DNA metabarcoding reveals greater plant diversity than morphological seed analysis of bird feces

Abstract Premise Fruit‐eating birds drive seed dispersal in recovering tropical ecosystems, shaping forest regeneration. Molecular techniques, such as DNA metabarcoding, enable diet analysis from feces and can provide complementary frugivory data where dispersal is infrequent, as well as aid in seed identification in hyper‐diverse regions lacking morphological reference collections. Methods We compared the plant taxa detected in bird droppings using DNA metabarcoding and morphological seed classification. Plant DNA extracted from 52 seed‐containing droppings was amplified using a universal plant primer for an rbcL mini‐barcode. Morphologically detected seeds were cross‐referenced with metabarcoding‐detected genera. Results DNA metabarcoding and morphological classification of seeds are shown to be complementary methods, with the same plant taxa detected in only 38% of dropping samples. Although metabarcoding did not recover DNA of some seeds present in the dropping samples, metabarcoding revealed an overall higher diversity of plant genera compared to morphological seed analysis. Discussion Our results suggest that the use of a metabarcoding approach can be complemented by established seed analysis methods. Diet information obtained from metabarcoding feces may shed light on cryptic bird–plant interactions and potential seed dispersal events, especially in high biodiversity areas.