Physiology and taxonomy of scleractinian corals: a case study in the genus Stylophora

The morphology and skeletal characteristics of colonies of the coral genus Stylophora living on the reef edge at 1 m depth on the Jordanian coast of the Gulf of Aqaba (Red Sea) are those of S. mordax (Dana 1846) which has not been reported previously from that area. These colonies were considered earlier as ecomorphs of S. pistillata (Esper 1797) which lives down to at least 67 m on the reef slopes. Growth, organic content and metabolism were compared in colonies living at different depths (1,5,10 and 30 m). The trends of twelve parameters between 1 and 5 m were different from the variation observed between 5 and 30 m. Colonies living at 1 m have a higher chlorophyll content but a lower metabolic activity and growth rate than colonies living at 5 m. Most of these pecularities cannot be explained by the influence of environmental factors. It is therefore suggested that S. mordax is a valid taxon.     

Merging taxonomy with ecological population prediction in a case study of Vibrionaceae

We synthesized population structure data from three studies that assessed the fine-scale distribution of Vibrionaceae among temporally and spatially distinct environmental categories in coastal seawater and animals. All studies used a dynamic model (AdaptML) to identify phylogenetically cohesive and ecologically distinct bacterial populations and their predicted habitats without relying on a predefined genetic cutoff or relationships to previously named species. Across the three studies, populations were highly overlapping, displaying similar phylogenetic characteristics (identity and diversity), and were predominantly congruent with taxonomic Vibrio species previously characterized as genotypic clusters by multilocus sequence analysis (MLSA). The environmental fidelity of these populations appears high, with 9 out of 12 reproducibly associating with the same predicted (micro)habitats when similar environmental categories were sampled. Overall, this meta-analysis provides information on the habitat predictability and structure of previously described species, demonstrating that MLSA-based taxonomy can, at least in some cases, serve to approximate ecologically cohesive populations.     

Inference in morphological taxonomy using collinear data and small sample sizes: Monogenean sclerites (Platyhelminthes) as a case study

Vignon, M. (2011) Inference in morphological taxonomy using collinear data and small sample sizes: Monogenean sclerites (Platyhelminthes) as a case study. —Zoologica Scripta, 40, 306–316. Taxonomists and evolutionary biologists frequently use a combination of morphological measurements to distinguish between species and investigate local adaptation. However, the entire set of characters often displays various degrees of collinearity. This paper discusses the effect of using collinear data in morphological taxonomy and ways to handle multicollinearity in a classification context, with special consideration for small sample size. In addition, I propose a robust and easy‐to‐use combination of dimension reduction using partial least squares (PLS) with traditional discriminant methods for morphological data. To do this, I investigated morphological variation patterns among four monogenean populations from the Pacific Ocean using the correlated morphological features of the sclerotized attachment organ. The new approach yielded better prediction results (lower classification error rates) than the traditional dimension reduction method based on principle component analysis (PCA) and is also much more robust for small sample size. This emphasizes that PLS may be more efficient than PCA in dealing with correlated data and extracting the most relevant morphological differences among groups.     

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

Background

The molecular operational taxonomic unit (MOTU) has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of “reverse taxonomy” has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of “reverse taxonomy” has not been sufficiently evaluated. Therefore, the practical applicability of “reverse taxonomy” is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts.

Methodology

Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types ( =  MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified.

Conclusions

That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.     

Salicylic acid is not a bacterial siderophore: a theoretical study

Using a newly available program for calculating the concentrations and speciation of various ions (Pettit, LD & Powell KJ, `SolEq' Academic Software, 1999), we have calculated that at pH 7 the amount of free Fe(III) present in an aqueous solution is 1.4×10^–9 M and not 10^–18 M as is usually quoted. In the presence of salicylic acid, included in the calculations at 10^–4 M, the solubility of Fe(III) is increased to only 9.8×10^–9 M suggesting that salicylate is unable to act as a siderophore although it is produced as an extracellular product by several bacterial genera when grown iron deficiently. In the presence of 40 mM phosphate, the soluble Fe(III) concentration is decreased by 10⁴ at pH 7 and again this is hardly affected by the presence of salicylate. Thus, for microorganisms grown either in vitro or in vivo, salicylate is unlikely to function as a iron solubilizing agent. The same conclusions may also apply to 2,3-dihydroxybenzoic acid.     

Becoming a Christian in Fiji: an ethnographic study of ontogeny

By means of an ethnographic and developmental analysis, this article shows how everyday ritual practice is fundamental to people's constitution over time of ideas that, in this case, inform a specifically Fijian Christianity. Focusing on the developmental process that is the fixation of belief, and on the significance of ritual for this process, it explores transformations in ideas about God, Sunday school, and death ceremonies held by Sawaieke girls and boys between 7 years, 10 months and 13 years old. The broader objective is to demonstrate, first, how data obtained systematically from children can illuminate our understanding of ritual and its significance, and, secondly, how an analysis of the developmental process necessarily entails a concomitant analysis of the social relations that inform it.     

Becoming a Christian in Fiji: an ethnographic study of ontogeny

By means of an ethnographic and developmental analysis, this article shows how everyday ritual practice is fundamental to people's constitution over time of ideas that, in this case, inform a specifically Fijian Christianity. Focusing on the developmental process that is the fixation of belief, and on the significance of ritual for this process, it explores transformations in ideas about God, Sunday school, and death ceremonies held by Sawaieke girls and boys between 7 years, 10 months and 13 years old. The broader objective is to demonstrate, first, how data obtained systematically from children can illuminate our understanding of ritual and its significance, and, secondly, how an analysis of the developmental process necessarily entails a concomitant analysis of the social relations that inform it.     

Sequencing as a tool in yeast molecular taxonomy

The literature on sequencing as a tool for yeast molecular taxonomy is reviewed. Ribosomal DNA has been preferred for sequencing over other molecules such as mitochondrial DNA, and a large database is now available. rDNA consists of regions that evolve at different rates, allowing comparison of different levels of relationship among yeasts. Sequences of the 18S rDNA and the 25S rDNA have been largely used for yeast systematics and phylogeny, but the search for regions with increased resolving power has led to the study of the spacer regions of the rDNA. Few studies are concerned with signature sequences.     

Folk taxonomy and evolutionary dynamics of cassava: A case study in Ubatuba, Brazil

A survey was conducted of Caicara farmers from Ubatuba in the Brazilian coastland between São Paulo and Rio de Janeiro States regarding the folk-taxonomy for cassava (Manihot esculenta Crantz) landraces they cultivate and cassava evolutionary dynamics in swidden cultivation. The accuracy of their folk taxonomy was assessed. Cluster analysis was used to make comparisons between names given by the farmers to sampled individuals and their isozyme phenotypes obtained with four isozyme systems. Interviews with farmers were done and ethnobiological data collected. These farmers possess a loose taxonomic system and tend to underestimate cassava genetic diversity in their gardens. However, classification skills vary considerably among them. The accuracy of their taxonomy along with the results of interviews with farmers and ethnobiological data are discussed in light of a proposed evolutionary dynamics model for cultivated cassava and its ecology in tropical swidden cultivation.     

Ascidian Budding as a Transdifferentiation-Like System: Multipotent Epithelium is not Undifferentiated

During bud development of the ascidian Polyandrocarpa misakiensis , most of the new tissues are formed from foldings of atrial epithelium. Although the atrial epithelium has been believed to be undifferentiated, we found that this epithelium of P. misakiensis strongly expressed a tissue-restricted antigen, named Pae 1. Cross-reactivity of the antibody was found only in a few differentiated tissues such as branchial epithelium and phagocyte-like cells. In developing buds, the antigen disappeared selectively from the regions where the atrial epithelium forms organ rudiments. These regions corresponded with that of mitotic activity, thickening of the epithelium, swelling of nuclei, the appearance of nucleoli and accumulation of a large amount of RNA. From these observations, we assume that the change in antigen expression indicates a change in the state of differentiation of the atrial epithelium. Although Pae 1 antigen was never detected in functional gut, it was detected in the invaginating gut epithelium. This result indicates that gut cells were derived from the cells which had expressed the antigen. We therefore conclude that the conversion of the atrial epithelium into gut can be regarded as a transdifferentiation-like process.     

Vocal turn-taking in a non-human primate is learned during ontogeny

Conversational turn-taking is an integral part of language development, as it reflects a confluence of social factors that mitigate communication. Humans coordinate the timing of speech based on the behaviour of another speaker, a behaviour that is learned during infancy. While adults in several primate species engage in vocal turn-taking, the degree to which similar learning processes underlie its development in these non-human species or are unique to language is not clear. We recorded the natural vocal interactions of common marmosets (Callithrix jacchus) occurring with both their sibling twins and parents over the first year of life and observed at least two parallels with language development. First, marmoset turn-taking is a learned vocal behaviour. Second, marmoset parents potentially played a direct role in guiding the development of turn-taking by providing feedback to their offspring when errors occurred during vocal interactions similarly to what has been observed in humans. Though species-differences are also evident, these findings suggest that similar learning mechanisms may be implemented in the ontogeny of vocal turn-taking across our Order, a finding that has important implications for our understanding of language evolution.     

Testing the island rule: primates as a case study

The island rule states that after island colonization, larger animals tend to evolve reduced body sizes and smaller animals increased sizes. Recently, there has been disagreement about how often, if ever, this rule applies in nature, and much of this disagreement stems from differences in the statistical tests employed. This study shows, how different tests of the island rule assume different null hypotheses, and that these rely on quite different biological assumptions. Analysis and simulation are then used to quantify the biases in the tests. Many widely used tests are shown to yield false support for the island rule when island and mainland evolution are indistinguishable, and so a Monte Carlo permutation test is introduced that avoids this problem. It is further shown that tests based on independent contrasts lack power to detect the island rule under certain conditions. Finally, a complete reanalysis is presented of recent data from primates. When head-body length is used as the measure of body size, reports of the island rule are shown to stem from methodological artefacts. But when skull length or body mass are used, all tests agree that the island rule does hold in primates.     

Cellular responses to naphthoquinones: juglone as a case study

The effects of juglone (JG) on the endogenous growth, growth in the presence of either indoleacetic acid (IAA) or fusicoccin (FC) and on proton extrusion were studied in maize coleoptile segments. In addition, membrane potential changes were also determined at chosen JG concentrations. It was found that JG, when added to the incubation medium, inhibited endogenous growth as well as growth in the presence of either IAA or FC. Simultaneous measurements of growth and external pH indicated that inhibition of either IAA-induced growth or proton extrusion by JG was a linear function of JG concentration. Addition of JG to the control medium caused depolarization of the membrane potential (E_m), value of which was dependent on JG concentration and time after its administration. Hyperpolarization of E_m induced by IAA was suppressed in the presence of JG. It was also found that for coleoptile segments initially preincubated with JG, although subsequently removed, addition of IAA was not effective in the stimulation of growth and medium acidification. Taken together, these results suggest that the mechanism by which JG inhibits the IAA-induced growth of maize coleoptile segments involves inhibition of PM H⁺-ATPase activity.     

Biohydrogen production in alkalithermophilic conditions: Thermobrachium celere as a case study

In the present work the hydrogenesis in the anaerobic alkalithermophilic bacterium Thermobrachium celere was studied. The impact of several factors on hydrogen production during glucose fermentation was investigated in batch conditions. The optimal hydrogen production occurred at pH_67 °C 8.2 with phosphate buffer concentration of 50 mM. Hydrogen yield reached the highest value of 3.36 mol H₂/mol glucose when the partial pressure in the gas headspace was reduced. Supplementation of nitrogen sources and iron affected hydrogen production. Under optimized conditions, the maximum H₂ accumulation and H₂ production rate were estimated to be respectively 124.3 mmol H₂/l culture and 20.7 mmol H₂/l/h. Considering the efficient and rapid hydrogen evolution, and the ability to grow in extreme environments, T. celere might be a good candidate for biohydrogen production in open (non-sterile) bioprocess system.     

Modeling density dependence in heterogeneous landscapes: Dispersal as a case study

Population models often pose density-dependent rates as relations between current population size on a habitat patch, n, and some threshold size defined by limiting resources, r. In fourteen recent modeling studies incorporating density-dependent dispersal, formulations of the density-dependent rate (or probability) fall into two distinct groups, expressing the rate as a function of n-r or n/r. These two depictions of the same process differ fundamentally: they can cause strikingly different dynamics in otherwise identical systems and they have different scaling properties in heterogeneous landscapes. Here I consider the implications of the two formulations under two broad ecological scenarios: scramble competition for an equally divided resource (e.g. food) and contest competition for an unequally divided resource (e.g. nest sites). In both cases, simple arguments show that the n/r form is preferable when density dependence is driven by individual access to resources. Other circumstances may require different formulations, but modelers must ensure that these have appropriate scaling and non-equilibrium behavior.