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

Citation

Flanders, Kelly; Olson, Zachary; Ono, Kathryn (2020), Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet, Dryad, Dataset, https://doi.org/10.5061/dryad.bzkh1896s

Abstract

Increasing grey seal (Halichoerus grypus) abundance in coastal New England is leading to social, political, economic, and ecological controversies. 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, U.S. 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.) was 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 been documented in U.S. grey seal diet previously. 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%), two particularly valuable species of concern.

Methods

This dataset is a fasta file that includes vertebrate DNA sequences (organized into Operational Taxonomic Units) found in grey seal scats collected from Monomoy Island, MA, USA. The scat collection methods, laboratory protocols, sequencing, and bioinformatic analyses are detailed in accompanying manuscript (MEPS-2020-01-052, in review). 

Usage Notes

Sequence names are in the following format: "denovoX_17.Mono.X..."

"Denovo" refers to each unique Operational Taxonomic Unit, and "17.Mono" refers to the scat samples from Monomoy Island collected in 2017. There are also some sequences with "16.Muski", which refers to seal scats from Muskeget Island that were not included in the aforementioned study. Several control samples are also included (please see manuscript), which are those that lack a Mono or Muski label.

This file contains the data as provided by the sequencing company, University of Minnesota Genomics Center.

Funding

University of New England

Lerner-Gray Fund for Marine Research

Lerner-Gray Fund for Marine Research