Assessment of the status and trends in abundance of a coastal pinniped, the Australian sea lion Neophoca cinerea

Australian sea lions Neophoca cinerea are endemic to Australia, with their contemporary distribution restricted to South Australia (SA) and Western Australia (WA). Monitoring of the species has proved challenging due to prolonged breeding events that occur non-annually and asynchronously across their range. The most recent available data from 80 extant breeding sites (48 in SA, 32 in WA) enabled us to estimate the species-wide pup abundance to be 2739, with 82% (2246) in SA and 18% (493) in WA, mostly based on surveys conducted between 2014 and 2019. We evaluated 1776 individual site-surveys undertaken between 1970 and 2019 and identified admissible time-series data from 30 breeding sites, which revealed that pup abundance declined on average by 2.0% yr-1 (range 9.9% decline to 1.7% growth yr-1). The overall reduction in pup abundance over 3 generations (42.3 yr) was estimated to be 64%, with over 98% of Monte Carlo simulations producing a decline >50% over a 3-generation period, providing strong evidence that the species meets IUCN ‘Endangered’ criteria (decline ≥50% and ≤80%). The population is much smaller than previously estimated and is declining. There is a strong cline in regional abundances (increasing from west to east), with marked within-region heterogeneity in breeding site pup abundances and trends. Results from this study should improve consistency in the assessment of the species and create greater certainty among stakeholders about its conservation status. To facilitate species management and recovery, we prioritise key data gaps and identify factors to improve population monitoring.

Cytokine RT-qPCR and ddPCR for immunological investigations of the endangered Australian sea lion (Neophoca cinerea) and other mammals

Measurement of cytokine gene expression by reverse transcription quantitative polymerase chain reaction (RT-qPCR) is used widely to assess the immune system of animals and to identify biomarkers of disease, but its application is limited in wildlife species due to a lack of species-specific reagents. The free-ranging endangered Australian sea lion (Neophoca cinerea) experiences significant clinical disease and high pup mortality due to intestinal hookworm infection. Developing immunological tools specific to the species will aid in the assessment of drivers of disease and its impact in population demographics. This study describes the development and validation of cross-reactive RT-qPCR assays to measure five important cytokines involved in innate and Th1/Th2 responses (IL-6, TNFα, IFNγ, IL-4 and IL-10) in unstimulated blood samples from a range of different mammalian species including the Australian sea lion. All RT-qPCR assays efficiencies ranged between 87% (Ovis aries TNFα) and 111% (Bos taurus IL-10) and had strong linearity (R2). IL-4 and IFNγ gene expression for N. cinerea fell below the dynamic range (and therefore quantifiable limits) of RT-qPCR assays but were able to be quantified using the novel droplet digital PCR (ddPCR). This study delivers new immunological tools for eco-immunologists studying cytokine gene expression in wildlife species and is to our knowledge, the first cytokine ddPCR approach to be reported in a pinniped species.

Morphometrical and molecular evidence suggests cryptic diversity among hookworms (Nematoda: Uncinaria) that parasitize pinnipeds from the south-eastern Pacific coasts

Hookworms of the genus Uncinaria parasitize pinniped pups in various locations worldwide. Four species have been described, two of which parasitize pinniped pups in the southern hemisphere: Uncinaria hamiltoni parasitizes Otaria flavescens and Arctocephalus australis from the South American coast, and Uncinaria sanguinis parasitizes Neophoca cinerea from the Australian coast. However, their geographical ranges and host specificity are unknown. Uncinaria spp. are morphologically similar, but molecular analyses have allowed the recognition of new species in the genus Uncinaria. We used nuclear genetic markers (internal transcribed spacer (ITS) and large subunit (LSU) rDNA) and a mitochondrial genetic marker (cytochrome c oxidase subunit I (COI)) to evaluate the phylogenetic relationships of Uncinaria spp. parasitizing A. australis and O. flavescens from South American coasts (Atlantic and Pacific coasts). We compared our sequences with published Uncinaria sequences. A Generalized Mixed Yule Coalescent (GMYC) analysis was also used to delimit species, and principal component analysis was used to compare morphometry among Uncinaria specimens. Parasites were sampled from A. australis from Peru (12°S), southern Chile (42°S), and the Uruguayan coast, and from O. flavescens from northern Chile (24°S) and the Uruguayan coast. Morphometric differences were observed between Uncinaria specimens from both South American coasts and between Uncinaria specimens from A. australis in Peru and southern Chile. Phylogenetic and GMYC analyses suggest that south-eastern Pacific otariid species harbour U. hamiltoni and an undescribed putative species of Uncinaria. However, more samples from A. australis and O. flavescens are necessary to understand the phylogenetic patterns of Uncinaria spp. across the South Pacific.

Fur seals and sea lions (family Otariidae) on the breakwaters at Adelaide

Long-nosed fur seals (Arctocephalus forsteri) and Australian sea lions (Neophoca cinerea) on the breakwaters at the mouth of the Port River estuary at Adelaide’s Outer Harbor were counted from 2004 to 2015. Observed counts were modelled using a generalised linear model. Fur seal numbers have been increasing since 2011; for sea lions there was a small discernible annual trend in counts. Counts of fur seals varied seasonally; most annual maxima were in August or September with modelled peak numbers around 9–11 September. The maximum count of fur seals was 79 in September 2015. For sea lions, the model predicts annual peaks in the period 28 August to 19 September. The maximum count of sea lions was nine in September 2009. The haulout sites on the Outer Harbor breakwaters are easily accessible by boats, including pleasure craft. In particular, the seaward end of the outer breakwater is a popular spot with recreational anglers whose lines are often within a few metres of the seals. We propose that a management plan should be developed involving a study of the effect of boat approaches on seals utilising the Outer Harbor area followed by education coupled with enforcement.