DOI: 10.5061/dryad.4rj2s
title: Data from: An holistic ecological analysis of the diet of Cory’s shearwaters using prey morphological characters and DNA barcoding

description: 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 intra-populational 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 (pre-laying 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.
description: Database
 1This
 file contains all the information from the individual diet samples of
 Cory's shearwaters analyzed, including morphological and genetic
 identifications of prey (and respective Genbank accession
 numbers).Database
 2This
 file includes the dataset used to calculate the frequencies of occurrence
 and numerical frequencies of prey (See the Results section and the Table
 2) and to build the figures 2 and 3.Frequency_of_Occurence_Alonso_et_alThis file contains the dataset used to perform all the analyses with the R Program (See Table 3 and Results subsections: "Diet of non-breeders", "Sex and inter-annual variations in diet", "Seasonal variations in diet").GLM_Analysis_Table3_AdonisThis file contains the R-codes and scripts used in the analysis present on Table 3 and Results subsections ("Diet of non-breeders", "Sex and inter-annual variations in diet", "Seasonal variations in diet".Alignment_CarangidaeFile containing alignment run in Clustal WAlignment_ExocoetidaeFile containing alignment run in Clustal WAlignment_HalosauridaeFile containing alignment run in Clustal WAlignment_HistioteuthidaeFile containing alignment run in Clustal WAlignment_MyctophidaeFile containing alignment run in Clustal WAlignment_OmmastrephidaeFile containing alignment run in Clustal WAlignment_SternoptychidaeFile containing alignment run in Clustal WAlignment_SynaphobranchidaeFile containing alignment run in Clustal WAlignment_TrichiuridaeFile containing alignment run in Clustal WNJTree_CarangidaeTree file constructed in Mega 6NJTree_ExocoetidaeTree file constructed in Mega 6NJTree_HalosauridaeTree file constructed in Mega 6NJTree_HistioteuthidaeTree file constructed in Mega 6NJTree_MyctophidaeTree file constructed in Mega 6NJTree_OmmastrephidaeTree file constructed in Mega 6NJTree_SternoptychidaeTree file constructed in Mega 6NJTree_SynaphobranchidaeNJTree_TrichiuridaeTreeTree file run in POYPOYAlignmentAlignments between reference and sample sequences to produce a tree in POYBootstrapTreeBootstrap tree consensus file produced in POY