Data from: Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias ...

• Main Authors: Thomas, Austen C., Jarman, Simon N., Haman, Katherine H., Trites, Andrew W., Deagle, Bruce E.
• Format: Dataset
• Language: English
• Published: Dryad 2013
• Subjects: Mallotus villosus; Diet Analysis; Clupea pallasii; Scomber japonicus; Wildlife Management; Phoca vitulina; Pacific
• Online Access: https://dx.doi.org/10.5061/dryad.h3k4n; https://datadryad.org/stash/dataset/doi:10.5061/dryad.h3k4n

Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals’ diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate ... : Tissue mix DNA amplicon pool (.fastq)This file contains the DNA sequences and quality scores that resulted from Ion Torrent amplicon sequencing of a fish tissue mixture that matched the seal diet in the study. See manuscript text for details.PDZA_mix.fastqSeal scat DNA amplicon pool (.fastq)This file contains the DNA sequences and quality scores that resulted from Ion Torrent amplicon sequencing of 48 individually amplified seal scats from the feeding trial. The harbour seals were fed: capelin (Mallotus villosus) (40%), Pacific herring (Clupea pallasii) (30%), chub mackerel (Scomber japonicus) (15%), and market squid (Loligo opalescens) (15%). See text for details.PDZA_scats.fastqFigure_DataData used to create figures 2-5. See Readme file for details ...