TY  - JOUR
T1  - Reproducible Phylogenomic Taxonomy Requires Traceable Links from Insect Genomes to Species Hypotheses and Formal Names
A1  - Sara Al-Fahd
A1  - Noura Al-Khalifa
A1  - Omar Al-Turki
JF  - Entomological Research Letters
JO  - Entomol Res Lett
SN  - 3108-639X
Y1  - 2025
VL  - 5
IS  - 1
DO  - 10.51847/FB0aiOqYhB
SP  - 142
EP  - 152
N2  - Phylogenomics has expanded the scale of insect systematics, but taxonomic reproducibility requires more than rerunning a tree-building pipeline. Auditability is weakened when specimen identity, sequence processing, orthology, alignment, tree estimation, species-hypothesis formation, and nomenclatural action are disconnected across files and repositories. This article develops a proposed traceability-centered methodology in which each inferential transition remains linked to the biological and computational objects from which it was derived. The approach separates genome quality from taxonomic identity, orthology hypotheses from source sequences, gene trees from species histories, branch support from genomic concordance, and candidate species hypotheses from formal names. It also identifies conditions under which apparently robust trees remain taxonomically insufficient because they depend on processing choices, alignment decisions, model assumptions, discordance, or incomplete specimen anchoring. The methodology is an auditable architecture rather than a universal decision rule: it prescribes no species thresholds and does not claim validated taxonomic performance. Its purpose is to preserve the evidence chain through which genomic observations become progressively stronger taxonomic propositions.
UR  - https://esvpub.com/article/reproducible-phylogenomic-taxonomy-requires-traceable-links-from-insect-genomes-to-species-hypothese-fnzrxhlhj9qplfx
ER  -