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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’.
Highlights
Generating an accurate ‘Tree of Life’ including every species that exists, and has ever existed, is an impossible challenge
We presented the largest Trichoptera phylogeny to date, which was built based on data from multiple genes for deep-level nodes and novel barcode data for terminal tips
Similar results were seen across Trichoptera [34] and in Chimarra [12]. All these studies noted that intermediate nodes were problematic when assessed by congruence to morphology and/or other molecular data
Summary
Generating an accurate ‘Tree of Life’ (phylogeny) including every species that exists, and has ever existed, is an impossible challenge. Because the COI gene has been shown to be homoplastic for recovering deep-level phylogenetic trees for Trichoptera [11,12], we applied a series of topological constraints to our analysis to concentrate the resolving power of the barcode data toward the tips of the tree. These constraints were generated from a variety rstb.royalsocietypublishing.org Phil. In a separate analysis with different input taxa, we generated trees for smaller, monophyletic groups within Trichoptera (usually families) For each of these groups, we downloaded the barcodes from BOLD, including several outgroups.
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