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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'.

SUBMITTER: Zhou X

PROVIDER: S-EPMC4971193 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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

Zhou Xin X Frandsen Paul B PB Holzenthal Ralph W RW Beet Clare R CR Bennett Kristi R KR Blahnik Roger J RJ Bonada Núria N Cartwright David D Chuluunbat Suvdtsetseg S Cocks Graeme V GV Collins Gemma E GE deWaard Jeremy J Dean John J Flint Oliver S OS Hausmann Axel A Hendrich Lars L Hess Monika M Hogg Ian D ID Kondratieff Boris C BC Malicky Hans H Milton Megan A MA Morinière Jérôme J Morse John C JC Mwangi François Ngera FN Pauls Steffen U SU Gonzalez María Razo MR Rinne Aki A Robinson Jason L JL Salokannel Juha J Shackleton Michael M Smith Brian B Stamatakis Alexandros A StClair Ros R Thomas Jessica A JA Zamora-Muñoz Carmen C Ziesmann Tanja T Kjer Karl M KM

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20160901 1702

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 mos ...[more]

PMID: 27481793

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Project description:Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].

Dataset Information

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

Publications

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

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