Environmental DNA and biodiversity patterns: a call for a community phylogenetics approach

Environmental DNA (eDNA) metabarcoding is a relatively new technology allowing effective non-invasive analyses and monitoring of biodiversity patterns. Studies on eDNA metabarcoding focus on using sequence data to delimit basic units (i.e., such as Molecular Operational Taxonomic Units – MOTUS – or Amplicon Sequence Variation – ASVs), and after this definition standard analytical approaches from community ecology are applied. However, there is more information inherent to eDNA data and it is now straightforward to use more general approaches in which analyses are based directly on phylogenies or genetic distances between MOTUs or ASVs, rather than in discrete units without any accounting for hierarchical structure, providing a more continuum understanding of biodiversity patterns. Here we briefly review the concepts and methods to incorporate phylogenetic patterns into eDNA metabarcoding analyses, illustrating some of the main issues with eukaryote diversity data along the Araguaia River Basin. Hopefully this perspective stimulates researchers obtaining eDNA metabarcoding data to perform their data under the community phylogenetics framework instead of (or in addition to) the more standard community ecology approach.