Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Non‐Bilaterian Animals
Abstract
Small subunit ribosomal RNA (SSU rRNA)—18S in eukaryotes—is a universally present gene that was central in resolving ancient relationships in early molecular phylogenies. Nowadays, despite multi‐locus phylogenomics dominating, SSU rRNA sequences still serve as a molecular identifier of biodiversity. Phylogenetic placement uses a reference phylogeny and a given evolutionary model to annotate taxonomically environmental DNA, enabling a more accurate identification of divergent sequences that may belong to unknown lineages. Here, we first created the largest dataset of 18S sequences belonging to non‐Bilateria metazoans by curating the sequences found in PR2 database. We then used it as a case study to test the performance of common 18S‐based barcodes (V4, V9, and full‐length 18S) within a phylogenetic placement framework. We found that the V9 region generally lacks sufficient phylogenetic signal for reliable placements. The V4 region is accurate when the environmental diversity is represented in the reference tree but struggles with divergent lineages. Full‐length 18S overcomes short‐read limitations and emerges as the most robust option to uncover major clades. Finally, we apply phylogenetic placement to empirical environmental 18S data. We observe geographical variation in non‐bilaterians communities and recover a putative clade sister to Ctenophora based on long‐sequence barcodes.
Related
- The endocranial anatomy of ‘thoracosaur’ crocodyliforms: implications for their ecology and phylogenetic affinities
- Injection-rate histories and well placement influence fault yielding during CO2 geological storage
- Phylogenetic signal in anteater snout morphology: Implications for interpreting rare vermilinguan fossils
- Tree traits drive phylogenetic and functional responses of soil fungal communities in Mediterranean forests subjected to recurrent fires
- Can’t see the forest for the trees: The influence of marker type on inferred phylogenetic relationships in a cosmopolitan bat genus
BibTeX
@article{aranoansola2026evaluating,
title = {{Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Non‐Bilaterian Animals}},
author = {Javier Arañó-Ansola and Inés Galán-Luque and Marc Domènech and Laura Rico-Martín and Edmund Moody and Megha Suresh and James Fleming and Daniel Vaulot and Javier del Campo and Mattia Giacomelli and Jesus Lozano-Fernandez},
journal = {Environmental DNA},
year = {2026},
month = aug,
doi = {10.1002/edn3.70350},
url = {https://hal.sorbonne-universite.fr/hal-05778274v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Non‐Bilaterian Animals
AU - Javier Arañó-Ansola
AU - Inés Galán-Luque
AU - Marc Domènech
AU - Laura Rico-Martín
AU - Edmund Moody
AU - Megha Suresh
AU - James Fleming
AU - Daniel Vaulot
AU - Javier del Campo
AU - Mattia Giacomelli
AU - Jesus Lozano-Fernandez
PY - 2026
DA - 2026/08/12
JO - Environmental DNA
DO - 10.1002/edn3.70350
UR - https://hal.sorbonne-universite.fr/hal-05778274v1
AB - Small subunit ribosomal RNA (SSU rRNA)—18S in eukaryotes—is a universally present gene that was central in resolving ancient relationships in early molecular phylogenies. Nowadays, despite multi‐locus phylogenomics dominating, SSU rRNA sequences still serve as a molecular identifier of biodiversity. Phylogenetic placement uses a reference phylogeny and a given evolutionary model to annotate taxonomically environmental DNA, enabling a more accurate identification of divergent sequences that may belong to unknown lineages. Here, we first created the largest dataset of 18S sequences belonging to non‐Bilateria metazoans by curating the sequences found in PR2 database. We then used it as a case study to test the performance of common 18S‐based barcodes (V4, V9, and full‐length 18S) within a phylogenetic placement framework. We found that the V9 region generally lacks sufficient phylogenetic signal for reliable placements. The V4 region is accurate when the environmental diversity is represented in the reference tree but struggles with divergent lineages. Full‐length 18S overcomes short‐read limitations and emerges as the most robust option to uncover major clades. Finally, we apply phylogenetic placement to empirical environmental 18S data. We observe geographical variation in non‐bilaterians communities and recover a putative clade sister to Ctenophora based on long‐sequence barcodes.
SN - 2637-4943
ER -