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

Vences, Miguel; Miralles, Aurélien; Brouillet, Sophie; Ducasse, Jacques; Fedosov, Alexander; Kharchev, Vladimir; Kostadinov, Ivaylo; Kumari, Sangeeta; Patmanidis, Stefanos; Scherz, Mark D.; Puillandre, Nicolas; Renner, Susanne S.

doi:10.11646/megataxa.6.2.1

Cited by 84 publications

(35 citation statements)

References 49 publications

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“…For COI and 16S , we retrieved sequences from the nucleotide archive of GenBank combining the search term (i) “Madagascar” successively with (ii) “Actinopterygii”, “Chondrichthyes”, “Bedotiidae”, “Cichlidae”, and “ Pachypanchax ”, and (iii) “ COI ”, “ cox1 ”, and “ 16S ”. Sequences were downloaded as GenBank flatfiles and transformed into a tab-delimited file using DNAconvert as implemented in iTaxoTools [ 38 ]. Furthermore, we downloaded in tsv format one data set [ 35 ] from the BOLD data portal ( https://www.boldsystems.org/ ) and added it to the table.…”

Section: Methodsmentioning

confidence: 99%

Towards a DNA barcode library for Madagascar’s threatened ichthyofauna

Vences¹,

Stützer²,

Raminosoa

et al. 2022

PLoS ONE

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In order to improve the molecular resources available for conservation management of Madagascar’s threatened ichthyofauna, we elaborated a curated database of 2860 mitochondrial sequences of the mitochondrial COI, 16S and ND2 genes of Malagasy fishes, of which 1141 sequences of freshwater fishes were newly sequenced for this data set. The data set is mostly composed of COI (2015 sequences) while 16S and ND2 sequences from partly the same samples were used to match the COI sequences to reliably identified reference sequences of these genes. We observed COI uncorrected pairwise genetic distances of 5.2‒31.0% (mean 20.6%) among species belonging to different genera, and 0.0‒22.4% (mean 6.4%) for species belonging to the same genus. Deeply divergent mitochondrial lineages of uncertain attribution were found among Malagasy freshwater eleotrids and gobiids, confirming these groups are in need of taxonomic revision. DNA barcodes assigned to introduced cichlids (tilapias) included Coptodon rendallii, C. zillii, Oreochromis aureus (apparently a new country record), O. cf. mossambicus, O. niloticus, and one undetermined species of Oreochromis, with sequences of up to three species found per location. In aplocheiloid killifishes of the genus Pachypanchax, most species from northern Madagascar had only low mitochondrial divergences, three of these species (P. omalonotus, P. patriciae, and P. varatraza) were not reciprocally monophyletic, and one genetically deviant lineage was discovered in a northern locality, suggesting a need for partial taxonomic revision of this genus. While the lack of voucher specimens for most of the samples sequenced herein precludes final conclusions, our first step towards a DNA barcoding reference library of Madagascar’s fishes already demonstrates the value of such a data set for improved taxonomic inventory and conservation management. We strongly suggest further exploration of Madagascar’s aquatic environments, which should include detailed photographic documentation and tissue sampling of large numbers of specimens, and collection of preserved voucher specimens as well as of living fish for the buildup of ex situ assurance populations of threatened species complying with the One Plan Approach proposed by the IUCN SSC Conservation Breeding Specialist Group (CBSG).

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Section: Methodsmentioning

confidence: 99%

Towards a DNA barcode library for Madagascar’s threatened ichthyofauna

Vences¹,

Stützer²,

Raminosoa

et al. 2022

PLoS ONE

Self Cite

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“…It does not require any dependencies besides standard python libraries. mold is also accessible through a graphical web interface (beta version currently at https://mold.testa pi.me/) and as an iTaxoTools module (Vences et al, 2021).…”

Section: Overview Of the Mold Softwarementioning

confidence: 99%

mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions

Fedosov

Achaz

Gontchar

et al. 2022

Molecular Ecology Resources

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DNA data are increasingly being used for phylogenetic inference, and taxon delimitation and identification, but scarcely for the formal description of taxa, despite their undisputable merits in taxonomy. The uncertainty regarding the robustness of DNA diagnoses, however, remains a major impediment to their use. We have developed a new program, mold, that identifies diagnostic nucleotide combinations (DNCs) in DNA sequence alignments for selected taxa, which can be used to provide formal diagnoses of these taxa. To test the robustness of DNA diagnoses, we carry out iterated haplotype subsampling for selected query species in published DNA data sets of varying complexity. We quantify the reliability of diagnosis by diagnosing each query subsample and then checking if this diagnosis remains valid against the entire data set. We demonstrate that widely used types of diagnostic DNA characters are often absent for a query taxon or are not sufficiently reliable. We thus propose a new type of DNA diagnosis, termed “redundant DNC” (or rDNC), which takes into account unsampled genetic diversity, and constitutes a much more reliable descriptor of a taxon. mold successfully retrieves rDNCs for all but two species in the analysed data sets, even in those comprising hundreds of species. mold shows unparalleled efficiency in large DNA data sets and is the only available software capable of compiling DNA diagnoses that suit predefined criteria of reliability.

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“…The proposed format is already implemented in several widely‐used SD programs. The matricial SPART output file is already generated by GUI‐driven standalone versions (https://github.com/iTaxoTools; http://itaxotools.org/ of ABGD, ASAP, GMYC, PTP, mPTP, TR2 and DELINEATE (Vences et al., 2021), by the native Python version of TR2, and in the web versions of ABGD and ASAP; and in progress for the Python versions of GMYC and PTP. The implementation of the SPART.XML output will become available by the end of 2021 for ABGD and ASAP.…”

Section: Tools Already Implementing Spart and Future Perspectivesmentioning

confidence: 99%

“…Ducasse et al., 2020) for species partitions from SPART files (including each one or several species partitions); (2) merge species partitions included in different SPART files into one SPART file, (3) import species partition(s) table(s) from spreadsheet editors such as Microsoft EXCEL and save it (them) into a single SPART file. A new software tool named SPARTMAPPER has also been developed (Vences et al., 2021); it takes SPART files as input along with a tab‐delimited series of geographical coordinates linked to specimen names, plots the distribution of alternative delimited species on a map, and exports a.kml file to visualize this information in Google Earth.…”

Section: Tools Already Implementing Spart and Future Perspectivesmentioning

confidence: 99%

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

Miralles

Ducasse²,

Brouillet

et al. 2021

Molecular Ecology Resources

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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.

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

Cited by 84 publications

References 49 publications

Towards a DNA barcode library for Madagascar’s threatened ichthyofauna

Towards a DNA barcode library for Madagascar’s threatened ichthyofauna

mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions

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

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