Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results: Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Metabolism of Rhizobium bacteroids

Nitrogen fixation within legume nodules results from a complex metabolic exchange between bacteria of the family Rhizobiaciae and the plant host. Carbon is supplied to the differentiated bacterial cells, termed bacteroids, in the form of dicarboxylic acids to fuel nitrogen fixation. In exchange, fixed nitrogen is transferred to the plant. Both the bacteroid and the plant-derived peribacteroid membrane tightly regulate the exchange of metabolites. In the bacteroid oxidation of dicarboxylic acids via the TCA cycle occurs in an oxygen-limited environment. This restricts the TCA cycle at key points, such as the 2-oxoglutarate dehydrogenase complex, and requires that inputs of carbon and reductant are balanced with outputs from the TCA cycle. This may be achieved by metabolism through accessory pathways that can remove intermediates, reductant, or ATP from the cycle. These include synthesis of the carbon polymers PHB and glycogen and bypass pathways such as the recently identified 2-oxoglutarate decarboxylase reaction in soybean bacteroids. Recent labeling data have shown that bacteroids synthesize and secrete amino acids, which has led to controversy over the role of amino acids in nodule metabolism. Here we review bacteroid carbon metabolism in detail, evaluate the labeling studies that relate to amino acid metabolism by bacteroids, and place the work in context with the genome sequences of Mesorhizobium loti and Sinorhizobium meliloti. We also consider a wider range of metabolic pathways that are probably of great importance to rhizobia in the rhizosphere, during nodule initiation, infection thread development, and bacteroid development.

Symposium on 'nutrition interventions in high-risk groups' - CVD risk in South Asians: the importance of defining adiposity and influence of dietary polyunsaturated fat

The prevalence of the metabolic syndrome (MetS), CVD and type 2 diabetes (T2D) is known to be higher in populations from the Indian subcontinent compared with the general UK population. While identification of this increased risk is crucial to allow for effective treatment, there is controversy over the applicability of diagnostic criteria, and particularly measures of adiposity in ethnic minorities. Diagnostic cut-offs for BMI and waist circumference have been largely derived from predominantly white Caucasian populations and, therefore, have been inappropriate and not transferable to Asian groups. Many Asian populations, particularly South Asians, have a higher total and central adiposity for a similar body weight compared with matched Caucasians and greater CVD risk associated with a lower BMI. Although the causes of CVD and T2D are multi-factorial, diet is thought to make a substantial contribution to the development of these diseases. Low dietary intakes and tissue levels of long-chain (LC) n-3 PUFA in South Asian populations have been linked to high-risk abnormalities in the MetS. Conversely, increasing the dietary intake of LC n-3 PUFA in South Asians has proved an effective strategy for correcting such abnormalities as dyslipidaemia in the MetS. Appropriate diagnostic criteria that include a modified definition of adiposity must be in place to facilitate the early detection and thus targeted treatment of increased risk in ethnic minorities.

Diet, immunity and functional foods

Functional foods (specific nutrient and/or food components) should beneficially affect one or more target functions in the body. The use of functional foods as a form of preventive medicine has been the subject of much research over the last two decades. It is well known that nutrition plays a vital role in chronic diseases, but it is only recently that data relating to the effects of specific nutrients or foods on the immune system have become available. This chapter aims to summarize the effects of some functional foods (e.g., prebiotics and micronutrients) on the immune system. It should be noted, however, that studies into the role of functional foods with regard to the human immune system are still in their infancy and a great deal of controversy surrounds the health claims attributed to some functional foods. Consequently, thorough studies are required in human and animal systems if we are to move towards developing a functional diet that provides maximal health benefits.

A refined LEED analysis of water on Ru{0001}: an experimental test of the partial dissociation model

Despite a number of earlier studies which seemed to confirm molecular adsorption of water on close-packed surfaces of late transition metals, new controversy has arisen over a recent theoretical work by Feibelman, according to which partial dissociation occurs on the Ru{0001} surface leading to a mixed (H2O + OH + H) superstructure. Here, we present a refined LEED-IV analysis of the (root3 x root3)R30degrees-D2O-Ru{0001} structure, testing explicitly this new model by Feibelman. Our results favour the model proposed earlier by Held and Menzel assuming intact water molecules with almost coplanar oxygen atoms and out-of-plane hydrogen atoms atop the slightly higher oxygen atoms. The partially dissociated model with an almost identical arrangement of oxygen atoms can, however, not unambiguously be excluded, especially when the single hydrogen atoms are not present in the surface unit cell. In contrast to the earlier LEED-IV analysis, we can, however, clearly exclude a buckled geometry of oxygen atoms.

Entropy versus APE production: on the buoyancy power input in the oceans energy cycle

This letter argues that the current controversy about whether Wbuoyancy, the power input due to the surface buoyancy fluxes, is large or small in the oceans stems from two distinct and incompatible views on how Wbuoyancy relates to the volume-integrated work of expansion/contraction B. The current prevailing view is that Wbuoyancy should be identified with the net value of B, which current theories estimate to be small. The alternative view, defended here, is that only the positive part of B, i.e., the one converting internal energy into mechanical energy, should enter the definition of Wbuoyancy, since the negative part of B is associated with the non-viscous dissipation of mechanical energy. Two indirect methods suggest that by contrast, the positive part of B is potentially large.

Cannabis sativa and the endogenous cannabinoid system: therapeutic potential for appetite regulation

The herb Cannabis sativa (C. sativa) has been used in China and on the Indian subcontinent for thousands of years as a medicine. However, since it was brought to the UK and then the rest of the western world in the late 19th century, its use has been a source of controversy. Indeed, its psychotropic side effects are well reported but only relatively recently has scientific endeavour begun to find valuable uses for either the whole plant or its individual components. Here, we discuss evidence describing the endocannabinoid system, its endogenous and exogenous ligands and their varied effects on feeding cycles and meal patterns. Furthermore we also critically consider the mounting evidence which suggests non‐tetrahydrocannabinol phytocannabinoids play a vital role in C. sativa‐induced feeding pattern changes. Indeed, given the wide range of phytocannabinoids present in C. sativa and their equally wide range of intra‐, inter‐ and extra‐cellular mechanisms of action, we demonstrate that non‐Δ9tetrahydrocannabinol phytocannabinoids retain an important and, as yet, untapped clinical potential.

Processing of regular and irregular past tense morphology in highly proficient second language learners of English: a self-paced reading study

Dual-system models suggest that English past tense morphology involves two processing routes: rule application for regular verbs and memory retrieval for irregular verbs (Pinker, 1999). In second language (L2) processing research, Ullman (2001a) suggested that both verb types are retrieved from memory, but more recently Clahsen and Felser (2006) and Ullman (2004) argued that past tense rule application can be automatised with experience by L2 learners. To address this controversy, we tested highly proficient Greek-English learners with naturalistic or classroom L2 exposure compared to native English speakers in a self-paced reading task involving past tense forms embedded in plausible sentences. Our results suggest that, irrespective to the type of exposure, proficient L2 learners of extended L2 exposure apply rule-based processing.

The water vapour continuum: brief history and recent developments

The water vapour continuum is characterised by absorption that varies smoothly with wavelength, from the visible to the microwave. It is present within the rotational and vibrational–rotational bands of water vapour, which consist of large numbers of narrow spectral lines, and in the many ‘windows’ between these bands. The continuum absorption in the window regions is of particular importance for the Earth’s radiation budget and for remote-sensing techniques that exploit these windows. Historically, most attention has focused on the 8–12 μm (mid-infrared) atmospheric window, where the continuum is relatively well-characterised, but there have been many fewer measurements within bands and in other window regions. In addition, the causes of the continuum remain a subject of controversy. This paper provides a brief historical overview of the development of understanding of the continuum and then reviews recent developments, with a focus on the near-infrared spectral region. Recent laboratory measurements in near-infrared windows, which reveal absorption typically an order of magnitude stronger than in widely used continuum models, are shown to have important consequences for remote-sensing techniques that use these windows for retrieving cloud properties.

Phylogenies reveal predictive power of traditional medicine in bioprospecting

There is controversy about whether traditional medicine can guide drug discovery, and investment in ethnobotanically led research has fluctuated. One view is that traditionally used plants are not necessarily efficacious and there are no robust methods for distinguishing the ones that are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogeny representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This strongly suggests independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in a random sample. Phylogenetic cross-cultural comparison can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalise the use of traditional knowledge in bioprospecting.

Registering scents as community trade marks

While the registrability of scents as Community trade marks has become source of much controversy, the possibility of trademarking scents represents a great potential for the industry. In the aftermath of the Sieckmann case, which has raised the threshold of registrability for scent marks, companies have refrained from submitting new smell-mark applications. Despite the difficulties in registering scents as trademarks, however, it is not impossible to meet the Sieckmann criteria and file successful scent mark applications. This article explains how this could be possible; it reviews all objections in registering scents as trademarks and brings new light into this topic by way of a comprehensive analysis of the conditions under which scents can be registered as Community trade marks.

When do export subsidies have a redistributional role? Reply

Our differences are three. The first arises from the belief that "... a nonzero value for the optimally chosen policy instrument implies that the instrument is efficient for redistribution" (Alston, Smith, and Vercammen, p. 543, paragraph 3). Consider the two equations: (1) o* = f(P3) and (2) = -f(3) ++r h* (a, P3) representing the solution to the problem of maximizing weighted, Marshallian surplus using, simultaneously, a per-unit border intervention, 9, and a per-unit domestic intervention, wr. In the solution, parameter ot denotes the weight applied to producer surplus; parameter p denotes the weight applied to government revenues; consumer surplus is implicitly weighted one; and the country in question is small in the sense that it is unable to affect world price by any of its domestic adjustments (see the Appendix). Details of the forms of the functions f((P) and h(ot, p) are easily derived, but what matters in the context of Alston, Smith, and Vercammen's Comment is: Redistributivep referencest hatf avorp roducers are consistent with higher values "alpha," and whereas the optimal domestic intervention, 7r*, has both "alpha and beta effects," the optimal border intervention, r*, has only a "beta effect,"-it does not have a redistributional role. Garth Holloway is reader in agricultural economics and statistics, Department of Agricultural and Food Economics, School of Agriculture, Policy, and Development, University of Reading. The author is very grateful to Xavier Irz, Bhavani Shankar, Chittur Srinivasan, Colin Thirtle, and Richard Tiffin for their comments and their wisdom; and to Mario Mazzochi, Marinos Tsigas, and Cal Turvey for their scholarship, including help in tracking down a fairly complete collection of the papers that cite Alston and Hurd. They are not responsible for any errors or omissions. Note, in equation (1), that the border intervention is positive whenever a distortion exists because 8 > 0 implies 3 - 1 + 8 > 1 and, thus, f((P) > 0 (see Appendix). Using Alston, Smith, and Vercammen's definition, the instrument is now "efficient," and therefore has a redistributive role. But now, suppose that the distortion is removed so that 3 - 1 + 8 = 1, 8 = 0, and consequently the border intervention is zero. According to Alston, Smith, and Vercammen, the instrument is now "inefficient" and has no redistributive role. The reader will note that this thought experiment has said nothing about supporting farm incomes, and so has nothing whatsoever to do with efficient redistribution. Of course, the definition is false. It follows that a domestic distortion arising from the "excess-burden argument" 3 = 1 + 8, 8 > 0 does not make an export subsidy "efficient." The export subsidy, having only a "beta effect," does not have a redistributional role. The second disagreement emerges from the comment that Holloway "... uses an idiosyncratic definition of the relevant objective function of the government (Alston, Smith, and Vercammen, p. 543, paragraph 2)." The objective function that generates equations (1) and (2) (see the Appendix) is the same as the objective function used by Gardner (1995) when he first questioned Alston, Carter, and Smith's claim that a "domestic distortion can make a border intervention efficient in transferring surplus from consumers and taxpayers to farmers." The objective function used by Gardner (1995) is the same objective function used in the contributions that precede it and thus defines the literature on the debate about borderversus- domestic intervention (Streeten; Yeh; Paarlberg 1984, 1985; Orden; Gardner 1985). The objective function in the latter literature is the same as the one implied in another literature that originates from Wallace and includes most notably Gardner (1983), but also Alston and Hurd. Amer. J. Agr. Econ. 86(2) (May 2004): 549-552 Copyright 2004 American Agricultural Economics Association This content downloaded on Tue, 15 Jan 2013 07:58:41 AM All use subject to JSTOR Terms and Conditions 550 May 2004 Amer. J. Agr. Econ. The objective function in Holloway is this same objective function-it is, of course, Marshallian surplus.1 The third disagreement concerns scholarship. The Comment does not seem to be cognizant of several important papers, especially Bhagwati and Ramaswami, and Bhagwati, both of which precede Corden (1974, 1997); but also Lipsey and Lancaster, and Moschini and Sckokai; one important aspect of Alston and Hurd; and one extremely important result in Holloway. This oversight has some unfortunate repercussions. First, it misdirects to the wrong origins of intellectual property. Second, it misleads about the appropriateness of some welfare calculations. Third, it prevents Alston, Smith, and Vercammen from linking a finding in Holloway (pp. 242-43) with an old theorem (Lipsey and Lancaster) that settles the controversy (Alston, Carter, and Smith 1993, 1995; Gardner 1995; and, presently, Alston, Smith, and Vercammen) about the efficiency of border intervention in the presence of domestic distortions.

The potential inefficiency of using marketing margins in applied commodity price analysis, forecasting and risk management

This paper examines the implications of using marketing margins in applied commodity price analysis. The marketing-margin concept has a long and distinguished history, but it has caused considerable controversy. This is particularly the case in the context of analyzing the distribution of research gains in multi-stage production systems. We derive optimal tax schemes for raising revenues to finance research and promotion in a downstream market, derive the rules for efficient allocation of the funds, and compare the rules with an without the marketing-margin assumption. Applying the methodology to quarterly time series on the Australian beef-cattle sector and, with several caveats, we conclude that, during the period 1978:2 - 1988:4, the Australian Meat and Livestock Corporation optimally allocated research resources.

Near-Earth initiation of a terrestrial substorm

Despite the characterization of the auroral substorm more than 40 years ago, controversy still surrounds the processes triggering substorm onset initiation. That stretching of the Earth's magnetotail following the addition of new nightside magnetic flux from dayside reconnection powers the substorm is well understood; the trigger for explosive energy release at substorm expansion phase onset is not. Using ground-based data sets with unprecedented combined spatial and temporal coverage, we report the discovery of new localized and contemporaneous magnetic wave and small azimuthal scale auroral signature of substorm onset. These local auroral arc undulations and magnetic field signatures rapidly evolve on second time scales for several minutes in advance of the release of the auroral surge. We also present evidence from a conjugate geosynchronous satellite of the concurrent magnetic onset in space as the onset of magnetic pulsations in the ionosphere, to within technique error. Throughout this time period, the more poleward arcs that correspond to the auroral oval which maps to the central plasma sheet remain undisturbed. There is good evidence that flows from the midtail crossing the plasma sheet can generate north-south auroral structures, yet no such auroral forms are seen in this event. Our observations present a severe challenge to the standard hypothesis that magnetic reconnection in stretched magnetotail fields triggers onset, indicating substorm expansion phase initiation occurs on field lines that are close to the Earth, as bounded by observations at geosynchronous orbit and in the conjugate ionosphere.

Pollen-based differentiation of Amazonian rainforest communities and implications for lowland palaeoecology in tropical South America

An ongoing controversy in Amazonian palaeoecology is the manner in which Amazonian rainforest communities have responded to environmental change over the last glacial–interglacial cycle. Much of this controversy results from an inability to identify the floristic heterogeneity exhibited by rainforest communities within fossil pollen records. We apply multivariate (Principal Components Analysis) and classification (Unweighted Pair Group with Arithmetic Mean Agglomerative Classification) techniques to floral-biometric, modern pollen trap and lake sediment pollen data situated within different rainforest communities in the tropical lowlands of Amazonian Bolivia. Modern pollen rain analyses from artificial pollen traps show that evergreen terra firme (well-drained), evergreen terra firme liana, evergreen seasonally inundated, and evergreen riparian rainforests may be readily differentiated, floristically and palynologically. Analogue matching techniques, based on Euclidean distance measures, are employed to compare these pollen signatures with surface sediment pollen assemblages from five lakes: Laguna Bella Vista, Laguna Chaplin, and Laguna Huachi situated within the Madeira-Tapajós moist forest ecoregion, and Laguna Isirere and Laguna Loma Suarez, which are situated within forest patches in the Beni savanna ecoregion. The same numerical techniques are used to compare rainforest pollen trap signatures with the fossil pollen record of Laguna Chaplin.