Abstract
BackgroundDecapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world.Methodology/Principal FindingsWe contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content.Conclusions/SignificanceDecapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.
Highlights
In recent decades, the loss of biodiversity has been recognized as a major global environmental problem, with much effort being targeted at biodiversity conservation [1,2,3,4,5]
The number of sequences per species varied between 1–32, with a mean of 5, and an average length of 620 base pairs. Within this newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification. Such cases were distributed throughout the Decapoda, including the long legged crabs Macropodia longipes
Our analysis shows a general increase in the molecular divergence of c oxidase subunit 1 (COI) with taxonomic rank, a trend that suggests that morphological taxonomy is roughly in agreement with DNA evolution
Summary
The loss of biodiversity has been recognized as a major global environmental problem, with much effort being targeted at biodiversity conservation [1,2,3,4,5]. The proposed threshold value of 2% COI sequence divergence [12], and 0.16 patristic distances for species delimitation in Crustacea [10] may, be problematic in some cases (i.e., heteroplasmy, hybridization, incomplete lineage sorting, nuclear introgression of mtDNA [38,39,40,41,42]) because DNA barcoding follows the typological species approach and species are entities continue to evolve To cope with such limitations, DNA barcode sequences have been analysed based on other species concepts [38], and referred to as Recognizable Taxonomic Units [43], or Molecular Operational Taxonomic Units [44]. It remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
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
