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SPART, a versatile and standardized data exchange format for species partition information

View ORCID ProfileAurélien Miralles, Jacques Ducasse, Sophie Brouillet, View ORCID ProfileTomas Flouri, View ORCID ProfileTomochika Fujisawa, View ORCID ProfilePaschalia Kapli, View ORCID ProfileL. Lacey Knowles, Sangeeta Kumari, View ORCID ProfileAlexandros Stamatakis, View ORCID ProfileJeet Sukumaran, Sarah Lutteropp, View ORCID ProfileMiguel Vences, View ORCID ProfileNicolas Puillandre
doi: https://doi.org/10.1101/2021.03.22.435428
Aurélien Miralles
1Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles 57 rue Cuvier, CP 50, 75005 Paris, France
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  • ORCID record for Aurélien Miralles
  • For correspondence: miralles.skink@gmail.com m.vences@tu-braunschweig.de nicolaspuillandre@gmail.com
Jacques Ducasse
249 rue Eugène Carrière, 75018 Paris, France
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Sophie Brouillet
1Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles 57 rue Cuvier, CP 50, 75005 Paris, France
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Tomas Flouri
3Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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Tomochika Fujisawa
4Center for Data Science and Education and Research, Shiga University, 1-1-1 Banba, Hikone, 522-8522, Shiga, Japan
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Paschalia Kapli
3Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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L. Lacey Knowles
5Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI 48109, USA
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Sangeeta Kumari
6Braunschweig University of Technology, Zoological Institute, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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Alexandros Stamatakis
7Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg Germany
8Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
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Jeet Sukumaran
9Biology Department, LS 262, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4614, USA
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Sarah Lutteropp
7Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg Germany
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Miguel Vences
6Braunschweig University of Technology, Zoological Institute, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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  • For correspondence: miralles.skink@gmail.com m.vences@tu-braunschweig.de nicolaspuillandre@gmail.com
Nicolas Puillandre
1Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles 57 rue Cuvier, CP 50, 75005 Paris, France
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  • For correspondence: miralles.skink@gmail.com m.vences@tu-braunschweig.de nicolaspuillandre@gmail.com
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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 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 to optionally report support values, 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.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 22, 2021.
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SPART, a versatile and standardized data exchange format for species partition information
Aurélien Miralles, Jacques Ducasse, Sophie Brouillet, Tomas Flouri, Tomochika Fujisawa, Paschalia Kapli, L. Lacey Knowles, Sangeeta Kumari, Alexandros Stamatakis, Jeet Sukumaran, Sarah Lutteropp, Miguel Vences, Nicolas Puillandre
bioRxiv 2021.03.22.435428; doi: https://doi.org/10.1101/2021.03.22.435428
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SPART, a versatile and standardized data exchange format for species partition information
Aurélien Miralles, Jacques Ducasse, Sophie Brouillet, Tomas Flouri, Tomochika Fujisawa, Paschalia Kapli, L. Lacey Knowles, Sangeeta Kumari, Alexandros Stamatakis, Jeet Sukumaran, Sarah Lutteropp, Miguel Vences, Nicolas Puillandre
bioRxiv 2021.03.22.435428; doi: https://doi.org/10.1101/2021.03.22.435428

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