Integrative Taxonomy: From FASTA Pain to Species Gain with the interactive ''IntegraTax''

Abstract

Here we present IntegraTax, a tool for analysing and managing taxonomic projects that combine DNA data with other evidence such as morphology to arrive at integrative species boundaries. IntegraTax visualizes genetic clusters through single-linkage clustering ("Objective Clustering") and provides an interactive browser interface that allows users to record taxonomic decisions regarding species limits. Projects can be saved at any stage, thus allowing continuous tracking of annotations and taxonomic decisions across many sessions. A typical IntegraTax session starts with a set of sequences that are visualized as a cluster fusion diagram revealing the genetic distances between the sequences and clusters. Users can define an "instability zone" to distinguish clusters that are clearly distinct, likely representing separate species, from those whose status is uncertain based on genetic data alone. Based on the instability zone setting, IntegraTax then suggests which and how many specimens should be studied with a second source of data to validate species hypotheses. This process is facilitated by an interactive html environment that enables detailed specimen-level annotations. For example, a taxonomist can label which specimens have been studied, which clusters have been validated as species, and which species can be identified. By combining clustering, intuitive visualization, and easy annotation in one interactive framework, IntegraTax treats species hypotheses as annotated objects that can be inspected, revised, and exported at any stage, with documentation of examined specimens. It simultaneously allows researchers to manage taxonomy projects with tens of thousands of specimens and hundreds of species. This will become increasingly important as taxonomists start resolving the species boundaries of the millions of undescribed species particularly within hyperdiverse dark taxa.