The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

Abstract

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue ‘From DNA barcodes to biomes’.

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

“…However, a fixed threshold of COI sequences is not appropriate for all taxonomic groups. In insects for instance, a 2% threshold provides effective identification at the species level of Ephemeroptera (Schmidt et al 2015;Webb et al 2012;Zhou et al 2010), Lepidoptera (Zahiri et al 2014) and Trichoptera (Zhou et al 2016), while a 2.2% threshold appears appropriate for Heteroptera (Knebelsberger et al 2014), 2.5% for aquatic beetles (Monaghan et al 2005), and >3% for various dipteran groups (Nzelu et al 2015;Renaud et al 2012). Furthermore, an average threshold of 4-5% appears appropriate for most Chironomidae (Lin et al 2015;Meier et al 2015), even if a 7% threshold has been reported for closely related species in this family (Carew & Hoffmann 2015).…”

Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands

“…Cristescu (2014) raised the urge for a coordinated progression of species barcoding that integrates taxonomic expertise and genetic data. For the family Chironomidae an extended and reliably curated barcode database (analogous to the Trichoptera Barcode of Life Database, Zhou et al 2016) would be highly useful for integrating chironomids in standard freshwater biomonitoring which enhance water quality assessments and might lead to better management of aquatic ecosystems.…”

Progress, pitfalls and parallel universes: a history of insect phylogenetics

“…Again, this study proved that such a thing can work, and supported several disputed internal relationships. Zhou et al [345] produced a phylogeny of over 16 000 barcode haplotypes from Trichoptera, but this study differed in that constraints were used to insulate the phylogeny from predictable errors. These studies provide evidence that producing huge phylogenies from public databases is feasible.…”