Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca)

Abstract

Background: Decapods 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 findings: We 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/significance: Decapod 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.

Figure 1. Intraspecific diversity assessment: the effect of sampling bias, non-monophyletic clades, putative cryptic species and congeneric species with low genetic distance.

Solid lines represent the raw data for the total data set (A_R, black lines) and for the dataset in which non-monophyletic clades, putative cryptic species and congeneric species with low genetic distance were removed (B_R, blue lines). The dashed lines represent results for the data in which all taxa have the same weight (mean values of genetic distance), for the total (black, A_M) and trimmed (blue, B_M) datasets respectively.

Figure 2. Frequency distribution of COI K2P distances (%) intraspecies (S), intragenus (G), and intrafamily (F) from 302 species, 154 genera, and 58 families.

Figure 3. Boxplot distribution of 11 selected families of the Decapoda order intraspecies (S), intragenus (G), and intrafamily (F) COI K2P distances (%).

The plot summarises median (central bar), position of the upper and lower quartiles (called Q1 and Q3, central box), extremes of the data (dots) and very extreme points of the distribution that can be considered as outliers (stars). Points are considered as outliers when they exceed Q3+1.5(Q3-Q1) for the lower part, where (Q3-Q1) is the inter quartile range. The number of sequences, species, and genera per family are given in Table 3. Mean K2P distance (%) ± SE within taxa are: Chirostylidae S = 0.701±0.028 and G = 8.999±.039; Lithodidae S = 0.416±0.021, G = 6.376±.137 and F = 11.392±0.063; Paguridae S = 0.686±.045 and G = 17.173±0.084; Parastacidae S = 1.375±0.131, G = 11.017±0.078 and F = 22.681±0.064; Majidae S = 0.547±0.028, G = 9.643±0.214 and F = 21.084±0.061; Portunidae S = 0.453±0.024, G = 14.826±0.311 and F = 28.929±0.047; Galatheidae S = 0.285±0.017, G = 16.839±0.04 and F = 22.355±0.033; Atyidae S = 0.758±0.041, G = 13.475±0.352 and F = 25.218±0.056; Pandalidae S = 0.49±0.042, G = 20.924±0.213 and F = 25.617±0.07; Palaemonidae S = 0.812±0.055, G = 20.157±0.108 and F = 25.398±0.048; Crangonidae S = 0.344, G = 19.991±0.514 and F = 25.241±0.103.

Figure 4. Boxplot distribution of ascending GC content (%) from 11 selected families.

The number of sequences, species, and genera per family is indicated in Table 3 and statistic values in Table 4.