Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

Novel alphaherpesvirus in a wild South American sea lion (Otaria byronia) with pulmonary tuberculosis

In 2017, an adult male South American sea lion (Otaria byronia), presenting emaciation and a cervical abscess, stranded alive in Florianópolis, southern Brazil. The animal was directed to a rehabilitation center, dying a few days later. On necropsy, the main gross findings were necrotizing lymphadenitis of the right prescapular lymph node and nodular bronchopneumonia. A novel alphaherpesvirus, tentatively named Otariid alphaherpesvirus 1, was amplified in several tissue samples. No histopathologic findings associated with viral infection were observed. Additionally, pulmonary tuberculosis by Mycobacterium pinnipedii was diagnosed by histopathological, immunohistochemical, and molecular techniques. Several bacteria were cultured from antemortem and postmortem samples, including Proteus mirabilis from the cervical abscess and cardiac blood, and Escherichia coli from the cervical abscess and pericardial effusion. Flavivirus, morbillivirus, and Apicomplexa were not detected by molecular techniques. Herein, we report a novel alphaherpesvirus in a pinniped species of the family Otariidae. Although previously described in Southern Hemisphere pinniped species, including South American sea lions, there is limited information regarding M. pinnipedii impact over this group. Further research is required to determine the associated pathogenesis of this novel herpesvirus, and prevalence of Otariid alphaherpesvirus 1 and M. pinnipedii in the reproductive colonies.

Phylogeography of Otaria flavescens (Carnivora: Pinnipedia): unravelling genetic connectivity at the southernmost limit of its distribution

The Pleistocene glacial period shaped the current genetic structure of numerous species. The last glacial dynamics has been proposed to have split the South American sea lion, Otaria flavescens, into two Evolutionarily Significant Units (ESUs), one on each side of the continent. However, previous studies have not provided genetic information on colonies found along 3000 km of coastline of the southernmost limit of the species distribution, where gene flow could occur. We conducted an exhaustive phylogeographical analysis of O. flavescens using a mtDNA marker, including, for the first time, data from colonies living south of latitude 45° S, in the Argentinian provinces of Santa Cruz and Tierra del Fuego. Our results indicated the presence of five Conservation Units across the distribution range of O. flavescens and suggest that the Patagonian population must have expanded about 150 000 BP. We found evidence for gene flow across the entire species range, supporting a scenario of secondary contact in Tierra del Fuego where representatives of the oldest lineages coexist. The presence of gene flow between oceans leads us to reject the assumption of complete reciprocal monophyly for mtDNA between the presumed ESUs, suggesting that the species constitutes a single Evolutionarily Significant Unit.

Analysing the natural population growth of a large marine mammal after a depletive harvest

An understanding of the underlying processes and comprehensive history of population growth after a harvest-driven depletion is necessary when assessing the long-term effectiveness of management and conservation strategies. The South American sea lion (SASL), Otaria flavescens, is the most conspicuous marine mammal along the South American coasts, where it has been heavily exploited. As a consequence of this exploitation, many of its populations were decimated during the early 20th century but currently show a clear recovery. The aim of this study was to assess SASL population recovery by applying a Bayesian state-space modelling framework. We were particularly interested in understanding how the population responds at low densities, how human-induced mortality interplays with natural mechanisms, and how density-dependence may regulate population growth. The observed population trajectory of SASL shows a non-linear relationship with density, recovering with a maximum increase rate of 0.055. However, 50 years after hunting cessation, the population still represents only 40% of its pre-exploitation abundance. Considering that the SASL population in this region represents approximately 72% of the species abundance within the Atlantic Ocean, the present analysis provides insights into the potential mechanisms regulating the dynamics of SASL populations across the global distributional range of the species.

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens)

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean.

Habitat use and spatial fidelity of male South American sea lions during the nonbreeding period

Conditions experienced during the nonbreeding period have profound long‐term effects on individual fitness and survival. Therefore, knowledge of habitat use during the nonbreeding period can provide insights into processes that regulate populations. At the Falkland Islands, the habitat use of South American sea lions (Otaria flavescens) during the nonbreeding period is of particular interest because the population is yet to recover from a catastrophic decline between the mid‐1930s and 1965, and nonbreeding movements are poorly understood. Here, we assessed the habitat use of adult male (n = 13) and juvenile male (n = 6) South American sea lions at the Falkland Islands using satellite tags and stable isotope analysis of vibrissae. Male South American sea lions behaved like central place foragers. Foraging trips were restricted to the Patagonian Shelf and were typically short in distance and duration (127 ± 66 km and 4.1 ± 2.0 days, respectively). Individual male foraging trips were also typically characterized by a high degree of foraging site fidelity. However, the isotopic niche of adult males was smaller than juvenile males, which suggested that adult males were more consistent in their use of foraging habitats and prey over time. Our findings differ from male South American sea lions in Chile and Argentina, which undertake extended movements during the nonbreeding period. Hence, throughout their breeding range, male South American sea lions have diverse movement patterns during the nonbreeding period that intuitively reflects differences in the predictability or accessibility of preferred prey. Our findings challenge the long‐standing notion that South American sea lions undertake a winter migration away from the Falkland Islands. Therefore, impediments to South American sea lion population recovery likely originate locally and conservation measures at a national level are likely to be effective in addressing the decline and the failure of the population to recover.