Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species

Abstract

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

“…The aims of DNA barcoding are identification of unknown specimens via DNA barcodes of a priori defined taxonomic entities in databases (Merckelbach & Borges, 2020). The method is being increasingly utilized to tackle many issues, including illegal species exploitation, food fraud, biological invasions, and biodiversity monitoring (Bohmann et al, 2014;Gonçalves et al, 2015;Hubert et al, 2015;Khaksar et al, 2015).…”

“…In fact, even though there is sufficient evidence to support the species hypothesis and species delimiting, there are still many newly discovered species that have not been described (Pante et al, 2015), a situation that hinders taxonomic progress, species identification, and biodiversity estimation (Schlick-Steiner et al, 2007). Thus, if a species is marked as merely presumed rather than formally described and therefore fully established, the taxonomy is still incomplete; so, the transition from species delimitation to species description is still a major task to be accomplished (Merckelbach & Borges, 2020;Miralles & Vences, 2013).…”

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

“…The diagnosis of new species – rather than its lengthy description – represents the most important part of the alpha-taxonomic process, and in all Nomenclatural Codes, diagnosis can be based on molecular, as well as morphological characters (Renner, 2016). Several software tools have been proposed to extract diagnostic nucleotide positions of clades and species, either phylogeny-based (caos; Sarkar et al 2008) or primarily alignment-based (MolD, Fastachar, DeSignate: Fedosov et al 2019; Merckelbach & Borges 2020; Hütter et al 2020). In order to facilitate the use of such DNA characters in differential diagnoses of new species, we implemented a crucial new tool for DNA taxonomy named dnadiagnoser .…”

Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

“…It can be identified in batches, and requires less professional knowledge (Takahara, Minamoto, & Doi, 2013 ;Tinacci et al, 2018 ). To be specific, the aims of DNA barcoding are identification unkonwn specimens with DNA barcodes of a priori defined taxonomic entities in databases (Merckelbach & Borges, 2020 ). It is being increasingly utilized to tackle many issues including illegal species exploitation, food fraud and biological invasions, and for biodiversity monitoring (Bohmann et al, 2014 ;Collins, Armstrong, Holyoake, & Keeling, 2013 ;Frantine-Silva, Sofia, Orsi, & Almeida, 2015 ;Goncalves, Oliveira-Marques, Matsumoto, & Miyaki, 2015 ;Hubert, Espiau, Meyer, & Planes, 2015 ;Khaksar et al, 2015 ;Xiong et al, 2016 ).…”

“…If a species is marked as merely presumed rather than formally described and therefore fully established, the taxonomy is still incomplete. In many cases, the transition from species delimitation to species description is a major task to be accomplished (Jorger & Schrodl, 2013 ;Merckelbach & Borges, 2020 ).…”