Applying taxonomic boundaries for species identification (ABIapp): A convenient and accurate application for species delimitation of parasitic helminths

Abstract

Background: Parasitic helminths are highly diverse and ubiquitously distributed in various environments and hosts. Their vast species diversity renders morphological and molecular species delimitation challenging, due to phenotypic and genotypic variations. Currently used approaches to species delimitation are generally computationally intensive. Here, using genetic distances, we developed and validated a simple and easy-to-use application, Applying taxonomic Boundaries for species Identification (ABIapp), to aid in helminth species delimitation. Methodology/Principal Findings: ABIapp uses a database of cut-off genetic distances obtained using the K-means algorithm to determine helminth taxonomic boundaries for ten genetic markers: The nuclear 18S and 28S rRNA genes, ITS1 and 2 regions, and the mitochondrial 12S and 16S rRNA, COI , COII, cytB, and ND1 genes. ABIapp was written in R, and the Shiny framework was used to produce an interactive and user-friendly interface. ABIapp requires just three types of input (genetic distance, genetic marker, helminth group) that are easily generated through basic morphological and molecular analysis. To validate ABIapp’s accuracy and robustness for use, validation was performed both in silico and with actual specimens. Prior to validation, ABIapp’s database of genetic distances and species used was increased to broaden the app’s applicability. In silico validation was conducted by obtaining 534 genetic distances from 91 publications and inputting these into ABIapp. Using confusion matrices, an overall classification accuracy of 79% was achieved, demonstrating the robustness and accuracy of ABIapp. Using sequences of the 12S, 16S, COI, and 18S rRNA genes obtained from ten representative helminth specimens, an overall classification accuracy of 75% was achieved. Conclusions/Significance: Our results demonstrate the applicability and robustness of ABIapp for helminth species delimitation using ten common genetic markers. With a user-friendly interface, coupled with minimal and simple data input and robust classification accuracy, ABIapp provides helminth researchers with a convenient tool for helminth species delimitation.