Testing the applicability of environmental DNA metabarcoding to
landscape genetics
Abstract
Landscape genetics is a field dealing with local genetic differences and
contributes to strategic conservation planning. Recently, environmental
DNA (eDNA) metabarcoding has proven useful not only for detecting
species but also for assessing genetic diversity and genetic structure
on a large scale such as in phylogeography. However, it remains unclear
whether eDNA analysis also has sufficient power to perform the landscape
genetics, which focuses on a local scale. To reveal the applicability of
eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis
of the mitochondrial DNA D-loop region of the fluvial sculpin
Cottus nozawae in the upper Sorachi River in Japan and compared
the results with inferences based on traditional tissue-based
approaches. As a result, the spatial distribution of haplotypes was
generally consistent between the eDNA- and tissue-based approaches. In
addition, the genetic differentiation statistics calculated using eDNA
and tissue samples were highly correlated when compared in the same
genetic region. Furthermore, if an inference based on genome-wide SNP
data from tissue samples was taken as known truth, the inference by eDNA
was not necessarily inferior to the inference by the same region from
tissue samples. Finally, we confirmed that analyses using eDNA data can
reveal patterns such as isolation-by-distance shown in previous studies
on this species, indicating the applicability of eDNA to basic landscape
genetics. Even though some limitations remain, eDNA may have great
potential for conducting basic landscape genetics.