SPART: A versatile and standardized data exchange format for species partition information

Area of Science:

• Taxonomy and Systematics
• Computational Biology
• Bioinformatics

Background:

• Species delimitation (SD) uses diverse data and computational tools to objectively define species.
• Current SD tools lack interoperability, hindering comparisons of different species partitions.
• Alpha-taxonomists do not routinely use formalized SD approaches due to these limitations.

Purpose of the Study:

• To introduce a standardized format, SPART, for species partitions.
• To enable compatibility and data exchange between different species delimitation software.
• To streamline the comparison of alternative species partitions for robust species boundary evaluation.

Main Methods:

• Development of the Species Partition (SPART) format.
• SPART allows reporting of inferred species assignments, support values, and analysis parameters.
• Two variants proposed: matricial SPART (human-readable) and SPART.XML (block format).

Main Results:

• SPART format successfully enables compatibility between various SD tools.
• ABGD, DELINEATE, GMYC, PTP, and TR2 adapted to output SPART files.
• LIMES software updated to import, export, merge, and split SPART files.

Conclusions:

• The SPART format addresses the critical need for interoperability in species delimitation.
• Facilitates objective comparison of species partitions derived from different methods.
• Promotes wider adoption of computational tools in taxonomic practice.