Data from: Longer amplicon metabarcoding primers enhance fish taxonomic resolution in eDNA samples

Many previously designed fish eDNA metabarcoding primers amplify short
regions ranging from 70-170 bp. However, the capacity to differentiate
related taxa is positively correlated with amplicon size. We collated an
alignment of full 12S gene sequences for 169 Canadian Freshwater species,
and used this to design and/or modify existing primers to develop two
novel primer pairs that target Canadian freshwater fish and which produce
amplicons approximately 210 and 315 bp in size. Together, these amplicons
covered ~57% of the 12S gene and included all but a single variable region
useful for differentiating taxa. Using an in-silico analysis of sequences
from 173 Canadian fish species, we demonstrated that these primer pairs
amplified more efficiently and can more readily distinguish closely
related taxa relative to commonly employed shorter-amplicon primer pairs.
We additionally validated their in-situ sensitivity in natural ecosystems
by sampling two urban pond ecosystems in Hamilton, Ontario, that were also
surveyed using conventional methods, including one pond that was drained
for a complete census. Both primer pairs detected all captured species,
including four rare species (1-3 individuals of ~1700).