Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere.

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.].

SURVEY FOR INFECTIOUS DISEASE IN THE SOUTH AMERICAN FUR SEAL (ARCTOCEPHALUS AUSTRALIS) POPULATION AT PUNTA SAN JUAN, PERU.

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.

Testing Bergmann's rule and the Rosenzweig hypothesis with craniometric studies of the South American sea lion.

We tested the validity of Bergmann's rule and Rosenzweig's hypothesis through an analysis of the geographical variation of the skull size of Otaria flavescens along the entire distribution range of the species (except Brazil). We quantified the sizes of 606 adult South American sea lion skulls measured in seven localities of Peru, Chile, Uruguay, Argentina, and the Falkland/Malvinas Islands. Geographical and environmental variables included latitude, longitude, and monthly minimum, maximum, and mean air and ocean temperatures. We also included information on fish landings as a proxy for productivity. Males showed a positive relationship between condylobasal length (CBL) and latitude, and between CBL and the six temperature variables. By contrast, females showed a negative relationship between CBL and the same variables. Finally, female skull size showed a significant and positive correlation with fish landings, while males did not show any relationship with this variable. The body size of males conformed to Bergmann's rule, with larger individuals found in southern localities of South America. Females followed the converse of Bergmann's rule at the intraspecific level, but showed a positive relationship with the proxy for productivity, thus supporting Rosenzweig's hypothesis. Differences in the factors that drive body size in females and males may be explained by their different life-history strategies. Our analyses demonstrate that latitude and temperature are not the only factors that explain spatial variation in body size: others such as food availability are also important for explaining the ecogeographical patterns found in O. flavescens.

Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator.

Hybridization is widespread and constitutes an important source of genetic variability and evolution. In animals, its role in generating novel and independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis is a marine apex predator of Pacific and Atlantic waters, with a disjunct set of populations in Peru and Northern Chile [Peruvian fur seal (Pfs)] with controversial taxonomic status. We demonstrate, using complete genome and reduced representation sequencing, that the Pfs is a genetically distinct species with an admixed genome that originated from hybridization between the SAfs and the Galapagos fur seal (Arctocephalus galapagoensis) ~400,000 years ago. Our results strongly support the origin of Pfs by homoploid hybrid speciation over alternative introgression scenarios. This study highlights the role of hybridization in promoting species-level biodiversity in large vertebrates.

Health evaluation of free-ranging Humboldt penguins (Spheniscus humboldti) in Peru.

As part of ongoing ecological studies of Humboldt penguins (Spheniscus humboldti) at Punta San Juan, Ica Department, Peru, health surveys were conducted in November 1992, 1993, and 1994. In the three surveys, 98 birds in total were handled for examination, and blood was collected for laboratory analysis from 90 of these birds. All birds seemed to be in good condition. Body weights of females were significantly lower in 1994 than in the other years. Fleas (Parapsyllus humboldti) and ticks (Ornithodoros amblus) were found on the penguins and in their nests. Females had significantly higher plasma calcium and phosphorus levels, and they had lower weights than males. No other differences were found between the sexes. Hematology, plasma chemistries, and plasma mineral levels varied between years. Positive antibody titers for Chlamydophila psittaci (62%), avian adenovirus (7%; 1994 only), paramyxovirus-2 (7%; 1993 only), and Salmonella Pullorum (7%) were found. Plasma chemistry and mineral levels differed between individuals testing positive vs. negative on serologic tests for avian adenovirus and Salmonella Pullorum. Serologic tests for antibodies to avian influenza A virus, avian encephalomyelitis virus, infectious bronchitis virus, avian reovirus, duck viral enteritis virus, equine encephalitis (eastern, western, and Venezuelan) viruses, infectious bursal disease virus, infectious laryngotracheitis virus, Aspergillus sp., and paramyxovirus-1 and -3 were negative. All chlorinated pesticide and polychlorinated biphenyl analyses were below detectable limits.

ASSESSMENT OF POLYCHLORINATED BIPHENYLS, ORGANOCHLORINE PESTICIDES, AND POLYBROMINATED DIPHENYL ETHERS IN THE BLOOD OF HUMBOLDT PENGUINS ( SPHENISCUS HUMBOLDTI) FROM THE PUNTA SAN JUAN MARINE PROTECTED AREA, PERU.

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 health and reproductive success; however, the identified concentrations of legacy and recently emerged toxicants underscore the need for temporal monitoring and diligence to protect this endangered species in the face of regional human population and industrial growth. These results also provide key reference values for spatial comparisons throughout the range of this 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.