Future challenges and perspectives
This study revealed the feasibility and usefulness of eDNA in landscape
genetics. Even if the degree of accuracy demonstrated in this study is
accepted by users as a usable level, there are certain limitations that
cannot be immediately resolved. The first is the low information content
of short DNA fragments available in eDNA. This study used a single
region of approximately 400 bp of mtDNA, but longer sequences would be
difficult to amplify due to the degradation of DNA in water (Jo et al.
2017). In addition, mtDNA, which is generally used in eDNA studies, has
limited information that is equivalent to that of a single locus (Andres
et al. 2023b). Landscape genetics studies after the 2010s are commonly
conducted by analyzing multiple independent loci (Wang 2011). For more
accurate analysis, it is essential to use loci in nuclear DNA, which is
not linked to mtDNA and is regarded as independent loci (Couton et al.
2023). The use of nuclear DNA in eDNA is still challenging, however,
this issue could be solved through the implementation of microsatellite
and SNP analysis currently under development (Andres et al. 2021; Liu et
al. 2024). Another limitation is that eDNA cannot provide individual
information. The statistics calculated in this study do not require
individual information because they deal with gene frequency in gene
pools, and eDNA sampling may even be possible to reduce bias due to the
selection of some individuals in the population. However, in order to
address more complex biological questions in the field, analyses
requiring individual information will sometimes be required (Couton et
al. 2023). Actually, in the studied species in the Sorachi River,
source-sink structures (asymmetric gene flow) from low-temperature
tributaries to high-temperature tributaries have been detected through
an analysis using the theory of assignment test (Paetkau et al. 1995),
which assigns individuals to groups (Nakajima et al. 2021), but this
analysis cannot be applied without individual information.
Nevertheless, this study shows that eDNA has the potential to perform
basic analyses via summary statistics with the same level of accuracy as
that seen in tissue samples. Given that the “basic landscape
genetics,” as practiced in the 2000s when only short sequence data
could be handled, could be rapidly performed through cost-efficient and
non-invasive sampling, the usefulness of eDNA analyses is evident. With
the increasing number of available markers, landscape genetics using
eDNA is expected to be more useful and be utilized for various purposes
such as the evaluation and conservation of habitat connectivity under
environmental changes.