluate survival to maturity and fecundity. Key results Sample size was a limiting factor as juvenile survival was very low, but a trend of improved survival was observed in the ivermectin-treated group. Year of birth was significant due to the effects of a bacterial epizootic in the first year of the trial. Reproductive rate was not significantly different between groups. Conclusions The effect of disease and parasitism on the survival of NZ sea lions is apparent, contributing to early pup mortality, with potentially wider-ranging implications for juvenile survival and beyond. Implications Further research is warranted to investigate anthelmintic treatment of NZ sea lion pups as a safe and effective management tool to improve survival and recruitment in declining populations.

Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots

Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce--in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers--and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority.

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.

Foraging behaviour of juvenile female New Zealand sea lions (Phocarctos hookeri) in contrasting environments

Foragers can show adaptive responses to changes within their environment through morphological and behavioural plasticity. We investigated the plasticity in body size, at sea movements and diving behaviour of juvenile female New Zealand (NZ) sea lions (Phocarctos hookeri) in two contrasting environments. The NZ sea lion is one of the rarest pinnipeds in the world. Most of the species is based at the subantarctic Auckland Islands (AI; considered to be marginal foraging habitat), with a recolonizing population on the Otago Peninsula, NZ mainland (considered to be more optimal habitat). We investigated how juvenile NZ sea lions adjust their foraging behaviour in contrasting environments by deploying satellite-linked platform transmitting terminals (PTTs) and time-depth recorders (TDRs) on 2–3 year-old females at AI (2007–2010) and Otago (2009–2010). Juvenile female NZ sea lions exhibited plasticity in body size and behaviour. Otago juveniles were significantly heavier than AI juveniles. Linear mixed effects models showed that study site had the most important effect on foraging behaviour, while mass and age had little influence. AI juveniles spent more time at sea, foraged over larger areas, and dove deeper and longer than Otago juveniles. It is difficult to attribute a specific cause to the observed contrasts in foraging behaviour because these differences may be driven by disparities in habitat/prey characteristics, conspecific density levels or interseasonal variation. Nevertheless, the smaller size and increased foraging effort of AI juveniles, combined with the lower productivity in this region, support the hypothesis that AI are less optimal habitat than Otago. It is more difficult for juveniles to forage in suboptimal habitats given their restricted foraging ability and lower tolerance for food limitation compared to adults. Thus, effective management measures should consider the impacts of low resource environments, along with changes that can alter food availability such as potential resource competition with fisheries.