The Old Pipe Gives the Sweetest Smoke: A Phylogenetic Turn for eDNA Metabarcoding
Abstract
Environmental DNA ( eDNA ) metabarcoding has emerged as a powerful tool for biodiversity monitoring because it is non‐invasive, applicable across broad taxonomic groups, and capable of detecting rare and cryptic species. However, the characteristics and limitations of eDNA vary among target organisms. Whereas studies of microorganisms and plankton often recover high‐quality DNA from whole or near‐whole organisms, surveys of marine macrofauna, particularly vertebrates, rely on trace, frequently degraded DNA . Combined with the lack of standardized protocols, inconsistent taxonomic resolution, limited quantitative information, and the absence of life‐stage information, these constraints hinder ecological interpretation and comparisons across studies. In this Perspective, we advocate a phylogenetic turn in eDNA analyses through the integration of phylogenetic diversity ( PD ), which quantifies the amount of evolutionary history represented by detected taxa. By considering evolutionary relatedness in addition to taxa identities, PD complements conventional taxonomic metrics and can provide additional ecological insight, particularly when taxonomic resolution is incomplete. We discuss both the opportunities and limitations of this approach, including its practical implementation in eDNA metabarcoding. To illustrate this framework, we compared five marine eDNA metabarcoding datasets (2021–2025) spanning tropical to Arctic ecosystems and contrasting anthropogenic contexts. Across these case studies, anthropized sites often showed higher taxonomic richness but reduced phylogenetic divergence, reflecting communities dominated by closely related evolutionary lineages, whereas less disturbed sites supported fewer taxa but encompassed broader evolutionary histories. These contrasting patterns illustrate how PD metrics can reveal ecological processes, including environmental filtering and community assembly, that may not be apparent from taxonomic richness alone. By proposing a reproducible workflow based on standardized eDNA datasets, we highlight the potential of phylogenetic diversity to strengthen biodiversity assessment from eDNA metabarcoding. Integrating evolutionary information alongside taxonomic information provides a complementary framework for biodiversity monitoring and offers promising perspectives for long‐term monitoring, conservation planning, and environmental policy.
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BibTeX
@article{haderle2026pipe,
title = {{The Old Pipe Gives the Sweetest Smoke: A Phylogenetic Turn for eDNA Metabarcoding}},
author = {Rachel Haderlé and Visotheary Ung and Jean‐luc Jung},
journal = {Environmental DNA},
year = {2026},
month = oct,
doi = {10.1002/edn3.70364},
url = {https://hal.science/hal-05842289v1},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - The Old Pipe Gives the Sweetest Smoke: A Phylogenetic Turn for eDNA Metabarcoding
AU - Rachel Haderlé
AU - Visotheary Ung
AU - Jean‐luc Jung
PY - 2026
DA - 2026/10/11
JO - Environmental DNA
DO - 10.1002/edn3.70364
UR - https://hal.science/hal-05842289v1
AB - Environmental DNA ( eDNA ) metabarcoding has emerged as a powerful tool for biodiversity monitoring because it is non‐invasive, applicable across broad taxonomic groups, and capable of detecting rare and cryptic species. However, the characteristics and limitations of eDNA vary among target organisms. Whereas studies of microorganisms and plankton often recover high‐quality DNA from whole or near‐whole organisms, surveys of marine macrofauna, particularly vertebrates, rely on trace, frequently degraded DNA . Combined with the lack of standardized protocols, inconsistent taxonomic resolution, limited quantitative information, and the absence of life‐stage information, these constraints hinder ecological interpretation and comparisons across studies. In this Perspective, we advocate a phylogenetic turn in eDNA analyses through the integration of phylogenetic diversity ( PD ), which quantifies the amount of evolutionary history represented by detected taxa. By considering evolutionary relatedness in addition to taxa identities, PD complements conventional taxonomic metrics and can provide additional ecological insight, particularly when taxonomic resolution is incomplete. We discuss both the opportunities and limitations of this approach, including its practical implementation in eDNA metabarcoding. To illustrate this framework, we compared five marine eDNA metabarcoding datasets (2021–2025) spanning tropical to Arctic ecosystems and contrasting anthropogenic contexts. Across these case studies, anthropized sites often showed higher taxonomic richness but reduced phylogenetic divergence, reflecting communities dominated by closely related evolutionary lineages, whereas less disturbed sites supported fewer taxa but encompassed broader evolutionary histories. These contrasting patterns illustrate how PD metrics can reveal ecological processes, including environmental filtering and community assembly, that may not be apparent from taxonomic richness alone. By proposing a reproducible workflow based on standardized eDNA datasets, we highlight the potential of phylogenetic diversity to strengthen biodiversity assessment from eDNA metabarcoding. Integrating evolutionary information alongside taxonomic information provides a complementary framework for biodiversity monitoring and offers promising perspectives for long‐term monitoring, conservation planning, and environmental policy.
SN - 2637-4943
ER -