Recurring Themes
Besides the insights made in each of the major theme areas above, there
were several recurring themes that emerged from multiple studies:
Importance of museum & associated reference
collections . Museums play a key role in metabarcoding approaches.
First, while many insights can be gained from molecular sequences alone,
the availability of a reference collection, ie, molecular barcodes for
identified specimens, adds unprecedented dimensionality to the data. The
availability of a reference collection allows us to infer the functional
traits and morphological attributes of every taxon in a sample, whether
it is native or not at a given site, its overall distribution and
trophic relationships. Moreover, it is critical that the identity of the
specimen has been thoroughly confirmed, as misidentification can lead to
flawed interpretations. Thus, rather than diminishing any role of
natural history museums in such approaches, the vast data that have been
generated through molecular profiling approaches have increasingly
highlighted the fundamental importance of barcodes from reliably
identified species and populations (Valdivia‐Carrillo, Rocha‐Olivares,
Reyes‐Bonilla, Domínguez‐Contreras, & Munguia‐Vega, 2021). The
importance of a reference collection is highlighted by Lue et al. (2022)
which describes the importance of a vetted and curated reference library
for biological control studies. Likewise, Lu et al. (2022) emphasize the
limitations of inference without a reference database, and introduce a
fungal rRNA operon database (FRODO) with 1116 linked to taxonomically
identified species.
A second role of museum specimens in these approaches is that they can
provide historic samples of past environments. For example,
metabarcoding of pollen loads from museum bee specimens has provided key
insights into environmental change over decadal scales, both in the
availability of plants, and changes in interaction networks (Bell et
al., 2022; Gous, Swanevelder, Eardley, & Willows‐Munro, 2019). This
work adds to the increasing body of research that shows how
metabarcoding of museum specimens can provide information on changes in
interactions through time, including diet and microbiome (Heindler et
al., 2018) and parasite-host interactions (Greiman et al., 2018).
Insights from clustering at different levels : Early
metabarcoding studies used clustering approaches and generally grouped
ASVs into Operational Taxonomic Units (OTUs), assumed to correspond to
species. The purpose of this step was to remove the known noise in the
data, while also grouping taxa into species. However, new denoising
approaches have presented the opportunity of analyzing ASVs and hence
gaining insights into population-level patterns (Noguerales et al.,
2023). The most important aspect of the ability to look at different
levels of genetic clustering is that the comparison can be tremendously
informative into the processes that govern species assembly.
Incorporation of Deep Learning / Artificial Intelligence
approaches applied to image analysis to study arthropod biodiversity
(Emerson et al., 2022). Supervised learning was used to make predictions
of sediment sample proximity to shipwrecks based on frequency of
microbial taxa (Hampel et al., 2022).