Antonio G. Valdecasas

On the extended depth of focus algorithms for bright field microscopy.

Microscopes offer a limited depth of focus which precludes the observation of a complete image of a three-dimensional (3D) object in a single view. Investigations, by a variety of researchers, have led to the development of extended depth of focus algorithms for serial optical slices of microscopic 3D objects in recent years. However, to date, no quantitative comparison of the different algorithms has been performed, generally leaving the evaluation to the subjective qualitative appreciation of the observer. In this paper we use three different tests for extended depth of focus algorithm evaluation and test 10 different algorithms, some of them have been adapted (by us) for a series of optical slices. However, the main contribution of the paper is a new improved algorithm for computing the extended depth of focus.

Mapping the biosphere: Exploring species to understand the origin, organization and sustainability of biodiversity

The time is ripe for a comprehensive mission to explore and document Earths species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.

Reliance on the citation index undermines the study of biodiversity

Sir — The popularity of the Science Citation Index (SCI) as a measure of ‘good’ science is damaging basic taxonomic work, without which the study of biodiversity would not be possible. Basic taxonomic work is not highly cited, except in ‘hot’ taxa like the genus Homo. The number of authors citing a paper during the short period of time (ten years) that the SCI uses for its statistics is relatively low. But taxonomy papers continue to be referred to and cited for more than a century after their publication. Almost every good taxonomic paper becomes a classic in the literature. High-quality basic taxonomic work — the description of new taxa and revision of older ones — is expensive and timeconsuming. Many of the most interesting finds are from ‘exotic’ locations, requiring travelling, sampling, preparing, sending back collections, writing descriptions, illustrating and so on. The resulting papers are rated low in the SCI, even when published in high-quality specialist journals, and are unlikely to impress managers or funding agencies. So a paradox arises: concern for biodiversity goes together with a dismissal of the foundation of any biodiversity work, which is the proper description of taxa. If there is reluctance to fund this kind of work because of low citations, and with fewer journals available to publish their findings, the most basic research in biodiversity is doomed to disappear, as is already happening. Antonio G. Valdecasas*, Santiago Castroviejo†, Leslie F. Marcus‡ *Museo Nacional de Ciencias Naturales (CSIC), José Gutierrez Abascal 2, 28006 Madrid, Spain †Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain ‡Department of Biology, Queens College of City University of New York, Flushing, New York 11367, USA

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.

Conservation to the Rescue of Taxonomy

Biodiversity studies and conservation measures depend on good and up-to-date taxonomic data. General faunistic lists are the result of long periods of sampling. How many species on a global list are actually living in an area can only be answered by updating inventories. The progressive disappearance of taxonomic specialists and the undervaluation of their work is not only unjustified, but could lead to specialists from other disciplines working with meaningless data.

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.

Diez retos para transformar la Taxonomía

Taxonomy is at a crossroads. Although taxonomy has an impressive past, having documented and organized knowledge of nearly two million species, most of the basic work required to describe Earth’s biodiversity remains undone. Factors that guide the choices of research topics in science are considered. Ten challenges are presented to the taxonomic community that we believe will accelerate its revitalization.

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-maché, 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.

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.

Parasitism by water mites in native and exotic Corixidae: are mites limiting the invasion of the water boatman Trichocorixa verticalis (Fieber, 1851)?

Abstract The water boatman Trichocorixa verticalis verticalis (Fieber 1851) is originally from North America and has been introduced into the southern Iberian Peninsula, where it has become the dominant Corixidae species in saline wetlands. The reasons for its success in saline habitats, and low abundance in low salinity habitats, are poorly known. Here we explore the potential role of water mites, which are typical parasites of hemipterans, in the invasion dynamics of T. v. verticalis. We compared infection levels between T. v. verticalis and the natives Sigara lateralis (Leach, 1817) and S. scripta (Rambur, 1840). No mites were found in saline wetlands where T. v. verticalis is highly dominant. Larvae of two mite species were identified infecting corixids in habitats of lower salinity: Hydrachna skorikowi and Eylais infundibulifera. Total parasite prevalence and prevalence of E. infundibulifera were significantly higher in T. v. verticalis compared with S. lateralis and S. scripta. Mean abundance of total infection and of E. infundibulifera and H. skorikowi were also higher in T. v. verticalis. When infected with H. skorikowi, native species harbored only one or two parasite individuals, while the smaller T. v. verticalis carried up to seven mites. When infected with E. infundibulifera, native species harboured only one parasite individual, while T. v. verticalis carried up to 6. Mite size didn’t differ among host species, suggesting that all are suitable for engorgement. Both mite species showed a negative correlation between prevalence and salinity. T. v. verticalis susceptibility to parasitic mites may explain its low abundance in low salinity habitats, and may contribute to the conservation of native corixids. The success of T. v. verticalis in saline wetlands may be partly explained by the absence of parasitic mites, which are less halotolerant.