Using patterns in prey DNA digestion rates to quantify predator diets

Abstract

Dietary metabarcoding-the process of taxonomic identification of food species from DNA in consumer guts or faeces-has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi-quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half-lives unique to each predator-prey combination. Because the feeding experiments required to deduce these half-lives are time-and resource-intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta-analysis of 24 spider prey DNA half-lives and show that these half-lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with halflives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half-lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.

High variation in handling times confers 35-year stability to predator feeding rates despite altered prey abundances and apparent diet proportions

“…At the species level, H. haustorium ’s detection times were estimated to vary between 1.6 and 130.8 hours. A wide range of detection times is typical for whelks (e.g., Yamamoto, 2004) and many other taxonomically-diverse consumers — from fishes to birds, seastars, spiders, and flies (e.g., Preston et al ., 2017; Hilton et al ., 1998; Uiterwaal & DeLong, 2020; Campos & Lounibos, 2000; Menge, 1972) — and is the consequence of a wide variety of both general and specific prey attributes. These include differences in digestible tissue mass (e.g., acorn barnacles are smaller than mussels), chemical defenses (e.g., H. scobina exudes a dark purple substance when consumed by H. haustorium ( pers.…”

Overcoming the pitfalls of merging dietary metabarcoding into ecological networks

“…First, the half‐life of DNA in the gut can be estimated empirically (Greenstone et al., 2007) to approximate the length of time for which a given length of DNA can be detected. Based on these data, semi‐quantitative predation rates can then be calculated (Egeter et al., 2015; Uiterwaal & DeLong, 2020). However, this is complicated as many species have highly variable metabolic rates (Greenstone et al., 2014; Sheppard et al., 2005).…”

Metabarcoding analysis of different portions of the digestive tract of scorpions (Scorpiones, Arachnida) following a controlled diet regime shows long prey DNA half‐life

“…The detectability of DNA of the ingested items also depends on how long the ingested DNA resides in the digestive tract of the consumer. One of the parameters to assess the detectability of ingested DNA is its half‐life ( D 50 ) (Greenstone et al, 2014; Uiterwaal & DeLong, 2020). The D 50 is the time at which sequences belonging to a consumed meal are detected in half of the consumers tested.…”

“…The D 50 is the time at which sequences belonging to a consumed meal are detected in half of the consumers tested. However, the D 50 parameter is sensitive to the type and size of the ingested meal (Schattanek et al, 2021), the digestion rates (Uiterwaal & DeLong, 2020), and the analyzed portion of the digestive tract (Macías‐Hernández et al, 2018).…”

“…However, the D 50 parameter is sensitive to the type and size of the ingested meal (Schattanek et al, 2021), the digestion rates (Uiterwaal & DeLong, 2020), and the analyzed portion of the digestive tract (Macías-Hernández et al, 2018).…”