Using multi-marker DNA metabarcoding to reveal the diet of a scarce woodland bird

Abstract

Understanding the role diet plays in the structure of food webs is vital, and dietary knowledge is key for conservation management success. There is limited knowledge of the diets of woodland bird species, due largely to difficulties in accurately identifying plant and invertebrate taxa being consumed. Here, we show the effectiveness of multi-marker faecal metabarcoding to provide the most in-depth dietary analysis of a generalist passerine, the Hawfinch (Coccothraustes coccothraustes, Linnaeus), to date. Faecal samples were obtained from 2016-2019 from Hawfinch populations prior to and during the breeding season throughout the UK. DNA was extracted from 263 samples and amplified using Internal Transcribed Spacer 2 (ITS2) and cytochrome C oxidase subunit I (COI) barcodes. Using high-throughput sequencing (HTS), we identified 49 and 97 ITS2 and COI zero radius operational taxonomic units (zOTUs) respectively which equated to reputed dietary items. The herbivorous element of Hawfinch diet was dominated by naturally occurring taxa such as beech (Fagus sylvatica, Linnaeus), hornbeam (Carpinus betulus, Linnaeus) and oak (Quercus sp., Linnaeus). The most taxon rich and commonly recorded invertebrate taxon identified was Lepidoptera. We found Hawfinch diet varied spatially, as well as between sexes. Hawfinch showed broad dietary plasticity and utilised multiple resources within their foraging environments. Our study shows the potential of multi-marker DNA metabarcoding to reveal subtle dietary differences, but also highlights the challenges of studying omnivorous species using metabarcoding methods.

DNA metabarcoding revealed how time and space do matter -sex does not- in the dietary variation of the endangered Dupont’s Lark

“…Sexual dietary differences have already been described for other bird species, including generalist medium-sized passerines such as the Black Wheatear (Oenanthe leucura [16] or the Hawfinch (Coccothraustes coccothraustes [67]). In contrast to our predictions, we revealed a high overlap between sexes in the diet of Dupont's Lark during the breeding season, suggesting that foraging behavior and nutritional requirements are probably equivalents in both sexes.…”

“…Spatial dietary differences of Dupont's Lark were observed at different scales, probably reflecting dietary plasticity in response to variations in prey availability [66,67].…”

The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?

“…The choice of either attempting to silence or potentially being swamped by predator DNA is an insidious one given the financial, practical and experimental implications. The increased adoption of multiprimer (often multimarker, i.e., across multiple genes) metabarcoding (e.g., Batuecas et al, 2022; Cuff, Tercel, et al, 2022; da Silva et al, 2019, 2020; Stenhouse et al, 2021; Tercel et al, 2022) offers the option of using both approaches in synergy, but is by no means a panacea. Multimarker metabarcoding has been more generally suggested as a means of overcoming the issues associated with PCR primer bias (Browett et al, 2021; Cuff, Windsor, et al, 2022; da Silva et al, 2019).…”