Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea)

[Display omitted] •Guidelines for the systematic integration of molecular signature characters in taxon diagnoses.•Novel bioinformatic tool assesses consistency of signature characters detected in different alignments.•Application exemplified by improved diagnoses in Oligotrichea (Alveolata, Ciliophora, Spirotricha)•Curated datasets of oligotrichean sequences and reference alignments annotated with consensus signature characters. Traditionally, taxa following the botanical or zoological codes of nomenclature are diagnosed mainly by morphological characters, although integrative taxonomy advocates including additional features. While many taxonomic studies include DNA sequence analyses, a systematic integration of diagnostic molecular characters (signature characters) is still rare. Here, we suggest a practical guideline for the detection and evaluation of signature characters that provides the means necessary to complement diagnoses and facilitates identifications. The guideline comprises generally applicable criteria exemplified by a case study on an ecologically important group of planktonic protists, the Oligotrichea. The detection of signature characters and their discrete states in multiple sequence alignments is facilitated by the recently developed tool DeSignate. Moreover, we introduce a novel bioinformatic approach to test the influence of different alignment programs on the consistency of signature characters. Our workflow enabled detection of consensus signature characters for most tested taxa and inclusion of such characters in the diagnoses of three orders, eight families, and two genera in the Oligotrichea. The suggested approach is a step towards an integrative taxonomy linking reliable molecular sequence data to organisms’ traits.