SEALNET: Facial recognition software for ecological studies of harbor seals

Methods for long-term monitoring of coastal species such as harbor seals, are often costly, time-consuming, and highly invasive, underscoring the need for improved techniques for data collection and analysis. Here, we propose the use of automated facial recognition technology for identification of individual seals and demonstrate its utility in ecological and population studies. We created a software package, SealNet, that automates photo identification of seals, using a graphical user interface (GUI) software to identify, align and chip seal faces from photographs and a deep convolutional neural network (CNN) suitable for small datasets (e.g., 100 seals with five photos per seal). We piloted the SealNet technology with a population of harbor seals located within Casco Bay on the coast of Maine, USA. Across two-years of sampling, 2019 and 2020, at seven haul-out sites in Middle Bay, we processed 1529 images representing 408 individual seals and achieved 88% (93%) rank-1 accuracy in closed set (open set) seal identification. We identified four seals that were photographed in both years at neighboring haul-out sites, suggesting that some harbor seals exhibit site fidelity within local bays across years, and that there may be evidence of spatial connectivity among haul-out sites. Using capture-mark-recapture (CMR) calculations, we obtained a rough preliminary population estimate of 4386 seals in the Middle Bay area. SealNet software outperformed a similar face recognition method developed for primates, PrimNet, in identifying seals following training on our seal dataset. The ease and wealth of image data that can be processed using SealNet software contributes a vital tool for ecological and behavioral studies of marine mammals in the emerging field of conservation technology.

Can harbor seals (Phoca vitulina) discriminate familiar conspecific calls after long periods of separation?

The ability to discriminate between familiar and unfamiliar calls may play a key role in pinnipeds’ communication and survival, as in the case of mother-pup interactions. Vocal discrimination abilities have been suggested to be more developed in pinniped species with the highest selective pressure such as the otariids; yet, in some group-living phocids, such as harbor seals (Phoca vitulina), mothers are also able to recognize their pup’s voice. Conspecifics’ vocal recognition in pups has never been investigated; however, the repeated interaction occurring between pups within the breeding season suggests that long-term vocal discrimination may occur. Here we explored this hypothesis by presenting three rehabilitated seal pups with playbacks of vocalizations from unfamiliar or familiar pups. It is uncommon for seals to come into rehabilitation for a second time in their lifespan, and this study took advantage of these rare cases. A simple visual inspection of the data plots seemed to show more reactions, and of longer duration, in response to familiar as compared to unfamiliar playbacks in two out of three pups. However, statistical analyses revealed no significant difference between the experimental conditions. We also found no significant asymmetry in orientation (left vs. right) towards familiar and unfamiliar sounds. While statistics do not support the hypothesis of an established ability to discriminate familiar vocalizations from unfamiliar ones in harbor seal pups, further investigations with a larger sample size are needed to confirm or refute this hypothesis.

If You Give a Clam an Estuary: The Story of Potamocorbula

When you look at San Francisco Bay, what animals do you see? You may see lots of fish, birds, harbor seals, and sea lions. What you do not see is a little clam (Potamocorbula amurensis) that changed the Bay. Many years ago, ships accidentally brought this clam into the Bay from Asia. Soon, they spread out all over in large numbers. Clams pump water through their gills and eat small particles of food that are in the water, like phytoplankton (microscopic aquatic plants) and other microscopic critters. Potamocorbula can pump water faster than other clams, and they can eat more than their share of phytoplankton. Sometimes, Potamocorbula eats phytoplankton faster than phytoplankton can grow! What problems does that cause for other animals that also eat phytoplankton? Does Potamocorbula’s invasion only have negative impacts? In this article, we dive to the bottom of the Bay to find some answers.

A Novel Orthoreovirus Isolated From Dead Stranded Harbor Seals From Puget Sound, Washington State, United States

As part of an ongoing investigation of harbor seal (Phoca vitulina) mortalities within Puget Sound, Washington State, United States, between October 2007 and July 2008, 25 seal cases were submitted for histopathology and ancillary diagnostic testing, including additional attempted virus isolation. In vitro granular and refractile cytopathic effects (CPE) were consistently observed in Vero.DogSLAMtag cells inoculated with tissue homogenates from three seals. Transmission electron microscopy of infected Vero.DogSLAMtag cells revealed cytoplasmic clusters of icosahedral viral particles morphologically consistent with members of the family Reoviridae. The complete genome of a novel species within the genus Orthoreovirus, tentatively named phocid orthoreovirus 1 (PhRV1), was determined by next-generation sequencing and confirmed by rt-PCR in isolates from the three harbor seals. This is the first report of an orthoreovirus infection associated with dead stranded harbor seals. Aside from the CPE and ultrastructural findings, no consistent signalment, gross pathology, histopathology, or ancillary diagnostic findings were identified with PhRV1 infection. Further research is needed to determine the prevalence, tissue tropism, transmission, pathogenicity, zoonotic potential, and host range of orthoreoviruses in pinnipeds. This study demonstrates the value of thorough necropsy investigations and a multidisciplinary team approach to advance our understanding of marine mammal health.