Environmental DNA and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems

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ABSTRACT Terrestrial mammals shape their ecosystems, and mammalian community assemblages can be important indicators of ecosystem functioning and ecosystem changes over time. Numerous taxa of terrestrial mammals are currently threatened by habitat loss and face displacement to new geographical areas or systems to which they are less suited and where they may affect the original communities. Understanding past ecosystem changes is important for predicting future responses of species assemblages to changes in their environments. Thus, ecological and evolutionary history, as well as adaptive capacity, are important predictors of future population viability. Genomic and metagenomic approaches using environmental or ancient DNA offer a wealth of information regarding genome‐wide variation of changing communities or of taxonomic groups over time, which may help explain past changes and predict future responses of communities to changes in their environment; however, to date, such studies are relatively scarce. We review studies on environmental DNA and environmental genomics of terrestrial mammals to assess the potential of such approaches regarding past, contemporary, and future terrestrial ecosystems, identify inherent challenges, and discuss potential applications. We elaborate on lessons to be learned from mammal genomics of past ecosystems and compare metabarcoding with general metagenetic and metagenomic techniques. We provide a comprehensive overview of current applications, challenges, and future potential of environmental DNA with regards to terrestrial mammals. As current major challenges regarding mammalian eDNA we identify its scarcity and patchy distribution, along with the persistent necessity of genomic reference data. While the latter are steadily increasing, the former can only be tackled by explicitly mapping the environment to gain understanding of spatial eDNA distribution. Such understanding may facilitate informed choices of sample sites and substrates and, together with new sequencing techniques, this can allow mammalian eDNA to be maximally exploited as a source of biodiversity data.