Enriching barcoding markers in environmental samples utilising a phylogenetic probe design: insights from mock communities

Hybridisation capture is a promising method that uses short oligonucleotide probes to enrich DNA libraries for specific genomic fragments, facilitating the detection of organisms in environmental samples. While it provides a primer-independent alternative to metabarcoding, there is limited empirical research on its biases and implications for biological interpretation. We used mock communities to test a new bait design for four plant orders and investigated potential capture biases. We show capture biases and which variables are at play, from GC-content, to number of baits overlapping a species.