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.

Selective biodegradation of keratin matrix in feather rachis reveals classic bioengineering

Flight necessitates that the feather rachis is extremely tough and light. Yet, the crucial filamentous hierarchy of the rachis is unknown—study hindered by the tight chemical bonding between the filaments and matrix. We used novel microbial biodegradation to delineate the fibres of the rachidial cortex in situ. It revealed the thickest keratin filaments known to date (factor >10), approximately 6 µm thick, extending predominantly axially but with a small outer circumferential component. Near-periodic thickened nodes of the fibres are staggered with those in adjacent fibres in two- and three-dimensional planes, creating a fibre–matrix texture with high attributes for crack stopping and resistance to transverse cutting. Close association of the fibre layer with the underlying ‘spongy’ medulloid pith indicates the potential for higher buckling loads and greater elastic recoil. Strikingly, the fibres are similar in dimensions and form to the free filaments of the feather vane and plumulaceous and embryonic down, the syncitial barbules, but, identified for the first time in 140+ years of study in a new location—as a major structural component of the rachis. Early in feather evolution, syncitial barbules were consolidated in a robust central rachis, definitively characterizing the avian lineage of keratin.

Langmuir turbulence and deeply penetrating jets in an unstratified mixed layer

The influence of surface waves and an applied wind stress is studied in an ensemble of large eddy simulations to investigate the nature of deeply penetrating jets into an unstratified mixed layer. The influence of a steady monochromatic surface wave propagating parallel to the wind direction is parameterized using the wave-filtered Craik-Leibovich equations. Tracer trajectories and instantaneous downwelling velocities reveal classic counterrotating Langmuir rolls. The associated downwelling jets penetrate to depths in excess of the wave's Stokes depth scale, δs. Qualitative evidence suggests the depth of the jets is controlled by the Ekman depth scale. Analysis of turbulent kinetic energy (tke) budgets reveals a dynamical distinction between Langmuir turbulence and shear-driven turbulence. In the former, tke production is dominated by Stokes shear and a vertical flux term transports tke to a depth where it is dissipated. In the latter, tke production is from the mean shear and is locally balanced by dissipation. We define the turbulent Langmuir number Lat = (v*/Us)0.5 (v* is the ocean's friction velocity and Us is the surface Stokes drift velocity) and a turbulent anisotropy coefficient Rt = /( + ). The transition between shear-driven and Langmuir turbulence is investigated by varying external wave parameters δs and Lat and by diagnosing Rt and the Eulerian mean and Stokes shears. When either Lat or δs are sufficiently small the Stokes shear dominates the mean shear and the flow is preconditioned to Langmuir turbulence and the associated deeply penetrating jets.

Linear amplification of marginally neutral baroclinic waves

Baroclinic wave development is investigated for unstable parallel shear flows in the limit of vanishing normal-mode growth rate. This development is described in terms of the propagation and interaction mechanisms of two coherent structures, called counter-propagating Rossby waves (CRWs). It is shown that, in this limit of vanishing normal-mode growth rate, arbitrary initial conditions produce sustained linear amplification of the marginally neutral normal mode (mNM). This linear excitation of the mNM is subsequently interpreted in terms of a resonance phenomenon. Moreover, while the mathematical character of the normal-mode problem changes abruptly as the bifurcation point in the dispersion diagram is encountered and crossed, it is shown that from an initial-value viewpoint, this transition is smooth. Consequently, the resonance interpretation remains relevant (albeit for a finite time) for wavenumbers slightly different from the ones defining cut-off points. The results are further applied to a two-layer version of the classic Eady model in which the upper rigid lid has been replaced by a simple stratosphere.

Periodic Reordering

For many networks in nature, science and technology, it is possible to order the nodes so that most links are short-range, connecting near-neighbours, and relatively few long-range links, or shortcuts, are present. Given a network as a set of observed links (interactions), the task of finding an ordering of the nodes that reveals such a range-dependent structure is closely related to some sparse matrix reordering problems arising in scientific computation. The spectral, or Fiedler vector, approach for sparse matrix reordering has successfully been applied to biological data sets, revealing useful structures and subpatterns. In this work we argue that a periodic analogue of the standard reordering task is also highly relevant. Here, rather than encouraging nonzeros only to lie close to the diagonal of a suitably ordered adjacency matrix, we also allow them to inhabit the off-diagonal corners. Indeed, for the classic small-world model of Watts & Strogatz (1998, Collective dynamics of ‘small-world’ networks. Nature, 393, 440–442) this type of periodic structure is inherent. We therefore devise and test a new spectral algorithm for periodic reordering. By generalizing the range-dependent random graph class of Grindrod (2002, Range-dependent random graphs and their application to modeling large small-world proteome datasets. Phys. Rev. E, 66, 066702-1–066702-7) to the periodic case, we can also construct a computable likelihood ratio that suggests whether a given network is inherently linear or periodic. Tests on synthetic data show that the new algorithm can detect periodic structure, even in the presence of noise. Further experiments on real biological data sets then show that some networks are better regarded as periodic than linear. Hence, we find both qualitative (reordered networks plots) and quantitative (likelihood ratios) evidence of periodicity in biological networks.

Experiences with sustainability indicators and stakeholder participation: A case study relating to a 'Blue Plan' project in Malta

The practical application of systemic sustainability analysis (SSA; Bell and Morse, 1999) as applied in-a project instigated and managed by 'Blue Plan', one of the regional activity centres of the Mediterranean Action Plan, is set out and explained in this paper. The context in which SSA was applied and adapted to SPSA (systemic and prospective sustainability analysis). is described in the Mediterranean, primarily in Malta. The SSA process is summarized, its extension and linkage to the prospective approach is described and the comments of stakeholders in the context are added. Some preliminary outcomes are suggested. The pauticular focus of the paper is on the lessons learned from doing SSA/SPSA within a classic blueprint project framework. It is-not assumed that SSA/SPSA is 'finished' or 'definitive'. Rather, we suggest that it is a developing and changing approach that practitioners can adapt and change to meet the specific needs of the circumstances that confront them. Copyright (C) 2004 John Wiley & Sons, Ltd and ERP Environment.

Croft Moraig and the chronology of stone circles

The Perthshire stone circle of Croft Moraig was excavated 40 years ago and is usually taken to illustrate the classic sequence at such monuments in Britain. A timber setting, accompanied by a shallow ditch, was replaced by two successive stone settings. The pottery associated with the earliest construction was dated to the Neolithic period. A new analysis of the excavated material suggests that, in fact, the ceramics are Middle or Late Bronze Age. They provide a terminus post quem for at least one of the stone settings on the site. Further study of the evidence suggests an alternative sequence of construction at Croft Moraig, involving a change in the axis of the monument. It seems possible that other stone and timber circles were equally late in date and that their period of use in Britain and Ireland may have been longer than is generally supposed.

An ichnofabric approach to the depositional interpretation of the intensely burrowed Bateig Limestone, Miocene, SE Spain

The foraminiferal-rich pelagic Bateig Limestone forms several varieties of the important building stones quarried at Bateig Hill in southeastern Spain. Three principal ichnofabrics (Bichordites, mottled-Palaeophycus and mottled-Ophiomorpha) are recognized, which are present in at least two (possibly up to four) repeated successions (cycles). Each succession begins with an erosional event. The Bichordites ichnofabric represents a new type of facies, formed as thin turbidity/grain flow, stratiform units derived from sediment slips off a fault into deep water. Each slipped unit became almost completely bioturbated by infaunal echinoids, colonizing by lateral migration. Because of the thinness of the units, successive colonizations tended to truncate the underlying burrows giving rise to a pseudo-stratification. As the Bichordites ichnofabric accumulated on the fault apron, thus reducing the effective height of the fault scarp, the substrate gradually came under the influence of currents traversing the shelf. This led to a change in hydraulic regime, and to the mottled-Palaeophycus and mottled-Ophiomorpha ichnofabrics in sediment deposited under bed load transport, and associated with laminar and cross-stratified beds and local muddy intervals. Reactivation of the fault triggered erosion and channeling and a return to grain flow sedimentation, and to the Bichordites ichnofabric of the succeeding cycle. The highest unit of the Bateig Limestone is formed entirely of cross-stratified calcarenites with occasional Ophiomorpha (Ophiomorpha-primary lamination ichnofabric) and is similar to many shallow marine facies but they still bear a significant content of pelagic foraminifera. The sedimentary setting bears resemblance with that described for the Pleistocene Monte Torre Paleostrait and the modem Strait of Messina (Italy), where the narrow morphology of the depositional area enhanced tidal currents and allowed for high-energy sandy deposition in relatively deep areas. More data on the Miocene paleogeography of the Bateig area should provide further testing for this hypothesis. The ichnofacies and stacking of the Bateig Limestone differ from the classic Seilacherian model in that they reflect changes in hydraulic process and are associated with faulting and subsidence and changes in sediment supply. Recognition of the unusual ichnofabrics and their relationships provides a clear indication of the overall dynamic setting. (c) 2006 Elsevier B.V. All rights reserved.

Aqueous geochemistry and oxygen isotope compositions of acid mine drainage from the Río Tinto, SW Spain, highlight inconsistencies in current models

The Rio Tinto river in SW Spain is a classic example of acid mine drainage and the focus of an increasing amount of research including environmental geochemistry, extremophile microbiology and Mars-analogue studies. Its 5000-year mining legacy has resulted in a wide range of point inputs including spoil heaps and tunnels draining underground workings. The variety of inputs and importance of the river as a research site make it an ideal location for investigating sulphide oxidation mechanisms at the field scale. Mass balance calculations showed that pyrite oxidation accounts for over 93% of the dissolved sulphate derived from sulphide oxidation in the Rio Tinto point inputs. Oxygen isotopes in water and sulphate were analysed from a variety of drainage sources and displayed delta O-18((SO4-H2O)) values from 3.9 to 13.6 parts per thousand, indicating that different oxidation pathways occurred at different sites within the catchment. The most commonly used approach to interpreting field oxygen isotope data applies water and oxygen fractionation factors derived from laboratory experiments. We demonstrate that this approach cannot explain high delta O-18((SO4-H2O)) values in a manner that is consistent with recent models of pyrite and sulphoxyanion oxidation. In the Rio Tinto, high delta O-18((SO4-H2O)) values (11.2-13.6 parts per thousand) occur in concentrated (Fe = 172-829 mM), low pH (0.88-1.4), ferrous iron (68-91% of total Fe) waters and are most simply explained by a mechanism involving a dissolved sulphite intermediate, sulphite-water oxygen equilibrium exchange and finally sulphite oxidation to sulphate with O-2. In contrast, drainage from large waste blocks of acid volcanic tuff with pyritiferous veins also had low pH (1.7). but had a low delta O-18((SO4-H2O)) value of 4.0 parts per thousand and high concentrations of ferric iron (Fe(III) = 185 mM, total Fe = 186 mM), suggesting a pathway where ferric iron is the primary oxidant, water is the primary source of oxygen in the sulphate and where sulphate is released directly from the pyrite surface. However, problems remain with the sulphite-water oxygen exchange model and recommendations are therefore made for future experiments to refine our understanding of oxygen isotopes in pyrite oxidation. (C) 2009 Elsevier B.V. All rights reserved.

Neocolonialism and international law, with specific reference to customary counterterrorism obligations and the principle of self-defence

Has international law ever, and, if it has not, can it ever, truly freed itself from the strictures of neocolonialism and the drive by a privileged elite to dominate the world scene? This article begins by inquiring into the nature of neocolonialism and, in so doing, pays particular attention to the writings of former Ghanaian President Kwame Nkrumah. It then proceeds to determine how neocolonialist designs surface in international law today by briefly looking at two aspects of international law in particular, namely customary international law, with specific reference to the counterterrorism context, and the principle of self-defence. In the final analysis, this article argues for a necessary and eternal scepticism of international law and the agendas of its privileged gatekeepers. Like classic State power, it opens itself to, and often operates as, neocolonial overreach, and to quote Nkrumah, “[t]he cajolement, the wheedlings, the seductions and the Trojan horses of neo-colonialism must be stoutly resisted, for neo-colonialism is a latter-day harpy, a monster which entices its victims with sweet music.”

Pathogenicity of the bacterium Xenorhabdus nematophila isolated from the entomopathogenic nematode Steinernema carpocapsae and its secretions against Galleria mellonella larvae

The entomopathogenic bacterium, Xenorhabdus nematophila was isolated from the hemolymph of Galleria mellonella infected with Steinernema carpocapsae. The bacterial cells and its metabolic secretions have been found lethal to the Galleria larvae. Toxic secretion in broth caused 95% mortality within 4 d of application whereas the bacterial cells caused 93% mortality after 6 d. When filter and sand substrates were compared, the later one was observed as appropriate. Similarly, bacterial cells and secretion in broth were more effective at 14% moisture and 25 °C temperature treatments. Maximum insect mortality (100%) was observed when bacterial concentration of 4×106 cells/ml was used. Similarly, maximum bacterial cells in broth (95%) were penetrated into the insect body within 2 h of their application. However, when stored bacterial toxic secretion was applied to the insects its efficacy declined. On the other hand, when the same toxic secretion was dried and then dissolved either in broth or water was proved to be effective. The present study showed that the bacterium, X. nematophila or its toxic secretion can be used as an important component of integrated pest management against Galleria.

Interference competition and high temperature reduce the ‘virulence’ of fig wasps and contribute to stability of a fig-wasp mutualism

Fig trees are pollinated by fig wasps, which also oviposit in female flowers. The wasp larvae gall and eat developing seeds. Although fig trees benefit from allowing wasps to oviposit, because the wasp offspring disperse pollen, figs must prevent wasps from ovipositing in all flowers, or seed production would cease, and the mutualism would go extinct. In Ficus racemosa, we find that syconia (‘figs’) that have few foundresses (ovipositing wasps) are underexploited in the summer (few seeds, few galls, many empty ovules) and are overexploited in the winter (few seeds, many galls, few empty ovules). Conversely, syconia with many foundresses produce intermediate numbers of galls and seeds, regardless of season. We use experiments to explain these patterns, and thus, to explain how this mutualism is maintained. In the hot summer, wasps suffer short lifespans and therefore fail to oviposit in many flowers. In contrast, cooler temperatures in the winter permit longer wasp lifespans, which in turn allows most flowers to be exploited by the wasps. However, even in winter, only in syconia that happen to have few foundresses are most flowers turned into galls. In syconia with higher numbers of foundresses, interference competition reduces foundress lifespans, which reduces the proportion of flowers that are galled. We further show that syconia encourage the entry of multiple foundresses by delaying ostiole closure. Taken together, these factors allow fig trees to reduce galling in the wasp-benign winter and boost galling (and pollination) in the wasp-stressing summer. Interference competition has been shown to reduce virulence in pathogenic bacteria. Our results show that interference also maintains cooperation in a classic, cooperative symbiosis, thus linking theories of virulence and mutualism. More generally, our results reveal how frequency-dependent population regulation can occur in the fig-wasp mutualism, and how a host species can ‘set the rules of the game’ to ensure mutualistic behavior in its symbionts.