Résumé
There is growing interest in the study of avian endoparasite communities, and me-tabarcoding is a promising approach to complement more conventional or targetedmethods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme,with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed thischallenge by comparing different primer sets across 16 samples from 5 bird species.Samples consisted of blood, feces, and controlled mixes with known proportions ofbird and nematode DNA. Illumina sequencing revealed that a 28S primer set used incombination with a custom blocking primer allowed detection of various plasmodiidparasites and filarioid nematodes in the blood, coccidia in the feces, as well as twopotentially pathogenic fungal groups. When tested on the controlled DNA mixes,these primers also increased the proportion of nematode DNA by over an order ofmagnitude. An 18S primer set, originally designed to exclude metazoan sequences,was the most effective at reducing the relative number of avian DNA sequences andwas the only one to detect Trypanosoma in the blood. Expectedly, however, it did notallow nematode detection and also failed to detect avian malaria parasites. This studyshows that a 28S set including a blocking primer allows detection of several majorand very diverse bird parasite clades, while reliable amplification of all major parasitegroups may require a combination of markers. It helps clarify options for bird parasitemetabarcoding, according to priorities in terms of the endoparasite clades and theecological questions researchers wish to focus on.