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

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.

iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

“…Various metrics and graphs defining the barcode gap in a given data set are also included in the output. The program furthermore performs a simple threshold-based clustering of DNA sequences into OTUs, following the approach previously implemented in TaxonDNA (http:// taxondna.sourceforge.net/; Meier et al 2006), and outputs the resulting species partition as SPArT file (Miralles et al 2021) morphometricanalyzer is our tool for exploratory analysis of morphometric datasets. Integrative taxonomists do not only use molecular data.…”

“…As far as possible, the exchange files between these different tools are based on compatible standards, in order to minimize the number of format conversion steps (e.g. FASTA or NExUS for sequences, NEWICK for tree topologies, and SPArT for species partitions: Lipman & Pearson 1985;Maddison et al 1997;Miralles et al 2021). Additional efforts to make analytical and integrative processes more fluid through an ergonomically designed architecture represent nevertheless a priority task for future versions of iTaxoTools.…”

“…By performing a series of autocorrections of possible typos and then using a heuristic approach, latlonconverter is able to recognize and transform many idiosyncratic formats of geographical coordinates as they are commonly found in specimen databases containing geographical information taken by different researchers. With spartmapper, geographical coordinates combined with a species partition file (SPArT; Miralles et al 2021) can be previewed on a map, and then transformed into a kml file that plots all localities on Google Earth and visualizes the geographical distribution of the respective species hypotheses (Fig. 4).…”

iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

“…For some of these tools (PTP, GMYC, tr2, DELINEATE) the current pre-release GUI versions are still basic and only run under default settings; options to change and refine parameters will be added to the first complete 6 release. iTaxoTools also includes LIMES 2.0, a program to handle and compare species partitions obtained by these various approaches (Ducasse et al 2020, Miralles et al 2021.…”

“…DNAconvert also supports tab-delimited table input and its conversion to common sequence formats such as FASTA, NEXUS, or PHYLIP, to facilitate storage and management of sequences and sequence metadata in spreadsheet editors such as Microsoft Excel FIGURE 4. Screenshot of spartmapper, a tool that plots distribution records from geographical coordinates on a map and categorizes the records based on a species hypothesis provided as SPART file (Miralles et al 2021). The program allows live view and produces a kml file to visualize the records in Google Earth or Google Maps.…”