DNA barcoding and taxonomy: dark taxa and dark texts

Abstract

Both classical taxonomy and DNA barcoding are engaged in the task of digitising the living world. Much of the taxonomic literature remains undigitised. The rise of open access publishing this century, and the freeing of older literature from the shackles of copyright has greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid-to late twentieth century remains offline ("dark texts"). DNA barcoding is generating a wealth of computable data that in many ways is much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These "dark taxa" hamper the classical method of integrating biodiversity data using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature, and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global "digital dashboard" to assess the extent to which biodiversity data is available online.

The systematics of Lobophora (Dictyotales, Phaeophyceae) in the western Atlantic and eastern Pacific oceans: eight new species

“…As a result, many molecularly defined PSH remain unnamed especially in organisms with simple morphologies and plagued with homoplasies such as algae (e.g., Lobophora: Vieira et al 2016Vieira et al , 2017Portieria: Payo et al 2013, Ostreobium: Sauvage et al 2016. These molecularly identified but unnamed species have been dubbed the "dark taxa" by Page (2016). Six of the eight newly described species in this study, L. colombiana, L. crispata, L. delicata, L. dispersa, L. panamensis, and L. tortugensis, were already identified as PSH in a worldwide Lobophora diversity assessment based primarily on cox3 DNA sequences .…”

“…DNA extraction from herbarium specimens was attempted using DNeasy Blood & Tissue Kit (Qiagen) and PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) as they were more efficient in older, or non-silica preserved, specimens. We chose to amplify two chloroplast genes (rbcL, psbA) and one mitochondrial gene (cox3) because of their successful use in recent Lobophora phylogenetic studies (e.g., Sun et al 2012, 2016. Information on primers, PCR, and sequencing conditions are listed in Table S2 in the Supporting Information.…”

“…Species delimitation analyses were conducted independently on the same alignments used for phylogenetic analyses, using three approaches: General Mixed Yule Coalescent (GMYC; Pons et al 2006); Automatic Barcode Gap Discovery (ABGD; Puillandre et al 2012); and the Poisson Tree Processes (PTP; Zhang et al 2013). These species delimitation methods (SDM) have been used previously to successfully delineate not only Lobophora species (e.g., Vieira et al 2014, 2016, Schultz et al 2015 but also species in other Dictyotales genera such as Dictyota (Tronholm et al 2010), and Padina (Silberfeld et al 2013).…”

“…The current known global Lobophora diversity is appraised to be in the range of 100-140 species but to date only 28 have been formally described (Guiry and Guiry 2018). The remaining molecularly defined species continue undescribed, contributing to what is known as "dark taxa" (Page 2016). The highest species diversity of Lobophora is the Central Indo-Pacific, while only 14 species are reported for the Western Atlantic Ocean (WA) and five in the Eastern Pacific Ocean (EP; Schultz et al 2015, 2017.…”

“…The three remaining undescribed species were originally recognized by Schultz et al (2015) and were not found in our extensive field and herbarium collections. It is hoped that our contribution will lessen the harmful effects of "dark taxa" sensu Page (2016) with respect to marine macroalgae diversity. However, our knowledge of Lobophora species richness in the WA and EP oceans is a work in progress.…”