Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal Halichoerus grypus diet

Increasing grey seal Halichoerus grypus abundance in coastal New England is leading to social, political, economic, and ecological controversies. Central to these issues is the foraging ecology and diet composition of the seals. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (n = 74) collected from a breeding colony on Monomoy Island in Massachusetts, USA, and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance Ammodytes spp. were the most frequently consumed prey group, with a frequency of occurrence (FO) of 97.3%, consistent with previous studies, but Atlantic menhaden Brevoortia tyrannus, the second most frequently consumed species (FO = 60.8%), has not previously been documented in US grey seal diet. Our results suggest that a metabarcoding approach to seal food habits can yield important new ecological insights, but that traditional hard parts analysis does not underestimate consumption of Atlantic cod Gadus morhua (FO = 6.7%, Gadidae spp.) and salmon Salmo salar (FO = 0%), 2 particularly valuable species of concern.

Diet of seals in the Baltic Sea region: a synthesis of published and new data from 1968 to 2013

A crucial first step in assessing and managing the role and impacts of predators on their environment is knowledge on their foraging behaviour and diet. Here, we synthesize previously published and newly generated data on the diet of harbour seals, grey seals, and ringed seals in the Baltic Sea region. More than 45 000 otoliths recovered from 3147 samples of scats and digestive tracts were collected throughout all seasons and most Baltic Sea sub-basins from 1968 to 2013. The data revealed a large extent of interspecific, spatial, and seasonal variation in seal diet, implying that caution should be made when extrapolating from one species, area or season, to others. Still, a few fish species, including Atlantic herring, sprat, cod, and sandeels had high occurrence across seal species and locations. The compiled data provide the first overview of seal diet across the entire Baltic Sea region, but also comes with several limitations. Thus, while the data presented here constitutes an important reference for future inference, it also illustrates an urgent need for standardizing methodology across studies on the diet of seals and other aquatic predators.

A review of spatial and temporal variation in grey and common seal diet in the United Kingdom and Ireland

Knowledge about the diet of fish-eating predators is critical when evaluating conflicts with the fishing industry. Numerous primary studies have examined the diet of grey seals Halichoerus grypus and common seals Phoca vitulina in a bid to understand the ecology of these predators. However, studies of large-scale spatial and temporal variation in seal diet are limited. Therefore this review combines the results of seal diet studies published between 1980 and 2000 to examine how seal diet varies at a range of spatial and temporal scales. Our results revealed extensive spatial variation in gadiform, perciform and flatfish consumption, likely reflecting variation in prey availability. Flatfish and gadiform consumption varied between years, reflecting changes in fish assemblages as a consequence of factors such as varying fishing pressures, climate change and natural fluctuations in populations. Perciform and gadiform consumption varied seasonally: in addition there was a significant interaction between season and seal species, indicating that grey and common seals exhibited different patterns of seasonal variation in their consumption of Perciformes and Gadiformes. Multivariate analysis of grey seal diet revealed spatial variation at a much smaller scale, with different species dominating the diet in different areas. The existence of spatial and temporal variation in seal diet emphasizes that future assessments of the impact of seal populations should not be based on past or localized estimates of diet and highlights the need for up-to-date, site specific estimates of diet composition in the context of understanding and resolving seal/fisheries conflict.

Spring diet of ringed seals (Phoca hispida) from northwestern Spitsbergen, Norway

Labansen, A. L., Lydersen, C., Haug, T., and Kovacs, K. M. 2007. Spring diet of ringed seals (Phoca hispida) from northwestern Spitsbergen, Norway. – ICES Journal of Marine Science, 64: 1246–1256. Complete gastro-intestinal tracts (GITs) from 267 ringed seals from five different locations in Spitsbergen were collected during spring of the years 2002–2004. Diet was assessed based on hard part remains from prey. Invertebrates constituted <2% of all prey (relative frequency, Ni). Fish otoliths were found in all seals; 1.7, 34.3, and 64.0% of the recovered otoliths were found in the stomach, small and large intestines, respectively, emphasizing the importance of analysing the whole GIT, not only the stomach. Otoliths from stomachs and small intestines with minimal signs of erosion were measured to back-calculate pre-ingested prey size and biomass. Based on measured polar cod (Boreogadus saida) otoliths (n = 7007), the ringed seals fed on fish in the length range 44.4–229.2 mm, primarily consuming the youngest year classes. Adult females ate smaller polar cod more often than adult males or juveniles. Polar cod dominated the diet, with a frequency of occurrence (FO) of 100%, Ni of 71.9%, and a biomass contribution of 77.2%. The taxon Stichaeidae was the second most frequent prey type (FO = 55.6%) followed by Cottidae (FO = 35.6%). The diet of ringed seals from one locality markedly differed from the others, with a greater species diversity, low Ni of polar cod (15%), and a dominance of Stichaeidae (Ni = 67%). Location of sampling, as well as sex and age of the seals, had significant influences on ringed seal diet in spring.