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

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 error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.

生态学家愈发关注基于膳食样本中的食物DNA与标记基因高通量测序技术，来量化消费者的饮食组成。尽管圈养饲喂研究已证实该假设并不成立，但学界仍容易默认从膳食样本中获取的食物DNA序列占比，可代表消费者的实际饮食占比。本研究通过在膳食样本同步测序已知组成的对照材料，旨在校正扩增子测序过程中引入的技术偏差，以及基因拷贝数变异这类生物学偏差。本研究使用Ion Torrent PGM©测序平台，对饲喂已知比例3种鱼类固定日粮的圈养斑海豹（*Phoca vitulina*）粪便中扩增得到的猎物DNA进行了测序。与此同时，我们还对与该海豹日粮匹配的猎物组织混合物进行测序，以此生成组织校正因子（Tissue Correction Factors, TCFs）。结果显示，组织校正因子可优化所有物种类别的饮食组成估算结果（基于序列占比），将平均估算误差从未经校正的28 ± 15%降至经TCF校正后的14 ± 9%。本实验设计还允许我们推断猎物特异性消化偏差的大小，并计算得到消化校正因子（Digestion Correction Factors, DCFs）。我们将消化校正因子与潜在的消化差异替代指标（如鱼类蛋白质占比、脂质占比）进行对比，发现DCFs与鱼类猎物的脂质占比之间存在显著相关性，这表明基于脂质含量的猎物特异性校正方法，可在本研究体系中获得精准的饮食组成估算结果。本研究结果证实了膳食研究中同步测序食物组织混合物的应用价值，并为定量DNA饮食分析领域的未来研究提供了全新方向。