Fishery bycatch is broadly defined as the incidental capture or discard of any living marine organism, including unobserved mortality, due to direct encounters with fishing vessels and gear (NMFS, 2016a). Bycatch of seals has been documented in several Northeastern US commercial fisheries where bycatch events can provide temporal and spatial context for analysis of seal distribution (Chavez-Rosales et al., 2018; Hayes et al., 2021; Precoda and Orphanides, 2022). Time and space are important factors in evaluating the diet of seals because of their life history where foraging patterns are largely dictated by the timing and location of reproduction and movements of their prey (Beck et al., 2007; Russell et al., 2015; Scharff-Olsen et al., 2018).

The western North Atlantic gray and harbor seal populations extend from eastern Canada to the mid-Atlantic US. Due to the semi-aquatic and wide-ranging movements of harbor (Phoca vitulina vitulina) and gray seals (Halichoerus grypus atlantica), utilizing dead specimens retained opportunistically from fishery bycatch events is a valuable resource because they provide rare insight to marine mammal trophic ecology that is otherwise difficult to obtain (Craddock et al., 2009; Wenzel et al., 2013; Orphanides et al., 2020). Williams (1999) and Ampela (2009) presented the first accounts of Northwest Atlantic harbor and gray seal diet utilizing stomach sample hard part remains obtained from Northeastern US incidental bycatch events (1991–2008). Our research will expand the time series by building off later research completed by Wenzel et al. (2015, 2017) including additional sampling from bycatch collected through 2018.

Cape Cod, coastal Maine, and nearby islands are home to several harbor and gray seal breeding colonies. These regions are adjacent to some of the most productive fishing grounds in the Northeastern US (NEFSC, 2023). Consequently, the resurgence of these transboundary seal populations has led to perceived competition for economically valuable prey between commercial fishermen and seals (Guerra, 2019; Behnke, 2021). While gray seals are exhibiting exponential rates of growth, there is increasing evidence of interspecific competition with gray seals outcompeting harbor seals for mutually desirable habitat and prey resources (Pace et al., 2019; Hayes et al., 2021; Wood et al., 2022). This could be contributing to an apparent decline or slowed growth of the Northwest Atlantic harbor seal population (Bowen et al., 2003; Johnston et al., 2015; Russell et al., 2015; Ampela et al., 2018; Jones et al., 2018; Pace et al., 2019; Wilson and Hammond, 2019; Hayes et al., 2021; Sigourney et al., 2022). Improving our understanding of forage diversity and consumption supporting the population growth of Northwest Atlantic harbor and gray seals is necessary to evaluate the magnitude of competition for both managed and protected resources in the Northeastern US region (Kusnierz et al., 2014; Hui et al., 2015; Swain and Benoît, 2015; Chasco et al., 2017). It is also necessary to improve our knowledge on key predator–prey linkages fundamental to the development of ecosystem-based fisheries management plans (Yodzis, 2001; Plaganyi and Butterworth, 2009; Fogarty, 2013; Free et al., 2021).

The success of the US Marine Mammal Protection Act of 1972 as amended (MMPA) has created a new set of challenges for natural resource managers (Gazit et al., 2013; Roman et al., 2013; Ferretti et al., 2015; Marshall et al., 2015; Jackman et al., 2018; Cammen et al., 2019; Guerra, 2019). Since the implementation of the MMPA, the US Northwest Atlantic harbor and gray seal populations have been recovering from near extirpation status. These species were considered extirpated from New England waters in the 1960s due to bounty hunting and overharvesting from legal hunting practices in coastal New England and Canadian provinces (Lelli et al., 2009). With the moratorium on the hunting of seals implemented under the MMPA, the recolonization of harbor and gray seals has been documented on several coastal beaches and islands throughout the Northeastern US and Canadian maritime region (Gilbert et al., 2005; Pace et al., 2019; den Heyer et al., 2020; Wood et al., 2020; Hayes et al., 2021; Sigourney et al., 2022).

The recovery of seals in Northeastern US waters has led to unintended negative interactions with stakeholder groups that range from landowners concerned about perceived impact on water quality around seal haul-out/pupping sites and beachgoers heightened awareness of sharks foraging in waters in search of seal prey adjacent to popular tourist beaches (Skomal et al., 2012; Bass et al., 2016; Jackman et al., 2018). Northwest Atlantic gray seal bycatch was over 2,000 individuals in 2019, the highest recent marine mammal bycatch in the US (Martins et al., 2019; Hayes et al., 2021). Increasing bycatch has also contributed to evidence of depredation due to apparent competition for resources that fishermen target for commercial and personal consumption and seals target to support their growth (Kaschner and Pauly, 2005; Konigson et al., 2009; Plaganyi and Butterworth, 2009; Rafferty et al., 2012; Gruber, 2014; Cosgrove et al., 2015; Sirak, 2015; Trull, 2015; Byron and Morgan, 2016).

The increasing interactions between recovering seal populations and fishermen are not unique to the Northeastern US. On the West Coast of the US, recovering seal populations have been blamed for impeding the recovery of protected salmon species (Chasco et al., 2017; Nelson et al., 2019). In Atlantic Canada, the Atlantic cod (Gadus morhua) has not recovered after two decades of moratorium on commercial harvest, and some of this decline has been attributed to predation by seals (Trzcinski et al., 2006; O’Boyle and Sinclair, 2012; Hammill et al., 2014; Neuenhoff et al., 2019; Rossi et al., 2021). In the Northeast Atlantic, Cook et al. (2015) stated that gray seal predation on Atlantic cod could impede recovery from overharvest by commercial fishing practices. In the Baltic Sea, researchers have documented economic losses to fishermen due to depredation and whole consumption of cod and salmon catches (Konigson et al., 2009, 2013).

The perceived increase in competition between marine mammal populations and fisheries has spurred new debate to legalize culling of seals in Northeastern US waters (Butterworth et al., 1988; Yodzis, 2001; Bowen and Lidgard, 2011; Schakner et al., 2016). However, contrasting studies suggest that changing environmental conditions and high fishing mortality outweigh the impact of natural mortality by predation from increasing higher trophic level predator populations (Kaschner and Pauly, 2005; Nye et al., 2013; Costalago et al., 2019). Furthermore, there is also evidence that marine mammal recovery has a positive impact on ecosystem health and trophic interactions potentially benefiting commercial fisheries (Trites et al., 1997; Morissette et al., 2012; Roman et al., 2013; Bass et al., 2016; Byron and Morgan, 2016). Thus, improving our understanding of the diversity and magnitude of seal prey consumption will move society further down the roadmap of an ecosystem-based approach to fisheries management (NMFS, 2016b; Gaichas et al., 2018).

Direct measurement of feeding by marine mammals in the wild is limited due to the nature of their habitat and how they interact with their environment (Boyle, 1997; Heithaus and Dill, 2009). Although pinnipeds spend a portion of their lives hauled out on land, they generally spend that time resting, mating, giving birth, and providing natal care. Consequently, scientists are mostly limited to indirect sampling approaches (e.g., hard part remains, stable isotopes, DNA, and fatty acids) to estimate the diet of marine mammals (Bowen and Iverson, 2013). There has been a growing body of literature from the Northeastern US region utilizing stable isotope and DNA techniques to infer the diet of US Northwest Atlantic gray seals. Hernandez et al. (2019a, 2019b) and Lerner et al. (2018) report the difficulty in obtaining taxonomic prey resolution using stable isotopes for a generalist predator. Ono et al. (2019) and McCosker et al. (2020) found several prey items present in Northwest Atlantic gray seal diet utilizing DNA techniques. However, obtaining estimates of prey abundance and biomass from DNA is still in the developmental stages (Deagle et al., 2018; Shelton et al., 2023). Consequently, there is uncertainty in 1) the relative magnitude of consumption and changes over time among prey types by Northwest Atlantic harbor and gray seals, 2) their interspecies prey foraging patterns, and 3) their competition with commercial fishermen for similar prey. In comparison to stable isotopes and DNA techniques, utilizing hard part remains obtained from seal scat and gastrointestinal samples provides an indirect and relatively inexpensive approach to investigate marine mammal diets. However, they are also not immune to sources of bias (e.g., digestive erosion of hard parts, poor evidence of depredation and scavenging, differential retention rates). Nonetheless, the use of hard part remains to infer the diet of marine mammals is extensively documented in the literature as providing high taxonomic resolution in conjunction with estimates of relative abundance and biomass of prey consumed. Pierce and Boyle (1991) and Bowen and Iverson (2013) provide comprehensive summaries with the pros and cons of indirect methods applied to the study of marine mammal diets.

Our primary aim with this research is to utilize stomach samples obtained opportunistically from harbor and gray seal commercial fishery bycatch events to improve our understanding of the foraging habits of Northwest Atlantic harbor and gray seals and their dietary role in the Northeastern US region ecosystems. The objectives of this study are to 1) quantify the mean length and weight, relative abundance, and biomass of prey consumed by harbor and gray seals using hard parts extracted from the stomachs of bycaught seals; 2) evaluate temporal, spatial, and seal demographic characteristics that may affect diet composition; 3) identify important prey and the magnitude of trophic niche overlap between the two seal species; and 4) compare the size distribution of prey consumed by these seals to the size of prey in commercial catches. Results from this study are expected to improve our scientific understanding of the extent of foraging and harvest competition for commercially important prey resources among these three predators: harbor seals, gray seals, and commercial fishermen.

Data available to infer marine mammal diet composition or consumption are often sparse and reflect varying degrees of temporal, spatial, and demographic resolution (Smith et al., 2015). This is true of the opportunistic samples obtained from bycatch events for this study ( Table 1 ). In most cases, there were no samples available to make 1:1 comparisons between harbor and gray seal diet that account for both intrinsic (age and sex) and extrinsic (season and region) factors ( Supplementary Table S3 ). However, these samples provide temporal and spatial contexts for analysis of the seals’ diet. The imbalance in the temporal and spatial distribution of stomach samples used in this study is explained by non-overlapping harbor and gray seal phenology and pup haul-out locations that are adjacent to high-density large mesh (>20 cm) gillnet fishing regions (Murray et al., 2021; Figure 1 ). This also explains why the majority of samples are from the pup and young-of-the-year age classes ( Table 1 ). In other words, these age classes appear in bycatch in opposite times and areas given the timing and location of their reproduction cycles. Evidence from tagged animals suggests that most weaned pups and young-of-the-year gray seals forage in Southern New England adjacent to Muskeget Island and Monomoy pupping habitats during late winter into spring and summer (Murray et al., 2021; Wood et al., 2022). On the other hand, most weaned pups and young-of-the-year harbor seals forage in the Gulf of Maine adjacent to coastal bays, ledges, and island pupping habitats in summer into fall seasons (Williams, 1999; Gilbert et al., 2005; Waring et al., 2006; Sigourney et al., 2022). Pup and young-of-the-year age classes from both seals generally overlap in the Gulf of Maine during summer and fall and less so in the southern region in winter and spring ( Figure 5 ). Given this bias toward pup and young-of-the-year age classes, it is not surprising that sex was not an important factor when contrasting patterns in diet between the two seal species (Beck et al., 2007). Both sexes are expected to have limited dive capacity and be equally naive in foraging and consequently subject to higher bycatch rates relative to older more experienced age classes (Frost et al., 2006; Murray et al., 2021).

The differences in important prey, also reflected in 55% overlap in diet, are also a function of when and where the seals show up in bycatch and mostly driven by samples from the pup and young-of-the-year age classes. This trophic niche separation is exhibited by gray seal consumption of more benthivorous prey species compared with harbor seals. The least dietary overlap in the Gulf of Maine during the summer and fall (C = 0.34) appears to be explained by harbor seals’ preference for redfish and small silver hake over sand lance, yellowtail flounder, and red hake consumed by gray seals. The most dietary overlap occurs in the southern region (C = 0.71) during winter and spring where both seals consume silver and red hake and gulf stream flounder. This is also when most of the squids are present in the harbor seal diet ( Table 3 and Figure 9 ). Pups rarely co-occur which explains low overlap in their diets (C = 0.27; Table 4 and Figure 5 ).

Consistent with Ampela (2009), diet data obtained from the stomachs of bycaught gray seals in our study paint a different picture of the relative abundance of prey in the diet when compared with data obtained from scat samples. Examples of this are shown by Ampela (2009) and Lerner et al. (2018) where a relatively high abundance of sand lance was found in gray seal scat samples obtained from sandbars off the coast of Chatham, Massachusetts. Bowen and Harrison (1994) show a similar pattern with a high proportion of sand lance found in scats collected on Sable Island, a sandy island habitat on the Scotian shelf. In contrast, sand lance relative abundance was low (<10%) in gray seal stomachs examined by Ampela (2009) and this study. We postulate that diet data obtained from Northeastern US bycatch events are more representative of offshore foraging on the continental shelf and banks away from haul-out sites, whereas diet from scats represents more nearshore foraging closer to haul-out sites (Pierce and Boyle, 1991; Ampela, 2009; Hammill et al., 2014; Johnston et al., 2015; Lerner et al., 2018; Hernandez et al., 2019a). These differences may also be confounded by the seal’s age and foraging experience (Beck et al., 2007). The majority of data in this study were obtained from young-of-the-year gray seals with limited foraging experience. Scat samples obtained off Chatham sandbars are generally obtained from mixed age groups with a likely bias toward the more numerous older gray seals. Older seals have more foraging experience and are likely more successful in capturing pelagic, fast swimming, or schooling prey. Sand lance are given their name because they burrow in the sand in shallow near-shore habitats (Robards et al., 1999; Staudinger et al., 2020). However, Bowen et al. (2002) documented mature harbor seals’ capture of sand lance both burrowed in the sand and as schooling prey in the water column. Although the sample sizes from the adult age class from our study are small, sand lance had the highest importance (iIMP) in the diet of adult gray seals (n = 7; Supplementary Table S3 and Supplementary Figure S7C ). Hammill et al. (2014) showed that sand lance also rank high in importance and mass consumed by older gray seals collected from digestive tracts obtained from the Cabot Strait and Cape Breton Island off of Canada (mean age ranged 7–12 years old). By comparison, sand lance were rarely found in the stomachs of bycaught harbor seals but historically were found in high abundance when recovered from their scats (Payne and Selzer, 1989). Ignoring all extrinsic and intrinsic factors, the occurrence of cod in gray seal diet (5.1%) is consistent with the findings in Flanders et al. (2020) where the relative contribution of cod (6.7%; resolved to the genus Gadidae spp.) to the diet of gray seals was inferred by DNA meta-barcoding techniques. This is also consistent with the findings in Canadian waters where cod was found to be important in adult gray seal diet (Bowen and Harrison, 1994; Hammill et al., 2014).

Consistent with Williams (1999) and Ampela (2009), prey sizes consumed by both seals in our study showed limited overlap with prey sizes caught by commercial gillnet fishermen. Sørlie et al. (2020) also reported evidence of harbor seal preference for smaller prey compared with the size of some species exploited by commercial fisheries off the coast of Norway and low levels of direct competition between harbor and gray seals and commercial fisheries. However, it is important to note that the majority of seals in our study were young-of-the-year animals, the age class most frequently caught as bycatch in NEUS commercial gillnet fisheries (Murray et al., 2021). It is generally understood that larger seals from the older age classes can consume larger prey. Hammill et al. (2014) showed that adult gray seals in the Cabot Straight and Cape Breton Island off of Canada on average consumed large white hake (29–35 cm) and Atlantic cod (28–39 cm). By comparison, adult gray seals in our study (albeit a small sample size, n = 7) indicate consumption of larger fish ( Supplementary Figure S8C ). Thus, it is important to consider the age distribution of the seals when utilizing results from seal diet studies to inform fish population and ecosystem dynamic models (Benoît et al., 2011).

If the dietary pattern of harbor seals is correlated to the relative abundance of prey in the ecosystems but also sensitive to gray seal population growth, this can provide insight into the resilience of US Northwest Atlantic harbor seals to gray seal recolonization in New England waters (Smout et al., 2014; Johnston et al., 2015; Russell et al., 2015; Ouellet et al., 2016; Pace et al., 2019; Murray et al., 2021). Consistent with other studies, our research shows that hake species rank at the top of the most important prey to harbor seals, similar to gray seals, regardless of sex and age class (Ampela, 2009; Hammill et al., 2014). Our study also shows that cod occurrence (16%) and abundance (2%) are three times greater in harbor seal diet compared with gray seals ( Table 2 ). The finding of the importance of cod in the diet of harbor seals is consistent with that reported by Williams (1999). The remaining most important prey unique to harbor seals—silver hake, redfish, red hake, herring, and squids—were also identified as the most important prey over 20 years ago by Williams (1999). Bowen and Harrison (1996) also identified cod, herring, and Illex squid among the most abundant prey in the diet of harbor seals in the Canadian maritime region. The persistence of important prey to the diet of harbor seals over recent decades provides evidence that they are resilient to the concurrent resurgence of the gray seal population in Northeastern US waters. Finally, mean harbor seal prey size and biomass were 8 cm and 0.09 kg smaller than gray seals, respectively. The significant difference in mean prey size and biomass between the two seal species was expected given the overall difference in body size and mass between the two seals, even at the younger age classes (Encyclopedia of Marine Mammals, 2^nd ed.; Perrin et al., 2009).

Williams (1999) and Ampela (2009) offer the only empirically based Northeastern US estimates of Northwest Atlantic harbor and gray seal diet composition based on biomass, respectively. In comparison to their research results, our more recent study found similar seal diet compositions, specifically for samples originating from bycatch. In contrast, seal diet composition from our study generally does not align with seal proportional prey composition for the Northeastern US estimated in Smith et al. (2015). There are likely several reasons for the differences. The most notable is that harbor and gray seal mean diet composition among prey groups in Smith et al. (2015) varies widely due to a large number of literature sources used to estimate diet composition. Most of those studies originated from regions outside of the Northeastern US, and several of the sources utilized scats to reconstruct the seal diets.

Using hard parts to evaluate marine mammal diet allows for the estimation of prey biomass consumed at a high taxonomic resolution ( Table 2 ). However, there are three primary shortcomings of using hard parts to estimate diet: 1) a bias toward cephalopod beaks and fish otoliths that have higher retention in the stomach lining and are more resistant to degradation, respectively; 2) underdetection of prey which have no hard part remains (e.g., elasmobranchs, crustaceans, and depredation); and 3) difficulty investigating for evidence of scavenging. Squid beaks have been reported to become lodged in the stomach lining and thereby can be overrepresented in diets inferred from stomach contents (Olesiuk et al., 1990; Bowen and Iverson, 2013). Pristine and otoliths with minor erosion likely reflect prey with more robust otolith size (e.g., gadoid species), but fragile otoliths are more likely to be underrepresented due to breakage, degradation, or fully digested in the stomach before passing through the intestines (e.g., clupeids; Murie and Lavigne, 1986; Pierce and Boyle, 1991; Hammill et al., 2007; Tollit et al., 2007). However, stomach content data are less biased than scats with respect to quantifying the minimum number and size of prey consumed simply because stomach content remains have not cycled through the entire digestive process (Jobling and Breiby, 1986; Olesiuk et al., 1990; Ampela, 2009).

Similar to the findings in Byron and Morgan (2016) and Pitchford et al. (2020), our study found evidence of elasmobranch prey present in gray seal stomach samples but very few in harbor seals. This is likely due to the high incidence of gray seal bycatch events in the southern region that co-occurred with large mesh skate and dogfish gillnet fisheries (Murray et al., 2021). With respect to depredation, only the lower portion or belly region of fish is consumed by predators. Consequently, there generally is no evidence of depredation (i.e., no otoliths consumed or located) in the stomach of the predator unless headless fish remains are found intact within the stomach. In contrast, consumption by scavenging may be detected when only heads of fish are recovered with no further co-occurring evidence of bony or flesh remains. Consumption by scavenging can occur when fishermen dress their fish catch for the market while at sea. The application of fatty acids as trophic markers provides both longer temporal insight into marine mammal foraging patterns and theoretically can limit the depredation source of bias when compared with techniques that involve analysis of hard parts (Kirsch et al., 2000; Dalsgaard et al., 2003; Thiemann and Iverson, 2008; Iverson, 2009; Thiemann et al., 2009; Bowen and Iverson, 2013). The DNA meta-barcoding of prey may also get at this source of bias; however, analytical techniques using DNA to quantify the abundance of prey in the diet are still under development (Jeanniard-du-Dot et al., 2017; Shelton et al., 2023).

In conclusion, this study demonstrates the importance and value of utilizing carcasses retained from bycatch events to fill data gaps in our understanding of the ecological role of recovering harbor and gray seal populations. This includes their impact on the natural mortality of prey important to commercial fisheries providing further insight into the connections between fisheries and protected species management potentially regulating food web dynamics in the Northeastern US region (Kulatska et al., 2021). Given the richness of their diets, these seals may be capable of shifting their diet to species that are predicted to be more abundant in the future as a result of changing environmental or habitat conditions (Nye et al., 2009; Zeppelin and Orr, 2010; Pinsky et al., 2013; Hare et al., 2016; Kleisner et al., 2017; Friedland et al., 2019; Lettrich et al., 2023). Finally, we recommend cross-validation studies comparing results from different diet sample types, locations, and methodologies to minimize bias and provide more robust evidence of the magnitude of natural mortality on commercially important species induced by top-level predators.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: FigShare, https://figshare.com/articles/dataset/Lyssikatos_and_Wenzel_2024/25097213.

The manuscript presents research on animal diet. No live animals were used or handled during the course of this study. Ethical approval was not required for the study.

ML: Conceptualization, Formal analysis, Investigation, Methodology, Writing – original draft, Writing – review & editing, Data curation. FW: Data curation, Investigation, Writing – review & editing.