One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire

Marko Mutanen,Sean W J Prosser,Paul D N Hebert,Mari Kekkonen,Lauri Kaila

doi:10.1111/1755-0998.12361

Marko Mutanen, Sean W J Prosser + Show 3 more

Open Access

https://doi.org/10.1111/1755-0998.12361

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Abstract

Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance‐based, tree‐based and character‐based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree‐, distance‐ and character‐based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.

Highlights

Since its introduction 12 years ago (Hebert et al 2003a,b), DNA barcoding has been widely applied by taxonomists as indicated by hundreds of published taxonomic studies utilizing DNA barcodes (Teletchea 2010)
The benefits of using DNA barcodes for species delineation are clear especially when employed with novel species delineation methods (e.g. General Mixed Yule-coalescent GMYC (Pons et al 2006; Monaghan et al 2009; Fujisawa & Barraclough 2013)
This study was initially motivated by the uncertain taxonomy of the Elachista dispunctella complex which likely derives from two factors

Summary

Introduction

Since its introduction 12 years ago (Hebert et al 2003a,b), DNA barcoding has been widely applied by taxonomists as indicated by hundreds of published taxonomic studies utilizing DNA barcodes (Teletchea 2010). This work has shown that DNA barcoding is useful in its main function, that is rapid identification of specimens. Many studies have shown that DNA barcodes allow the unambiguous identification of more than 90% of species and typically place the remainder to a very small number of closely related species (Barrett & Hebert 2005; Kerr et al 2009; Lukhtanov et al 2009; Dinca et al 2011; Hausmann et al 2011, 2013). DNA barcodes help to support several other taxonomic tasks. The benefits of using DNA barcodes for species delineation are clear especially when employed with novel species delineation methods (e.g. General Mixed Yule-coalescent GMYC (Pons et al 2006; Monaghan et al 2009; Fujisawa & Barraclough 2013). As delineation methods generate a clearly defined result, the outcome is

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