Marine Biology

, 166:106 | Cite as

Metabarcoding analysis of the Pacific harbor seal diet in Mexico

  • Elizabeth Brassea-Pérez
  • Yolanda Schramm
  • Gisela Heckel
  • Jennyfers Chong-Robles
  • Asunción Lago-LestónEmail author
Original Paper


Massive sequencing has improved the predator diet analysis, making it possible to identify taxa with low or no detectability via traditional scatological methods. In Mexico, the Pacific harbor seal (Phoca vitulina richardii) diet has been understudied, with the importance of invertebrates or cartilaginous fish as prey currently unknown. This study aims to characterize the harbor seal diet through metabarcoding and to compare results with those obtained via the analysis of the hard remains taken from the same samples. Samples were collected at four breeding colonies during the molting season. Libraries were constructed following an Illumina dual-indexed strategy using specific eukaryote (18S rRNA), chordate and cephalopod (16S mtDNA) primers to amplify the prey’s DNA, and blocking primers to avoid predator DNA amplification. Libraries were sequenced on the MiSeq® platform (Illumina), generating 848,411 reads. The quality control and taxonomic assignment for the sequences were performed in silico using bioinformatic tools. The present study, identified 49 prey (mostly bony fish), including 14 species of invertebrates, hagfish, and elasmobranchs, thus widening knowledge of the Pacific harbor seal’s diet. While 19 prey species were identified using both the hard remains and metabarcoding analysis, methods (with only four identified to genus level), lower prey richness was found in the hard remains. The main prey items around all islands were longfin sanddab (Citharichthys xanthostigma) and California lizardfish (Synodus lucioceps). Metabarcoding analysis is a new approach for studying the diet of key species in a highly productive and changing ecosystem, such as the California Current System.



This study was supported by the Consejo Nacional de Ciencia y Tecnologia (CONACyT or Mexican National Council for Science and Technology), through project 179451 (Basic Science 2012) and a scholarship number 339294 awarded to EBP. Permits were provided by the Mexican Ministry for Environment and Natural Resources (SEMARNAT, SGPA/DGVS/12269/13 and SGPA/DGVS/08370/14), the Ministry of the Interior (SEGOB, UG/211/0087/2014 and UG/211/01022/2014), and the El Vizcaino Biosphere Reserve (F00.DRPBCPN-000027 and F.00.1.DRPBCPN.00004/2014). We thank Axayácatl Rocha and Clara Galindo for their valuable comments, which helped to improve this study. We are grateful to the fishing cooperatives California de San Ignacio, Litoral, and Pacifico Aquaculture for providing logistical support during the surveys, and to all those who participated in the field work: Denise Lubinsky; Maricela Juárez; Claudia Tapia; Eva Fernández; Paulette Durazo; Alejandro Arias; and, Guadalupe Ruiz. We also thank Dr. Dante Magdaleno for his help and advice during data pre-processing and the professional copy editor Benjamin J. Stewart for the revision of this manuscript. Finally, we greatly appreciated the valuable comments and suggestions made by the reviewers to improve this paper.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All samples were collected without disturbing any animal or causing them any stress or harm.

Data accessibility

Accession Number PRJNA417449.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Centro de Investigación Científica y de Educación Superior de EnsenadaEnsenadaMexico
  2. 2.Universidad Autónoma de Baja CaliforniaEnsenadaMexico

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