DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish

Abstract

Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter-and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.

VTAM: A robust pipeline for validating metabarcoding data using controls

“…Apart from finding adequate parameters for data analyses, mock samples are also useful in ensuring that sufficient sequencing coverage has been achieved. Furthermore, in large-scale studies involving several distinct high-throughput sequencing runs, the systematic use of identical mock samples as standards for parametrization of the filtering should minimize the effect of random fluctuations and make samples comparable between runs [12] , [40] .…”

“…While the stringent filtering of VTAM decreases (within-sample) α-diversity and increases (between-samples) β-diversity, it has proven to provide accurate estimates to conduct robust ecological studies (e.g. [40] ). We, therefore, believe VTAM represents an innovative and so-expected tool for the robust validation of metabarcoding data and for conducting ecological analyses.…”

“…In particular, accurate and exhaustive curation of FP and ensuring repeatability by using technical replicates have proven essential for producing accurate ecological estimates [25] , [8] . These bioinformatic curation steps involve a series of good practices in study design, notably, the systematic use of mock community samples, negative controls, and technical replicates [29] , [40] , [5] . However, the use of mock community and negative control samples in bioinformatics pipelines was often limited to post-hoc analyses by the user to verify the quality expectations (e.g.…”

“…Yet, control samples have been shown extremely useful for determining data filtering thresholds and discarding false positives from metabarcoding data [11] . Moreover, mock community samples can be used to ensure the comparability of data between distinct high-throughput sequencing runs [12] , [40] . In these latter cases, negative and mock community samples were processed explicitly to set optimal parameters for validating metabarcoding data and standardizing biodiversity analyses across samples and High Throughput Sequencing (HTS) runs.…”

Modeling and comparing the distributions and associations of two co‐occurring catshark species off South Africa

“…The present study modeled the distribution of two co-occurring benthic catshark species to investigate intra-and interspecific spatial associations between coasts, maturity stages, and across depth ranges. Numerous studies have reported that ecologically and morphologically similar species may facilitate successful co-existence through partitioning their ecological niches (Holmgren, 1995;Pilfold et al, 2014;Villsen et al, 2022;Weideli et al, 2023). This appears to be the case in the present study, with catsharks displaying differential habitat occupancy, specifically intra-and interspecific differences in co-occurrence patterns and spatial associations between coasts, maturity stages, and across the depth ranges explored.…”