Molecular sequencing and morphological identification reveal similar patterns in native bee communities across public and private grasslands of eastern North Dakota

Bees play a key role in the functioning of human-modified and natural
ecosystems by pollinating agricultural crops and wild plant communities.
Global pollinator conservation efforts need large-scale and long-term
monitoring to detect changes in species’ demographic patterns and shifts
in bee community structure. The objective of this project was to test a
molecular sequencing pipeline that would utilize a commonly used locus,
produce accurate and precise identifications consistent with morphological
identifications, and generate data that are both qualitative and
quantitative. We applied this amplicon sequencing pipeline to native bee
communities sampled across Conservation Reserve Program (CRP) lands and
native grasslands in eastern North Dakota. We found the 28S LSU locus to
be more capable of discriminating between species than the 18S SSU rRNA
locus, and in some cases even resolved instances of cryptic species or
morphologically ambiguous species complexes. Overall, we found the
amplicon sequencing method to be a qualitatively accurate representation
of the sampled bee community richness and species identity, especially
when a well-curated database of known 28S LSU sequences is available. Both
morphological identification and molecular sequencing revealed similar
patterns in native bee community structure across CRP lands and native
prairie. Additionally, a genetic algorithm approach to compute
taxon-specific correction factors using a small subset of the most
concordant samples demonstrated that a high level of quantitative accuracy
could be possible if the specimens are fresh and processed soon after
collection. Here we provide a first step to a molecular pipeline for
identifying insect pollinator communities. This tool should prove useful
for future national monitoring efforts as use of molecular tools becomes
more affordable and as numbers of 28S LSU sequences for pollinator species
increase in publicly-available databases.