Fur Seals Research Articles

Habitat selection and influence on hunting success in female Australian fur seals

Determining the factors influencing habitat selection and hunting success in top predators is crucial for understanding how these species may respond to environmental changes. For marine top predators, such factors have been documented in pelagic foragers, with habitat use and hunting success being linked to chlorophyll-a concentrations, sea surface temperature and light conditions. In contrast, little is known about the determinants of benthic marine predators. The Australian fur seal (Arctocephalus pusillus doriferus) is a benthic-diving forager that has a breeding and foraging distribution largely restricted to Bass Strait, the shallow (max. depth 80 m) continental shelf region between the Australian mainland and Tasmania. The species forages mostly on benthic prey and represents the greatest resident marine predator biomass in south-eastern Australia. The region is also one of the world’s fastest-warming marine areas and oceanographic changes are influencing shifts in prey distribution and abundance. In the present study, GPS-derived locations of benthic dives (n = 288,449) and dive behaviour metrics were used to determine seafloor habitat selection and factors influencing hunting success in 113 lactating adult females from Kanowna Island during the winters of 2006–2021. Individuals non-randomly selected foraging habitats comprised of deeper, steeper sloped, muddy-sandy areas with less gravel and highly disturbed regions (P < 0.01). Hunting success was greatest in shallower rocky reefs (< 30 m) and deep areas (> 40 m) characterised by moderate presence of gravel (25–50%) and substantial rock composition (50–75%) on the seabed. These findings suggest that habitat use and hunting success in adult female Australian fur seals could be impacted by predicted oceanographic changes, such as rising temperature, altered currents and waves which may modify seafloor characteristics and benthic communities.

Northern Fur Seal Whisker Bioaccumulation and Partitioning of Polybrominated Diphenyl Ethers and Organochlorines

Northern Fur Seal Whisker Bioaccumulation and Partitioning of Polybrominated Diphenyl Ethers and Organochlorines

Surveillance for Toxoplasma gondii, Brucella spp., and Chlamydia spp. in Australian Fur Seal (Arctocephalus pusillus doriferus) Abortions.

The intracellular pathogens Toxoplasma gondii, Brucella spp., and Chlamydia spp. are all known causative agents of abortion in wildlife. Both T. gondii and Brucella spp. have been identified in marine mammal abortions and a limited number of studies have detected their potential presence in Australian fur seals (Arctocephalus pusillus doriferus), but data are sparse for these pathogens in Australian fur seal breeding colonies. Australian fur seals have been shown to have a high degree of third-trimester pregnancy loss in one of their largest breeding colonies. Additionally, pup production has declined at the largest breeding colony for the species. This study surveyed the presence of T. gondii, Brucella spp., and Chlamydia spp. as potential infectious causes of this reproductive loss. Aborted fetuses were collected from two of the largest breeding colonies for the species, Seal Rocks (n=19) and Kanowna Island (n=34). These were examined grossly and through histopathological evaluation, in conjunction with molecular testing for all three pathogens. Placentas were collected from full-term births during the pupping season from Kanowna Island (n=118). These were used to compare the molecular prevalence of the three pathogens in presumed successful pregnancies. Chlamydia spp. was not detected in aborted fetuses in this study. Brucella spp. was detected with PCR in both aborted fetuses (9.4%) and placentas from full-term births (3.4%), and T. gondii was detected using routine histopathology (n=2/53), immunohistochemistry (n=3/4), and PCR (n=4/53) in tissues from aborted fetuses. Toxoplasma gondii was present in 7.5% of third-trimester abortions and absent from all full-term placentas. Brucella spp. was detected in both aborted fetuses and full-term placentas. This is the first description of vertical transmission of T. gondii in a marine mammal from the southern hemisphere.

A case study of highly pathogenic avian influenza (HPAI) H5N1 at Bird Island, South Georgia: the first documented outbreak in the subantarctic region

ABSTRACT Capsule HPAI H5N1 was documented for the first time in the subantarctic region on Bird Island, South Georgia, resulting in the mortality of Brown Skuas Stercorarius antarcticus, Gentoo Penguins Pygoscelis papua, Snowy Albatrosses Diomedea exulans, and Antarctic Fur Seals Arctocephalus gazella. Aims The spread of the HPAI H5N1 subtype has had dramatic impacts on numerous populations of wild birds and mammals. We describe a case study that can inform the management of HPAI for conservation practitioners and researchers globally. Methods We documented the detection, monitoring, and impact of the first known outbreak of H5N1 HPAI in the subantarctic region, at Bird Island in South Georgia (−54.3582, −36.5112) during 2023–2024. Deaths from HPAI were first suspected in September 2023 and later confirmed by genetic analysis. Results In total, 77 Brown Skuas, 38 Gentoo penguins, and 58 Snowy Albatrosses were suspected to have died from HPAI infection, and HPAI was confirmed in 5 dead Antarctic Fur Seals. Total mortality was unknown for all species, as other individuals will have been scavenged before discovery, or died at sea. Conclusion This case study provides lessons for the management, risk, safety considerations, and ethical decisions regarding animal welfare that may help guide research and management responses to HPAI outbreaks elsewhere, particularly in remote areas or in species of conservation concern.

Host genetic diversity and body condition influence parasite resistance and clearance in a wild marine mammal population.

Host genetic variability can modulate infection resistance, although its role in infection clearance remains unclear. Hookworm disease (Uncinaria sp.) is the leading cause of pup mortality in several otariid species, although the parasite can be cleared through immune-mediated processes. We evaluated the association of host genetic diversity, body condition and immune response with hookworm resistance and/or clearance in the South American fur seal (Arctocephalus australis). Uninfected pups had higher heterozygosity than parasitized individuals, indicating a negative relationship between heterozygosity and the chances of infection. Likewise, pups that died of hookworm infection had lower heterozygosity than those that died of non-infectious causes. Interestingly, once infected, pups that survived hookworm infection had heterozygosities similar to pups that died of hookworm disease. However, pups that cleared the infection had a higher body mass and parasite-specific immunoglobulin G levels than those that did not recover or died of hookworm disease. Thus, although heterozygosity predicted resistance to and mortality from hookworm infections, it did not affect parasite clearance, which was facilitated by better body condition and adaptive immune responses. This demonstrates that host genetic variability and host-environment interactions influence disease dynamics, acting at different, well-defined stages of infection.

Prevalence and source of entanglements in Cape fur seals (Arctocephalus pusillus pusillus) in South Africa

Global pollution is increasing, and marine mammals are commonly affected by marine debris. This study combined data from multiple sources to help understand the prevalence, characteristics and demographic profile of Cape fur seals (Arctocephalus pusillus pusillus) entangled in anthropogenic items. Overall, 383 cases of entanglement in seals were identified with a regional prevalence for South Africa of 0.12 %, i.e., just over one in every thousand animals. Fishing materials were the primary cause of entanglements (70 %), with most entanglements observed on adults (n = 249, 65 %), particularly adult females (n = 95, 66 % of all sex-determined entangled seals). This study highlights the need for correct disposal of waste, particularly that derived from the fishing industry to mitigate the impact of marine pollution on the welfare and conservation of marine fauna in South Africa.

Behavioural response of Australian fur seals (Arctocephalus pusillus doriferus) to vessel noise during peak and off-peak human visitation

Vessel traffic is the greatest contributor to marine anthropogenic noise pollution, and particularly affects species utilising coastal areas. Seal Rocks (Victoria), the largest Australian fur seal breeding colony, has a relatively small vessel exclusion zone during the pupping and breeding season, when vessel traffic is at its peak. It is necessary to understand the impacts of visitation at sensitive marine sites to ensure they are adequately protected from human disturbance. This study assessed the behavioural response of hauled-out Australian fur seals at Seal Rocks to controlled vessel noise exposure during peak and off-peak vessel visitation periods. High level noise exposure (76–80 dB) resulted in increased vigilance and interruption to vital behaviours in both peak and off-peak periods. These behavioural responses were limited to the period of noise exposure but are nevertheless indicative of disturbance. It is important to ensure regulations intended to protect sensitive sites are up-to-date and evidence based.

Faecal source apportionment using molecular methods: A proof of concept using the FEAST algorithm

Faecal contamination of freshwater and marine environments represents a significant risk for public health, recreational activity and food safety, and tools for evaluating complex multi-source contamination remain largely in the development phase. We evaluated the efficacy of the Fast Expectation Maximization (FEAST) microbial source tracking (MST) algorithm to apportion sources of faecal contamination among four mammalian species of interest in coastal waters in New Zealand. Using 16S ribosomal DNA metabarcoding of faecal samples from cows, fur seals, and sheep, as well as human wastewater, we aimed to differentiate and quantify the contribution of these sources in mixed faecal samples. Multivariate analysis confirmed significant differences in the microbial communities associated with each mammalian source, with specific bacterial classes indicative of different sources. The FEAST algorithm was tested using mixed DNA and mixed faecal samples, and we found that the algorithm correctly assigned the dominant source from all samples, but underestimated the dominant source's proportional contribution. This underestimation suggests the need for further refinement and validation to ensure accurate source apportionment in environmental samples where the faecal signal is likely to be a minor component. Despite these limitations, the findings of our study, in combination with the evidence from others who have tested the FEAST algorithm in environmental settings, indicates that it represents an advance on existing tools for microbial source tracking and may become a useful addition to the toolbox for environmental management.

Unveiling mercury levels: Trophic habits influence on bioaccumulation in two Otariid species

Mercury, a toxic metal released by various human activities, exerts environmental stress through its bioaccumulation and biomagnification, particularly in marine habitats. South American fur seals (Arctocephalus australis) and sea lions (Otaria flavescens) reproduce on the Atlantic coast of Uruguay. As top predators, they can accumulate toxic levels of mercury and are often used as sentinel species for monitoring ecosystem health. Fur seals prey on pelagic species, such as fish and squid, while sea lions consume coastal-benthic prey. We analyzed the total mercury concentration (THg) in hair and the trophic habits (δ13C and δ15N) of females from both species. The average THg concentration in adult female sea lions (30.5 ± 9.3 μg/g dry weight) was significantly higher than in fur seals (6.3 ± 2.5 μg/g dry weight). Additionally, the mean δ15N and δ13C values were significantly higher in sea lion (δ15N: 19.2 ± 0.6‰, δ13C: −13.8 ± 0.2‰) compared to fur seals (δ15N: 16.5 ± 0.5‰, δ13C: −15.5 ± 0.6‰). Our results suggest that different trophic levels and feedings areas affect the THg concentration in Uruguayan Otariids. Notably, at the intraspecific level, the THg concentration in sea lions increased with δ13C values, suggesting a link to coastal feeding habits. This indicates that coastal feeding behaviors, compared to feeding in pelagic environments, enhance mercury bioaccumulation in Otariids along the Uruguayan coast, with the discharge of freshwater from the Río de la Plata (one of the largest estuaries in South America) basin identified as a potential mercury source. THg concentrations found in female sea lion hair are the highest reported in Otariids globally. Mercury levels exceeded toxic thresholds observed in other mammals and could pose significant health risks. Our findings may explain why sea lions were particularly affected by the avian influenza outbreak in Uruguay compared to fur seals. Monitoring the declining sea lion population is crucial, making our results significant for integrated conservation and management strategies.

Traversing the land-sea interface: A climate change risk assessment of terrestrially breeding marine predators.

Terrestrially breeding marine predators have experienced shifts in species distribution, prey availability, breeding phenology, and population dynamics due to climate change worldwide. These central-place foragers are restricted within proximity of their breeding colonies during the breeding season, making them highly susceptible to any changes in both marine and terrestrial environments. While ecologists have developed risk assessments to evaluate climate risk in various contexts, these often overlook critical breeding biology data. To address this knowledge gap, we developed a trait-based risk assessment framework, focusing on the breeding season and applying it to marine predators breeding in parts of Australian territory and Antarctica. Our objectives were to quantify climate change risk, identify specific threats, and establish an adaptable assessment framework. The assessment considered 25 criteria related to three risk components: vulnerability, exposure, and hazard, while accounting for uncertainty. We employed a scoring system that integrated a systematic literature review and expert elicitation for the hazard criteria. Monte Carlo sensitivity analysis was conducted to identify key factors contributing to overall risk. We identified shy albatross (Thalassarche cauta), southern rockhopper penguins (Eudyptes chrysocome), Australian fur seals (Arctocephalus pusillus doriferus), and Australian sea lions (Neophoca cinerea) with high climate urgency. Species breeding in lower latitudes, as well as certain eared seal, albatross, and penguin species, were particularly at risk. Hazard and exposure explained the most variation in relative risk, outweighing vulnerability. Key climate hazards affecting most species include extreme weather events, changes in habitat suitability, and prey availability. We emphasise the need for further research, focusing on at-risk species, and filling knowledge gaps (less-studied hazards, and/or species) to provide a more accurate and robust climate change risk assessment. Our findings offer valuable insights for conservation efforts, given that monitoring and implementing climate adaptation strategies for land-dependent marine predators is more feasible during their breeding season.

Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness.

The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome ("arcGaz3") shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome ("arcGaz4_h1"). The new assembly is 2.53Gb long, has a scaffold N50 of 55.6Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs (BUSCO) score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of eleven pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling (GERP). We then implemented Gene Ontology (GO) enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the two major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome.

Coastal connectivity of marine predators over the Patagonian Shelf during the highly pathogenic avian influenza outbreak

Animal movement and population connectivity are key areas of uncertainty in efforts to understand and predict the spread of infectious disease. The emergence of highly pathogenic avian influenza (HPAI) in South America poses a significant threat to globally significant populations of colonial breeding marine predators in the South Atlantic. Yet, there is a poor understanding of which species or migratory pathways may facilitate disease spread. Compiling one of the largest available animal tracking datasets in the South Atlantic, we examine connectivity and inter‐population mixing for colonial breeding marine predators tagged at the Falkland Islands. We reveal extensive connectivity for three regionally dominant and gregarious species over the Patagonian Shelf. Black‐browed albatrosses (BBA), South American fur seals (SAFS) and Magellanic penguins (MAG) used coastal waters along the Atlantic coast of South America (Argentina and Uruguay). These behaviours were recorded at or in close proximity to breeding colonies and haul‐out areas with dense aggregations of marine predators. Transit times to and from the Falkland Islands to the continental coast ranged from 0.2–70 days, with 84% of animals making this transit within 4 days ‐ a conservative estimate for HPAI infectious period. Our findings demonstrate BBA, SAFS and MAG connectivity between the Falkland Islands and mainland South America over an expansive spatial network and numerous pathways, which has implications for infectious disease persistence, transmission and spread. This information is vital in supporting HPAI disease surveillance, risk assessment and marine management efforts across the region.

Subnational governments and non-state actors in environmental governance: Japan, Russia, and the Northern fur seal

Russia's invasion of Ukraine in 2022 put to test the North Pacific regional governance structure, with environmental cooperation overshadowed by security concerns. In this paper, the central government, subnational and non-state actors' potential in finding ways out of environmental governance crises is explored. The authors turn for possible clues to the Northern fur seal conservation and management regimes, which existed in 1911–40 and 1957–84 and laid the groundwork for marine wildlife conservation and management in the North Pacific, in the century replete with military conflicts and international tension. The focus is on Japan and Russia's subnational and non-state actors (private companies, experts, NGOs and indigenous communities), who have received much less attention than their US and Canadian counterparts. Their roles in negotiation, operation and dismantlement of these regimes, are analyzed in domestic and international contexts by applying Putnam's “two-level game” metaphor. Their motives and tactics, interconnections and clout are examined in the light of both states' domestic and foreign policy goals and constraints, and regional and global trends in environmental governance. The recent multi-actor undertakings for marine mammal conservation and management in Japan and Russia are also explored from the multilevel governance perspective. It is hoped that the current diplomatic deadlock may be overcome by utilizing sub-state and supra-state frameworks and channels for communication.

ECR Spotlight – Mathilde Martin

ECR Spotlight is a series of interviews with early-career authors from a selection of papers published in Journal of Experimental Biology and aims to promote not only the diversity of early-career researchers (ECRs) working in experimental biology but also the huge variety of animals and physiological systems that are essential for the ‘comparative’ approach. Mathilde Martin is an author on ‘ Use of acoustic signals in Cape fur seal mother–pup reunions: individual signature, signal propagation and pup home range’, published in JEB. Mathilde conducted the research described in this article while a PhD student in Dr Isabelle Charrier's lab at the Institute of Neurosciences Paris-Saclay (NeuroPSI), CNRS &amp; Paris-Saclay University, France. She is now a postdoctoral researcher in the lab of Prof. Marta Manser at the University of Zurich, Switzerland, investigating acoustic communication to decipher how vocal signals modulate social interactions in group-living mammals, in relation to the species' ecological constraints.

Use of acoustic signals in Cape fur seal mother-pup reunions: individual signature, signal propagation and pup home range.

The Cape fur seal (Arctocephalus pusillus pusillus) is one of the most colonial mammals, with colonies of up to hundreds of thousands of individuals during the breeding season. During the lactation period, mothers and pups are regularly separated as females undertake multi-day foraging trips at sea. Mothers and pups use a mutual vocal recognition system to reunite after separation. Such communication is highly constrained by both high background noise and risk of individual confusion owing to the density of seals. This study aimed to experimentally assess the acoustic features relevant for mother-pup vocal identification and the propagation properties of their calls. Playback experiments revealed that mother and pup individual vocal signatures rely on both temporal and frequency parameters: amplitude and frequency modulations, timbre and fundamental frequency (f0). This is more parameters than in any colonial species studied so far. The combinational use of acoustic features reinforces the concept that both environmental and social constraints may have acted as selective pressures on the individual vocal recognition systems. Theoretical propagation distances of mother and pup vocalisations were estimated to be below the range of distances at which mother-pup reunions can occur. This suggests that Cape fur seals may have strong abilities to extract vocal signals from the background noise, as previously demonstrated in the highly colonial king penguin. Investigating the transmission of information throughout the propagation of the signal as well as the ability of the receiving individual to decipher vocal signatures is crucial to understanding vocal recognition systems in the wild.

Life-history stage influences immune investment and oxidative stress in response to environmental heterogeneity in Antarctic fur seals

Immune defenses are crucial for survival but costly to develop and maintain. Increased immune investment is therefore hypothesized to trade-off with other life-history traits. Here, we examined innate and adaptive immune responses to environmental heterogeneity in wild Antarctic fur seals. In a fully crossed, repeated measures design, we sampled 100 pups and their mothers from colonies of contrasting density during seasons of contrasting food availability. Biometric and cortisol data as well as blood for the analysis of 13 immune and oxidative status markers were collected at two key life-history stages. We show that immune responses of pups are more responsive than adults to variation in food availability, but not population density, and are modulated by cortisol and condition. Immune investment is associated with different oxidative status markers in pups and mothers. Our results suggest that early life stages show greater sensitivity to extrinsic and intrinsic effectors, and that immunity may be a strong target for natural selection even in low-pathogen environments such as Antarctica.

Sea-ice and macrozooplankton distribution as determinants of top predator community structure in Antarctic winter

The Antarctic Peninsula marine ecosystem is highly productive, with large populations of commercially and ecologically important species including Antarctic krill Euphausia superba, Adélie penguins Pygoscelis adeliae, and crabeater seals Lobodon carcinophagus. The ecology of the peninsula is rapidly changing due to accelerating climate change and fishing pressure. Systematic ecosystem surveys have focused on austral spring and summer, leaving an information gap on winter ecosystem dynamics. Using data from 5 consecutive ecosystem surveys, we quantified the composition and distribution of winter predator communities and investigated the physical and biological influences on community structure. Seabirds and marine mammals clustered into 3 communities: an ice-associated community represented by Adélie penguins and crabeater seals; a diverse marginal ice zone community dominated by fur seals and several species of seabirds including 3 petrels, kelp gulls Larus dominicanus, and Antarctic terns Sterna vittata; and an open water community consisting of southern fulmars Fulmarus glacialoides and 4 species of petrels. These communities were distributed along an environmental gradient ranging from ice-covered, cold, saline water to ice-free, warmer, and fresher water with greater chlorophyll concentrations. Predator communities were also associated with different communities of macrozooplankton: ice-associated predators with an extremely diverse assemblage of typically mesopelagic zooplankton; marginal ice zone predators with a community of large-bodied euphausiids (E. superba, E. crystallorophias); and open water predators with a community of small-bodied euphausiids (Thysanoessa macrura). Our synthesis of integrated winter predator and macrozooplankton communities relative to sea-ice concentration provides reference points for future ecosystem assessments within this rapidly changing region.

Bacterial septicemia and herpesvirus infection in Antarctic fur seals (Arctocephalus gazella) stranded in the São Paulo coast, Brazil

In August 2021, two juvenile male Antarctic fur seals (Arctocephalus gazella) stranded in the southeastern Brazilian coast and were referred to rehabilitation centers. The animals presented increased body temperature, prostration, respiratory distress and despite treatment died. A necropsy following a standardized protocol was performed, and formalin-fixed tissues were processed for microscopic examination. Samples were screened for morbillivirus, herpesvirus, and Brucella spp. by molecular analyses (PCR, RT-PCR). Bacteriological culture was performed in samples collected from the lungs, trachea, and lymph nodes of both cases. The main histopathologic findings were of infectious nature, including multifocal necrotizing and fibrinous mixed interstitial pneumonia, bronchiolitis, and bronchitis, with intralesional myriad bacteria associated with vascular fibrinoid necrosis. Pseudomonas aeruginosa was isolated from tracheal and lung swabs of Case 1, and Klebsiella oxytoca was found in nostril swabs, tracheobronchial lymph nodes, and lung of Case 2. Gammaherpesvirus infection was detected in both cases, and the sequences retrieved were classified into the genus Percavirus. All tested samples were PCR-negative for Brucella spp. and morbillivirus. We hypothesize that the deficient immunological status in association with starvation predisposed the reactivation of herpesvirus and secondary bacterial co-infections. To the authors’ knowledge, this is the first molecular detection of herpesvirus in an Antarctic pinniped. These findings reinforce that Otariid gammaherpesvirus circulating in the Southern Hemisphere are likely endemic in the Arctocephalus genus. This report contributes to the current knowledge of health aspects affecting wild pinnipeds, especially in the poorly studied Antarctic species.

Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups

Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability. We investigated inbreeding effects in a declining population of Antarctic fur seals (Arctocephalus gazella) at Bird Island, South Georgia. Here, localised warming has reduced the availability of the seal’s staple diet, Antarctic krill, leading to a temporal increase in the strength of selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population. However, it remains unclear whether selection operates before or after nutritional independence at weaning. We therefore used microsatellite data from 885 pups and their mothers, and SNP array data from 98 mother–offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth. We did not find any clear or consistent effects of offspring or maternal inbreeding on any of these traits. This suggests that selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment. Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.

Unraveling the gut microbiota of Mexican pinnipeds: the dominance of life histories over phylogeny.

Studying how phylogeny influences the composition and functions of microbiotas within animal hosts is essential for gaining insights into the connection between genetics, ecology, and health in the animal kingdom. However, due to limited comprehensive studies, this influence remains unclear for many wild mammals, including Mexican pinnipeds. We employed 16S rRNA gene deep-sequencing to investigate the impact of phylogeny on the gut microbiota of four pinniped species inhabiting Mexican shores: the Pacific harbor seal (Phoca vitulina richardii), the northern elephant seal (Mirounga angustirostris), the California sea lion (Zalophus californianus), and the Guadalupe fur seal (Arctocephalus philippii townsendi). Our results indicated that factors such as diets and shared life histories exerted more influence on microbiota composition than phylogeny alone. Notably, otariid species sharing similar life histories displayed greater microbiota similarity than phocids, which have distinct life histories and fewer microbiota similarities. Furthermore, harbor seals have more microbial similarities with the two otariid species than with elephant seals. Of particular concern, we observed a higher abundance of potentially pathogenic bacteria (e.g., Photobacterium damselae and Clostridium perfringens) in harbor seals and Guadalupe fur seals compared to other pinnipeds. This finding could pose health threats to these species and nearby human populations.IMPORTANCEPinnipeds in Mexico host microbial communities that remain understudied. While several factors can influence microbiota composition, the role of phylogenetic relationships among these pinnipeds remains unclear due to limited knowledge of the microbiota in certain species. This study aimed to fill this gap by characterizing the composition and function of the gut microbiota in the four pinniped species that occur in Mexico. Our analysis reveals that shared diets and life histories contribute to similarities in the composition of gut microbial communities. This study also highlights the potential differences in the metabolic capabilities and adaptations within the gut microbiota of pinnipeds. Understanding how phylogeny impacts microbial communities enhances our insights into the evolutionary dynamics of marine mammals.