The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.]

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.

The Peruvian population of the South American fur seal ( Arctocephalus australis ) is a distinct evolutionarily significant unit that is endangered. One of the largest rookeries for this species in Peru is located within the Punta San Juan marine protected area (15°22'S, 75°12'W). To better understand the current health status of this population, exposure to 10 pinniped pathogens was evaluated in adult female fur seals (n=29) via serology and polymerase chain reaction (PCR) techniques in November 2010. The results suggest this population is naïve to canine and phocine distemper viruses (serum neutralization test), five Leptospira interrogans serovars (microscopic agglutination test), and Brucella canis (card test). Indirect fluorescent antibody testing for Toxoplasma gondii , Neospora caninum , and Sarcocystis neurona was also uniformly negative. PCR testing of nasal swabs using previously described Mycoplasma spp. primers was positive in 37.9% (11/29) of samples. One animal was positive via card test for Brucella abortus , whereas 53.7% (15/28) were positive or suspect using a marine Brucella competitive enzyme-linked immunosorbent assay. Antibody to phocine herpesvirus-1 (PHV-1) was identified in 85.7% (24/28) of the sampled population by serum neutralization testing. Overall, exposure to Mycoplasma spp., Brucella spp., and PHV-1 was observed, but results demonstrated low to no exposure to many key pinniped pathogens. The expansion of human populations, agriculture, and industry along the Peruvian coast may lead to increased pathogen exposure from human, domestic, and wild animal sources. The naïve nature of this key population of South American fur seals raises concerns about potential risk for disease outbreaks.

Persistent organic pollutants were assessed in Humboldt Penguins (Spheniscus humboldti) from the Punta San Juan Marine Protected Area, Peru, in the austral winter of 2009. Plasma samples from 29 penguins were evaluated for 31 polychlorinated biphenyl (PCB) congeners and 11 organochlorine pesticides (OCPs) by using gas chromatography coupled to an ion trap mass spectrometer and for 15 polybrominated diphenyl ether (PBDE) congeners by using gas chromatography coupled with high-resolution mass spectrometry. The detection rate for PCBs in the samples was 69%, with congeners 105, 118, 180, and 153 most commonly detected. The maximum ΣPCB concentration was 25 ng/g. The detection rate for DDT, DDD, and/or DDE was higher than for other OCP residues (90%; maximum concentration=10 ng/g). The detection rate for PBDEs was 86%, but most concentrations were low (maximum ΣPBDE concentration=3.81 ng/g). This crucial breeding population of S. humboldti was not exposed to contaminants at levels detrimental to heal...

Peru’s coastal waters are characterized by significant environmental fluctuation due to periodic El Niño- La Niña- Southern Oscillation (ENSO) events. This variability results in ecosystem-wide food web changes which are reflected in the tissues of the Peruvian fur seal (Arctocephalus australis). Stable isotope ratios (δ¹³C and δ¹⁵N) in Peruvian fur seal vibrissae (whiskers) are used to infer temporal primary production and dietary variations in individuals. Sea surface temperature anomaly (SSTA) recordings from the Niño 1+2 Index region captured corresponding ENSO conditions. Fluctuations in δ¹⁵N values were correlated to SSTA records, indicating that ENSO conditions likely impact the diet of these apex predators over time. Anomalous warm phase temperatures corresponded to decreased δ¹⁵N values, whereas cold phase anomalous conditions corresponded to increased δ¹⁵N values, potentially from upwelled, nutrient-rich water. Vibrissae δ¹³C values revealed general stability from 2004 to 2012, a moderate decline during 2013 (La Niña conditions) followed by a period of increased values concurrent with the 2014–2016 El Niño event. Both δ¹³C and δ¹⁵N values were inversely correlated to each other during the strongest El Niño Southern Oscillation event on record (2014–2016), possibly indicating a decline in production leading to an increase in food web complexity. Lower δ¹³C and δ¹⁵N values were exhibited in female compared to male fur seal vibrissae. Findings suggest ENSO conditions influence resource availability, possibly eliciting changes in pinniped foraging behavior as well as food web of the endangered Peruvian fur seal.