Abstract
DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.
Highlights
A shortage of taxonomic expertise is one of the current challenges facing those engaged in identifying, classifying, utilising and conserving the world’s biodiversity (Giangrande 2003, Vernooy et al 2010, Cardoso et al 2011, Ebach et al 2011, Wägele et al 2011, Sluys 2013)
As mitochondrial pseudogenes are common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers
Specimens for DNA barcoding were collected during two workshops of the Training in Tropical Taxonomy programme run by the Smithsonian Tropical Research Institute in Bocas del Toro, Panama
Summary
A shortage of taxonomic expertise is one of the current challenges facing those engaged in identifying, classifying, utilising and conserving the world’s biodiversity (Giangrande 2003, Vernooy et al 2010, Cardoso et al 2011, Ebach et al 2011, Wägele et al 2011, Sluys 2013). The recent application of DNA techniques, the compilation of large taxonomic databases (Costello et al 2013) and the use of bioinformatics approaches like GIS, have rejuvenated interest in taxonomic data. This increase in relevance and interest has been counteracted by the gradual loss of integrative taxonomic expertise (Drew 2011, Coleman 2015). This recent decline has limited attempts to document the world's biodiversity and limits the rate at which high-profile initiatives, such as the Census for Marine Life, Barcode of Life (BOLD; Ratnasingham and Hebert 2007) and WoRMS, can generate, agglomerate and synthesise biodiversity knowledge. There is a particular shortage of taxonomists and data from developing countries and countries with economies in transition
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
