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

Miralles, Aurelien; Ducasse, Jacques; Brouillet, Sophie; Flouri, Tomas; Fujisawa, Tomochika; Kapli, Paschalia; Knowles, L Lacey; ... Puillandre, Nicolas; + view all (2022) SPART: A versatile and standardized data exchange format for species partition information. Molecular Ecology Resources , 22 (1) pp. 430-438. 10.1111/1755-0998.13470. Green open access

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Abstract

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.

Type: Article
Title: SPART: A versatile and standardized data exchange format for species partition information
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1111/1755-0998.13470
Publisher version: https://doi.org/10.1111/1755-0998.13470
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: integrative taxonomy, LIMES v2.0, SPART, species delimitation programs, species partition format
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10167205
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