An holistic ecological analysis of the diet of Cory's shearwaters using prey morphological characters and DNA barcoding

Abstract

Knowledge of the dietary choices and trophic niches of organisms is the key to understanding their roles in ecosystems. In seabird diet studies, prey identification is a difficult challenge, often yielding results with technique-specific biases. Additionally, sampling efforts are often not extensive enough to reveal intrapopulational variation. Immature animals, which may constitute up to 50% of a population, may occupy a significantly different trophic niche to more experienced birds, but this remains largely unexplored. We investigated the diet of Cory's shearwater (Calonectris diomedea) from Selvagem Grande, an island located off the northwest African coast, collecting a total of 698 regurgitate samples over three consecutive breeding seasons. The diet was assessed using two complementary approaches for prey identification: conventional morphological analysis (using fish vertebrae, otoliths and cephalopod beaks) and DNA barcoding of the 16S rRNA mitochondrial gene, in cases where a positive identification could not be retrieved. Species assignments employed BLAST and distance-based methods, as well as direct optimization of the tree length based on unaligned sequences in POY. This method resulted in robust tree estimates and species assignments, showing its potential for DNA barcoding of stomach contents using hypervariable markers such as the 16S. The molecular approach increased taxonomic resolution and revealed an additional 17 taxa. Diet differed significantly according to breeding status, sex, breeding phase (prelaying and chick rearing) and year. Such direct evidence of trophic segregation within the same population has rarely been shown in seabirds and highlights the importance of including such variables in ecosystem-based management approaches.

A switch in the Atlantic Oscillation correlates with inter-annual changes in foraging location and food habits of Macaronesian shearwaters ( Puffinus baroli ) nesting on two islands of the sub-tropical Atlantic Ocean

“…juvenile, sub-adult or adult, according to the darkness of the lower beaks: initially from the tip of the rostrum, when juvenile, up to the wing, only darkened in adults), following the guidelines of Cherel (2009), Xavier et al (2011) and using beak collections at the Institute of Marine Research, University of Coimbra, Portugal and at the Centre d'Etudes Biologiques de Chizé,9 France. Fish species were identified from vertebrae and one individual from otoliths using reference collections (Alonso et al, 2014). As one squid species was clearly dominant, we used molecular methods to verify the identification obtained with the lower beaks (Appendix 1).…”

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

“…DNA-based approaches have also yielded breakthrough dietary analyses in complex freshwater systems (e.g., Corse et al 2010;Carreon-Martinez et al 2011;Bartley et al 2015). Most of the studies to date attest to the effectiveness of DNA-based analysis, especially when combined with morphological analysis (e.g., Casper et al 2007;Braley et al 2010;Alonso et al 2014), and they offer new insights in trophic ecology.…”

“…A few studies to date have sampled specific aquatic predator taxa more deeply, and demonstrated the occurrence of trophic segregation between different life stages (e.g., age, breeding status, and sex; Alonso et al 2014;Jo et al 2014). Thus, they suggest that different population segments choose different diets.…”

“…Here, the results indicated the presence of ontogenetic diet shifts. Alonso et al (2014) combined DNA sequencing (16S rRNA mitochondrial gene) with conventional, morphological analysis to investigate the diet of Cory's shearwater (Calonectris diomedea). The molecular approach increased taxonomic resolution by revealing 17 additional prey taxa, and provided direct evidence of trophic segregation according to breeding status, sex, breeding phase (pre-laying versus chick rearing), and year within the same population.…”

DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses

“…These problems apply in particular to items originating as fisheries offal, as viscera float and are therefore easier to ingest than fish heads with otoliths, particularly those from large species (Thompson and Riddy, 1995). More recent studies have used DNA analysis to identify parts that were not taxonomically diagnostic (Alonso et al, 2014). However, studies using stomach samples are usually restricted to the chick-rearing period, thus focusing on chick rather than adult diet across the annual cycle and usually requires handling of birds.…”