Monday reads on a Tuesday? Well, I was a little busy yesterday and just managed to get a job ad out. As a result here my reading suggestions with a slight delay:
DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.
DNA barcoding of crickets, katydids, and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany, and Switzerland
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life, and Swiss Barcode of Life. Our dataset includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. 93 of these 122 species (76.2%, including all Ensifera), can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.
The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding
Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.
Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes
Species diversity in most protistan groups has been underestimated. Many morpho-species are in fact complexes that require detailed morphometric studies to be discriminated. However, which traits can be used for species descriptions remains in many cases unclear. The testate amoeba genus Quadrulella produces self-secreted, siliceous plates with a very characteristic square shape—such plates were assumed to be synapomorphic of the genus. Here we demonstrate that Quadrulella symmetrica (the most common Holarctic species) is not monophyletic. Square plate size and arrangement, test size and general shape are efficient criteria for species discrimination. Based on morphology and sequence data, we describe Quadrulella variabilis sp. nov. from Switzerland, and Quadrulella madibai sp. nov. from South Africa, and confirm the validity of Q. alata. The former species Q. subcarinata does not belong to the genus Quadrulella. We therefore transfer this species to the new genus Mrabella gen. nov. Our results show that hyalosphenids presenting siliceous square shell plates do not form a monophyletic clade. Several possible hypotheses about the origins of square plates are discussed. Additionally, this comprehensive phylogenetic analysis of the family Hyalospheniidae confirms that the genus Nebela is paraphyletic and needs to be divided into genera based on general shell shape: Nebela sensu stricto, Longinebela gen. nov., Planocarina gen. nov., Gibbocarina gen. nov., Cornutheca gen. nov. and Mrabella gen. nov.
Not DNA barcoding per se but a very interesting conceptual study:
Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning
Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity–ecosystem-function literature.