An evaluation of errors in the mitochondrial COI sequences of Hydrachnidia (Acari, Parasitengona) in public databases.

Public molecular databases are fundamental tools for modern taxonomic studies whose usefulness rely on the soundness of the data within them. Here, we study potential errors that can arise along the data pipeline from sampling, specimen identification and molecular processing (digestion, amplification and sequencing) to the submission of sequences to these databases by using the DNA sequences of Hydrachnidia (Acari, Parasitengona) as a case study. Our results indicate that molecular information is available for only about 3% of the Hydrachnidia species known to date; yet, within this small percentage, errors are present in almost 5% of the species analyzed (0.5% of the sequences and almost 11% of the genera). This study underscores the scarcity of genetic data available for Hydrachnidia, but also that the proportion of errors in DNA sequences is relatively small. Even so, it highlights the danger associated with using DNA sequences from public databases, particularly for species identification, and reinforces the need for greater quality control measures and/or protocols to avoid an intensification of errors in the (post) genomics era. Finally, our study emphasizes that potential errors may also reveal cryptic diversity within a species.

Extended depth of focus ultraviolet imaging compared with laser scanning confocal microscopy for the study of micro-Arthropoda surface texture, with the description of a new species of Brachypodopsis (Acari: Hydrachnidia).

Visualization and representation are two processes at the core of basic biodiversity studies. Visualization involves the examination, sorting, and evaluation of similarities and differences among specimens by specialists who then assign them to the same or different species. It is a cognitive process. Representing involves transmitting the knowledge obtained in the first step to others, usually specialists of the group under study, generally through written descriptions aided by representative drawings and/or images. In this work, I describe a new species of water mite, Brachypodopsis guillermoi n. sp. (Acari, Hydrachnidia), from the island of Coiba off the Pacific coast of Panama, using both laser scanning confocal microscopy and extended depth of focus microscopy with visible (wavelength: 400-700 nm) and ultraviolet (wavelength: 365 nm) light. A comparison of the surface texture representation obtained from these imaging methods suggests that extended depth of focus ultraviolet microscopy can be a cost-effective alternative to laser scanning confocal microscopy for the description of exoskeletal features of micro-arthropods.

Molecular Correlation between Larval, Deutonymph and Adult Stages of the Water Mite Arrenurus (Micruracarus) Novus.

The systematics of many groups of organisms has been based on the adult stage. Morphological transformations that occur during development from the embryonic to the adult stage make it difficult (or impossible) to identify a juvenile (larval) stage in some species. Hydrachnidia (Acari, Actinotrichida, which inhabit mainly continental waters) are characterized by three main active stages-larval, deutonymph and adult-with intermediate dormant stages. Deutonymphs and adults may be identified through diagnostic morphological characters. Larvae that have not been tracked directly from a gravid female are difficult to identify to the species level. In this work, we compared the morphology of five water mite larvae and obtained the molecular sequences of that found on a pupa of the common mosquito Culex (Culex) pipiens with the sequences of 51 adults diagnosed as Arrenurus species and identified the undescribed larvae as Arrenurus (Micruracarus) novus. Further corroborating this finding, adult A. novus was found thriving in the same mosquito habitat. We established the identity of adult and deutonymph A. novus by morphology and by correlating COI and cytB sequences of the water mites at the larval, deutonymph and adult (both male and female) life stages in a particular case of 'reverse taxonomy'. In addition, we constructed the Arrenuridae phylogeny based on mitochondrial DNA, which supports the idea that three Arrenurus subgenera are 'natural': Arrenurus, Megaluracarus and Micruracarus, and the somewhat arbitrary distinction of the species assigned to the subgenus Truncaturus.

Water boatman survival and fecundity are related to ectoparasitism and salinity stress.

Salinity is increasing in aquatic ecosystems in the Mediterranean region due to global change, and this is likely to have an important impact on host-parasite interactions. Here we studied the relationships between infection by ectoparasitic water mites and salinity variation, on survival and fecundity of water boatmen Corixidae in the laboratory. Larvae of Sigara lateralis parasitised by larval mites (Hydrachna skorikowi) had lower survivorship, and failed to moult to the adult stage. In adult corixids (S. lateralis and Corixa affinis) fitness was reduced at high salinities and in individuals infected by H. skorikowi, both in terms of survival and fecundity. We also found evidence for parasitism-salinity interactions. Our results suggest that ongoing increases in salinity in Mediterranean ponds due to climate change and water abstraction for agriculture or urban use have a strong impact on water bugs, and that their interactions with ectoparasites may modify salinity effects.

Minimal barcode distance between two water mite species from Madeira Island: a cautionary tale.

In this work, we compare morphological and molecular data in their ability to distinguish between species of water mites (Acari, Prostigmata, Hydrachnidia). We have focused on the two species of the genus Lebertia inhabiting the island of Madeira. While traditional morphological traits were initially sufficient to distinguish between these two species, the molecular data were more dependable on the kind of analysis carried out. Single arbitrary genetic distance (e.g. a K2P distance below 2%) may lead to the conclusion that the specimens under study belong to the same species. Analysing the same specimens with the coalescent model has proved the evolutionary independence of both Lebertia clades in Madeira. Furthermore, multi-rate Poisson Tree Process analysis confirmed both lineages as independent species. Our results agree with previous studies warning of the dangers of rigid species delimitation based on arbitrary molecular distances. In addition, the importance of different molecular data approaches for correct species delimitation in water mites is highlighted.

What's in a (biological) name? The wrath of Lord Rutherford.

Names in taxonomy have seven different and important properties, some due to their existence in the context of classifications. Names confer or facilitate individuation, information storage and retrieval, and set theories of relationships, explanatory power, testable predictions, conceptual power, and language. No other way of naming in science is so powerful. And this is possible because taxonomic naming is done with full consideration of the theoretical specification of empirical data (characters) and their correspondence among taxa via homology statements. Since Darwin and Hennig, sets of homologous characters distributed among taxa allow precise hypotheses of a genealogical relationship, and this relationship is reflected in the way naming results in a classification.

Does counting species count as taxonomy? On misrepresenting systematics, yet again.

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as "metrics". As such, their one-dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end-user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top-ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.

Exceptionally well-preserved giant spermatozoa in male and female specimens of an ostracod Cypria ophtalmica (Crustacea: Ostracoda) from Late Glacial lacustrine sediments of Southern Carpathians, Romania.

Exceptionally well-preserved giant spermatozoa observed between abundant decalcified carapace valves of ostracods (Crustacea: Ostracoda) were found in Late Glacial to Holocene (14,400 to 10,000 cal years BP) lacustrine sediments in the southern Romanian Carpathians. Analysis by scanning electron microscopy and laser scanning confocal microscopy revealed good preservation of the appendages enabling specific identification as Cypria ophtalmica (Candonidae) and indication of the presence of both female and male specimens based on the sexual dimorphism of the second antenna. This record represents the oldest and richest direct evidence of virtually morphologically unaltered animal spermatozoa preserved in females after mating.

Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation.

There has been much discussion of the "taxonomic impediment". This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding. © The Willi Hennig Society 2011.

Morphological confocal microscopy in arthropods and the enhancement of autofluorescence after proteinase K extraction.

Procedures to study the molecular and morphological characteristics of microscopic organisms are often incompatible with each other. Therein, the realization of alternatives that make the characterization of these features compatible and simultaneously permit the deposition of the original material as a voucher sample into a reference collection is one of the foremost goals of biodiversity studies. In this study, we show that genomic extraction does not necessarily compromise the detailed study of the external morphology of microscopic organisms, and to do so, we used a group of aquatic mites (Acari, Hydrachnidia) as a test group. Hydrachnidia morphology is difficult to study when specimens have been stored in pure ethanol; however, proteinase K extraction leaves them flexible and easy to dissect, while, at the same time, maintaining all of their diagnostic features intact. Furthermore, autofluorescence is significantly enhanced after proteinase extraction. Our study was conducted with aquatic mites that were stored in absolute ethanol in the field and processed for DNA extraction using a Qiagen QIAamp minikit. Before and after molecular extraction, a laser scanning confocal microscopy morphological examination was carried out.

Science literacy and natural history museums.

It appears that developed countries, such as the US, the UK and Italy, are losing the race against irrationalism and arbitrary thinking in regard to nature and human interactions. The incidence of misguided beliefs and the detachment from and, in some cases, outright hostility toward science are on the rise. Paradoxically, this is probably the period in the history of advanced countries in which increasing public and personal efforts have been directed toward the dissemination of scientific knowledge to increase public understanding of science. This article vindicates the role of natural history museums in consolidating rational and critical scientific thinking while briefly examining scientific illiteracy in developed countries. It also discusses methods to improve the involvement of natural history museums in the promotion of rational thinking, the only appropriate avenue for objective knowledge.

Understanding complex systems: lessons from Auzoux's and von Hagens's anatomical models.

Animal and human anatomy is among the most complex systems known, and suitable teaching methods have been of great importance in the progress of knowledge. Examining the human body is part of the process by which medical students come to understand living forms. However, the need to preserve cadavers has led to the development of various techniques to manufacture models for teaching purposes. A variety of materials, such as wax, wood, papier-mache, or glass, have long been used to construct animal and plant models. In the case of the human body, the most innovative, yet controversial, method of preservation has been plastination, invented by the German physician Gunther von Hagens, by which actual human bodies are preserved as odourless and aesthetic models for teaching and exhibitions. We point out in our study that the 'hands-on' approach that some anatomical models allow, namely, the (clastic) disassembly and reassembly of the parts of complex systems and their models, is not only a crucial tool for learning, but is far superior to the simple passive observation that rigid, single-piece models allow. And what is valid for the learning of anatomy can be generalized to the acquisition of knowledge of other complex physical systems.

Traditional water mite fixatives and their compatibility with later DNA studies.

This work compares frozen water, 70% alcohol, Koenike's and Angelier's fluid as preservation media for water mites in terms of their eventual facilitation of DNA extraction and amplification. The time the mites spent in the fixatives ranged between 1 week and 25 years. Two molecular markers were amplified: 16S ribosomal DNA and CoI mitochondrial DNA. DNA was extractable and could be sequenced from specimens fixed in all the above media, although this generally became more difficult as time progressed. In the light of the known characteristics of these media, the results suggest Angelier's fluid to be the most practical, especially on long expeditions.