Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks

Copyright © 2006 The Natural History MuseumThe majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon–Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.Y. Bertrand, F. Pleijel and G. W. Rous

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases

Does Party Support Help Candidates Win?

The parties’ congressional campaign committees have made it their business to strategically provide contributions to candidate campaigns in order to help their candidates win. However, the effectiveness of these contributions in terms of increasing the competitiveness of party-sponsored candidates remains untested. Using contribution data from the U.S. Federal Election Commission in a series of mixed effects models as well as a matching analysis, the receipt of direct party contributions and coordinated support is shown to significantly improve the competitive position of challengers but not open seat candidates in races for the House. Further, independent expenditures by the parties do not significantly increase candidates’ competitiveness. The implications of these results for future party strategies are explored

Characterization of inhibitors and substrates of Anopheles gambiae CYP6Z2

Three CYP6Z genes are linked to a major pyrethroid resistance locus in the mosquito Anopheles gambiae. We have expressed CYP6Z2 in Escherichia coli and produced a structural model in order to examine its role in detoxification. E. coli membranes co-expressing CYP6Z2 and An. gambiae P450 reductase (AgCPR) catalysed the dealkylation of benzyloxyresorufin with kinetic parameters K(m) = 0.13 microM; K(cat) = 1.5 min(-1). The IC(50) values of a wide range of compounds were measured. Pyrethroids cypermethrin and permethrin produced low IC(50) values, but were not metabolized. Plant flavanoids were the most potent inhibitors. Several compounds were shown to be substrates, suggesting that CYP6Z2 has broad substrate specificity and plays an important chemo-protective role during the herbivorous phase of the life-cycle

Isolation and molecular characterisation of Dunaliella tertiolecta with truncated light-harvesting antenna for enhanced photosynthetic efficiency

Here we report the development of a high-throughput selection protocol using random mutagenesis and live single-cell sorting to isolate cell lines from the algae Dunaliella tertiolecta with reduced chlorophyll content, with the aim to optimise the antenna size for increased photosynthetic efficiency. Two promising cell lines (lca1 and lca2) have been isolated that display a truncated light-harvesting antenna, and hence improved photosynthetic energy conversion efficiency by increasing the light intensity at which photosynthesis becomes saturated (Is). lca1 and lca2 differ significantly: the lca2 phenotype retains an ability to alter its antenna size in response to varying light intensity, whereas lca1 appears to have lost this ability and is ‘locked’ to a truncated antenna and high-light phenotype. Despite these clear differences, transcriptomic analysis shows that the expression profiles for differentially expressed nuclear-encoded photosynthetic genes is similar in both lca1 and lca2, possibly suggesting underlying mutations in the regulation of photosynthesis are causing the observed changes in phenotype rather than mutations impacting specific components of the photosynthetic apparatus. The combination of approaches presented here offer the capacity to substantially improve photosynthetic efficiency from any microalgal species irrespective of the extent to which it has been characterised genetically or the availability of molecular tools for rational engineering. It thus offers the potential to begin to exploit the huge natural diversity of microalgae for enhanced biomass production