Investigation of a Mass Stranding Event Reveals a Novel Pattern of Cascading Comorbidities in Northern Fulmars (Fulmarus glacialis).

During 2018, a seabird mortality event occurred in central California, US, that affected Northern Fulmars (Fulmarus glacialis), Common Murres (Uria aalge), and Cassin's Auklets (Ptychoramphus aleuticus). An increase in beachcast birds were reported on standardized surveys in conjunction with an increased number of live-stranded birds admitted to rehabilitation centers. Neurologic symptoms were noted during intake examination for some birds. Coincident with the mortality event, increased levels of the harmful algal bloom toxins domoic acid and saxitoxin were recorded in Monterey Bay and Morro Bay. Birds that died in care and beachcast carcasses were submitted to the California Department of Fish and Wildlife-Marine Wildlife Veterinary Care and Research Center for postmortem examination (n=24). All examined birds were emaciated. Examined Common Murres and Cassin's Auklets had no gross evidence of preexisting disease; however, all examined Northern Fulmars exhibited severe pyogranulomatous inflammation of the urogenital system at gross postmortem exam. Tissues from nine Northern Fulmars were examined by histopathology, and samples from two Northern Fulmars were tested for the presence of domoic acid and saxitoxin. Histopathology revealed moderate to severe kidney infection by Eimeria sp. and gram-negative bacteria, intratubular urate stasis, ureter rupture, and emaciation. Additionally, domoic acid and saxitoxin were detected simultaneously in tissues of some tested birds. This communication highlights a novel pattern of cascading comorbidities in native seabirds from a mass stranding event.

Molecular and morphological confirmation of Profilicollis altmani as the cause of acanthocephalan peritonitis in California sea otters (Enhydra lutris nereis).

Acanthocephalan peritonitis (AP; trans-intestinal migration of acanthocephalan parasites into the peritoneal cavity resulting in severe peritonitis), is a common cause of mortality in southern sea otters (Enhydra lutris nereis). Although Profilicollis spp. acanthocephalans have been implicated in these infections, the species causing AP has been an important unresolved question for decades. We used morphological and molecular techniques to characterize acanthocephalans from the gastrointestinal (GI) tract and peritoneal omentum of eighty necropsied southern sea otters. Only P. altmani was found to have perforated through the intestinal wall and migrated into the peritoneal cavity of examined sea otters, resulting in AP. Morphological and molecular criteria confirmed that Profilicollis kenti was synonymous with P. altmani. A second Profilicollis sp., likely P. botulus, was present only in the intestinal lumen, did not penetrate through the intestinal wall, and was not associated with AP.

Nasopulmonary mites (Acari: Halarachnidae) as potential vectors of bacterial pathogens, including Streptococcus phocae, in marine mammals.

Nasopulmonary mites (NPMs) of the family Halarachnidae are obligate endoparasites that colonize the respiratory tracts of mammals. NPMs damage surface epithelium resulting in mucosal irritation, respiratory illness, and secondary infection, yet the role of NPMs in facilitating pathogen invasion or dissemination between hosts remains unclear. Using 16S rRNA massively parallel amplicon sequencing of six hypervariable regions (or "16S profiling"), we characterized the bacterial community of NPMs from 4 southern sea otters (Enhydra lutris nereis). This data was paired with detection of a priority pathogen, Streptococcus phocae, from NPMs infesting 16 southern sea otters and 9 California sea lions (Zalophus californianus) using nested conventional polymerase chain reaction (nPCR). The bacteriome of assessed NPMs was dominated by Mycoplasmataceae and Vibrionaceae, but at least 16 organisms with pathogenic potential were detected as well. Importantly, S. phocae was detected in 37% of NPM by nPCR and was also detected by 16S profiling. Detection of multiple organisms with pathogenic potential in or on NPMs suggests they may act as mechanical vectors of bacterial infection for marine mammals.

Genetics and pathology associated with Klebsiella pneumoniae and Klebsiella spp. isolates from North American Pacific coastal marine mammals.

Southern sea otters (SSO: Enhydra lutris nereis) are a federally-listed threatened subspecies found almost exclusively in California, USA. Despite their zoonotic potential and lack of host specificity, K. pneumoniae and Klebsiella spp. have largely unknown epizootiology in SSOs. Klebsiella pneumoniae is occasionally isolated at necropsy, but not from live SSOs. Hypermucoviscous (HMV) K. pneumoniae strains are confirmed pathogens of Pacific Basin pinnipeds, but have not been previously isolated from SSOs. We characterized the virulence profiles of K. pneumoniae isolates from necropsied SSOs, evaluated killing of marine mammal K. pneumoniae following in vitro exposure to California sea lion (CSL: Zalophanus californianus) whole blood and serum, and characterized lesion patterns associated with Klebsiella spp. infection in SSOs. Four of 15 SSO K. pneumoniae isolates were HMV and all were recovered from SSOs that stranded during 2005. Many K. pneumoniae infections were associated with moderate to severe pathology as a cause of death or sequela. All HMV infections were assessed as a primary cause of death or as a direct result of the primary cause of death. Klebsiella-infected SSOs exhibited bronchopneumonia, tracheobronchitis and/or pleuritis, enteritis, Profilicollis sp. acanthocephalan peritonitis, septic peritonitis, and septicemia. All SSO HMV isolates were capsular type K2, the serotype most associated with HMV infections in CSLs. Multiplex PCR revealed two distinct virulence gene profiles within HMV isolates and two within non-HMV isolates. In vitro experiments investigating CSL whole blood and serum killing of K. pneumoniae suggest that HMV isolates are more resistant to serum killing than non-HMV isolates.

Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.).

Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories, yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here, we analyse the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located within the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression, and hybridization) using nuDNA and mtDNA data analysed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (structure), bidirectional estimates of gene flow (migrate-n and IMa2) and phylogeny-based methods (*beast, bucky) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.

A single nucleotide polymorphism assay for the identification of unisexual Ambystoma salamanders.

Unisexual (all female) salamanders in the genus Ambystoma are animals of variable ploidy (2N-5N) that reproduce via a unique system of 'leaky' gynogenesis. As a result, these salamanders have a diverse array of nuclear genome combinations from up to five sexual species: the blue-spotted (A. laterale), Jefferson (A. jeffersonianum), smallmouth (A. texanum), tiger (A. tigrinum) and streamside (A. barbouri) salamanders. Identifying the genome complement, or biotype, is a critical first step in addressing a broad range of ecological and evolutionary questions about these salamanders. Previous work relied upon genome-related differences in allele size distributions for specific microsatellite loci, but overlap in these distributions among different genomes makes definitive identification and ploidy determination in unisexuals difficult or impossible. Here, we develop the first single nucleotide polymorphism assay for the identification of unisexual biotypes, based on species-specific nucleotide polymorphisms in noncoding DNA loci. Tests with simulated and natural unisexual DNA samples show that this method can accurately identify genome complement and estimate ploidy, making this a valuable tool for assessing the genome composition of unisexual samples.

Efficacy of land-cover models in predicting isolation of marbled salamander populations in a fragmented landscape.

Amphibians worldwide are facing rapid declines due to habitat loss and fragmentation, disease, and other causes. Where habitat alteration is implicated, there is a need for spatially explicit conservation plans. Models built with geographic information systems (GIS) are frequently used to inform such planning. We explored the potential for using GIS models of functional landscape connectivity as a reliable proxy for genetically derived measures of population isolation. We used genetic assignment tests to characterize isolation of marbled salamander populations and evaluated whether the relative amount of modified habitat around breeding ponds was a reliable indicator of population isolation. Using a resampling analysis, we determined whether certain land-cover variables consistently described population isolation. We randomly drew half the data for model building and tested the performance of the best models on the other half 100 times. Deciduous forest was consistently associated with lower levels of population isolation, whereas salamander populations in regions of agriculture and anthropogenic development were more isolated. Models that included these variables and pond size explained 65-70% of variation in genetically inferred isolation across sites. The resampling analysis confirmed that these habitat variables were consistently good predictors of isolation. Used judiciously, simple GIS models with key land-cover variables can be used to estimate population isolation if field sampling and genetic analysis are not possible.