Table 1.

Data types used and/or produced in the context of taxonomy, currently or potentially in the future, their predicted storage requirements and main issues to be solved to allow their efficient storage and reuse

	Current use in alpha-taxonomy	Potential and prospective use in taxonomy	Storage requirements (per specimen)	Established specialized repositories	Issues and gaps
Regular images (e.g., .jpeg, .pdf, .tiff)	Regularly used	Images of different kinds will continue to be a main workhorse of taxonomic description and identification; new perspectives by machine-learning character extraction	Moderate to very high, depending on image quality and quantity	Yes (many specialized and generalist repositories will accept images)	Images produced in taxonomic revisions are rarely submitted to repositories; images are often not linked to specimen identifiers
High-resolution images (stacks etc.) (e.g., .tiff)	Increasingly used, e.g. in insects	As with regular images	High to very high	Yes (many specialized and generalist repositories will accept images)	As with regular images
Annotated images	Very rarely used	Documentation of morphology of small-sized organisms (e.g., on a microscopic slide)	High to very high	Only few specialized repositories	Requires development of standards for repositories and submitters
3D microCT, photogrammetry, and laser scanners (e.g., stack of .tiff, polygon mesh such as .ply, .bend, .obj)	Used rarely but regularly, especially in vertebrates. Increasing use in invertebrates.	High importance to visualize internal features of an organism or 3D morphometrics, key method in cyberspecimen approaches	High to very high, depending on storage modality (e.g., polygon mesh vs. raw data) and level of resolution	Yes, several	Requires development of standards for repositories and submitters.See commentary by Hipsley and Sherratt (2019).
DNA sequences (Sanger) (e.g., .fasta, .fastq, .gb)	Regularly used for most organism groups, almost omnipresent in mycological taxonomy	DNA barcodes will continue to drive species identification and discovery, multigene phylogenies important for inferring relationships	Very low to low depending on the number of loci sequenced	Yes, several very well established ones	Sequences deposited in databases are not always curated postsubmission, leading to mismatches after taxonomic changes.
RNAseq (raw) (e.g., .fastq)	Not used	Potentially useful after read mapping and variant calling, but currently rarely used.	High	Yes (e.g., Sequence Read Archive)	No issues
RNAseq (assembly) (e.g., .fasta)	Very rarely used	Valuable source of sequences for phylogenomics and species delimitation	Low	Yes (e.g., Transcriptome Shotgun Assembly Sequence Database)	Assemblies are often not submitted to repositories, although they could be a valuable source of sequences for machine-learning species discovery pipelines
Amplicon (raw) (e.g., .fastq)	Not used	Not straightforward; requires filtering and preprocessing	High	Yes (e.g., Sequence Read Archive)	No issues
Amplicon (consensus OTUs) (e.g., .fasta)	Not used	Metabarcoding data helps ascertaining distribution and ecology of taxa	Low	Not really. Sequences 200 bp could be submitted to GenBank.	OTU consensus sequences from metabarcoding studies are in most cases not submitted to a repository, but could be important for DNA-based assessments of distribution of taxa; targeted and searchable repositories do not exist (GenBank does not accept sequences <200 bp)
Bait capture—raw (e.g., .fastq)	Not used	Only usable after assembly	High	Yes (e.g., Sequence Read Archive)	No issues
Bait capture—assembled (e.g., .fasta)	Rarely used (e.g., sequencing of historical types)	Very valuable source of sequences for phylogenomics and species delimitation—next-generation DNA barcoding	Low to moderate	Yes, well established, same ones as for Sanger sequences	Similar as for Sanger sequences
Genomes—raw (e.g., .fastq)	Not used	Only usable after assembly	Very high	Yes (e.g., Sequence Read Archive)	Similar as for Sanger sequences
Genomes—assembled (e.g., .fasta)	Very rarely used	Valuable source of sequences for phylogenomics and species delimitation	High	Yes	Similar as for Sanger sequences
Maldi-TOF (e.g., .raw, .mzXML, .mzML)	Sometimes used in mycology; commonly in prokaryotes.	Useful for chemotaxonomic approaches	Moderate to very high, depending of storage of spectra vs. raw data.	No	Requires development of standards for repositories and submitters
Near-infrared spectroscopy (e.g., .snirf, .csv, .spc, and many others)	Not used	Possibly useful for “metabolomic barcoding”	Moderate	No	Requires development of standards for repositories and submitters
GC-MS/ (e.g., .raw, .cdf, .D, .mzxml)	Sometimes used in mycology; commonly in prokaryotes.	Useful for chemotaxonomic approaches, e.g., fatty acid profiling in yeasts, and in bacterial taxonomy	Moderate to very high, depending of storage of spectra vs. raw data.	No	Requires development of standards for repositories and submitters; reference databases do exist.
NMR/TLC/HPLC (e.g., .raw , .data, ..cdf)	Rarely used (e.g., TLC and HPLC in lichenology)	Possibly useful for chemotaxonomic approaches	Moderate to very high, depending of storage of spectra vs. raw data.	No	Requires development of standards for repositories and submitters
Sounds (e.g., .wav, .mp3)	Regularly used in sound-producing animals	Very useful for species delimitation of sound-producing animals	Moderate to high, depending on file format and sound duration	Yes	Most repositories do not feature user-friendly submission procedures and often data are not open access
Videos (.avi, .mov, .mp4)	Very rarely used (e.g., to document specific behavior)	Limited value	Moderate to very high, depending on definition and duration	Yes	Extend image databases to accept videos if linked to specimens
Measurements (e.g., .csv, .xls. .txt)	Regularly used	Very useful basic data for diagnosis and identification of species	Very low	No	Requires development of standards for repositories and submitters
2D geometric morphometric data sets (e.g., .csv)	Very rarely used	Increasingly used for resolving species complexes	Very low to low	Yes	No issues
3D geometric morphometric data sets (e.g., .csv)	Very rarely used	Increasingly used for resolving species complexes, especially in combination with microCT scans	Very low to low	Yes	No issues

Note: Note that the second column specifically focuses on the current use of data types in alpha-taxonomic studies (mostly based on our survey reported below), not other taxonomy-related activities such as species identification or phylogenetics. Storage capacity required per specimen: very low (<0.1 MB), low (0.1–1 MB), moderate (1–10 MB), high (10–100 MB), and very high (100 MB).