Atlantic Puffin Fecal DNA Metabarcoding: 2021-2022, Maine, USA
Abstract
These data include quantifications of prey types identified through metabarcoding using 12S and 18S genes and the DNA present in Atlantic puffin (Fratercula arctica) feces. Fecal samples were collected on Matinicus Rock, Maine during the incubation and chick-rearing periods of 2021 and 2022. Fecal samples were stored in DNA/RNA shield and were processed within 12 weeks of collection, with processing performed at the Cornell Lab of Ornithology and sequencing performed on an Illumina Hi-seq 2500 at the University of New Hampshire. Samples have been rarefied to an even read depth (600 reads for 12S, 2500 for 18S) and all bioinformatics work was performed by GVC in Qiime2. Data are presented here in separate csv files for each year and gene region examined, as well as corresponding metadata relating to sample collection (date and age of bird).
Subject keywords
Biological sciences, DNA metabarcoding, Fratercula arctica, Gulf of Maine, seabird diet
README: Atlantic Puffin Fecal DNA Metabarcoding: 2021-2022, Maine, USA
CSV files included display rows representing unique fecal samples, with ID numbers corresponding to individual fecal samples obtained from breeding Atlantic puffins (Fratercula arctica). Columns represent the DNA sequence reads belonging to each prey type, as identified in the top row. This data structure enables easy calculation of RRA values using the number of taxa-specific DNA sequences within an individual sample or conversion to binary presence/absence for FOO calculations. All samples have been rarefied to equal read depths for each gene region (12S - 600 reads, 18S - 2500 reads). CSVs containing sample information include the data of sample collection, the age of the bird the sample is from, and the position of the samples on the plate during processing. All samples were collected fresh and so the sample collection date is the same as sample deposition date.
Code/Software
Following sequencing, these data were processed in Qiime2 using scripts accessible at:
Straightforward use of R package 'vegan' allowed for calculation of species diversity metrics and nonparametric tests (ANOSIM, PERMANOVA, and more) examining community similarity. Other packages used with this dataset include 'stats' and 'ggplot2' but the data presented here have only been processed using Qiime2.
