An improved method to detect damage using modal strain energy based damage index

This paper presents two novel concepts to enhance the accuracy of damage detection using the Modal Strain Energy based Damage Index (MSEDI) with the presence of noise in the mode shape data. Firstly, the paper presents a sequential curve fitting technique that reduces the effect of noise on the calculation process of the MSEDI, more effectively than the two commonly used curve fitting techniques; namely, polynomial and Fourier’s series. Secondly, a probability based Generalized Damage Localization Index (GDLI) is proposed as a viable improvement to the damage detection process. The study uses a validated ABAQUS finite-element model of a reinforced concrete beam to obtain mode shape data in the undamaged and damaged states. Noise is simulated by adding three levels of random noise (1%, 3%, and 5%) to the mode shape data. Results show that damage detection is enhanced with increased number of modes and samples used with the GDLI.

A molecular phylogeny for the Tribe Dacini (Diptera: Tephritidae) : systematic and biogeographic implications

With well over 700 species, the Tribe Dacini is one of the most species-rich clades within the dipteran family Tephritidae, the true fruit flies. Nearly all Dacini belong to one of two very large genera, Dacus Fabricius and Bactrocera Macquart. The distribution of the genera overlap in or around the Indian subcontinent, but the greatest diversity of Dacus is in Africa and the greatest diversity of Bactrocera is in south-east Asia and the Pacific. The monophyly of these two genera has not been rigorously established, with previous phylogenies only including a small number of species and always heavily biased to one genus over the other. Moreover, the subgeneric taxonomy within both genera is complex and the monophyly of many subgenera has not been explicitly tested. Previous hypotheses about the biogeography of the Dacini based on morphological reviews and current distributions of taxa have invoked an out-of-India hypothesis; however this has not been tested in a phylogenetic framework. We attempted to resolve these issues with a dated, molecular phylogeny of 125 Dacini species generated using 16S, COI, COII and white eye genes. The phylogeny shows that Bactrocera is not monophyletic, but rather consists of two major clades: Bactrocera s.s. and the ‘Zeugodacus group of subgenera’ (a recognised, but informal taxonomic grouping of 15 Bactrocera subgenera). This ‘Zeugodacus’ clade is the sister group to Dacus, not Bactrocera and, based on current distributions, split from Dacus before that genus moved into Africa. We recommend that taxonomic consideration be given to raising Zeugodacus to genus level. Supportive of predictions following from the out-of-India hypothesis, the first common ancestor of the Dacini arose in the mid-Cretaceous approximately 80 mya. Major divergence events occurred during the Indian rafting period and diversification of Bactrocera apparently did not begin until after India docked with Eurasia (50–35 mya). In contrast, diversification in Dacus, at approximately 65 mya, apparently began much earlier than predicted by the out-of-India hypothesis, suggesting that, if the Dacini arose on the Indian plate, then ancestral Dacus may have left the plate in the mid to late Cretaceous via the well documented India–Madagascar–Africa migration route. We conclude that the phylogeny does not disprove the predictions of an out-of-India hypothesis for the Dacini, although modification of the original hypothesis is required.

An invasive grass shows colonization advantages over native grasses under conditions of low resource availability

Increased or fluctuating resources may facilitate opportunities for invasive exotic plants to dominate. This hypothesis does not, however, explain how invasive species succeed in regions characterized by low resource conditions or how these species persist in the lulls between high resource periods. We compare the growth of three co-occurring C4 perennial bunchgrasses under low resource conditions: an exotic grass, Eragrostis curvula (African lovegrass) and two native grasses, Themeda triandra and Eragrostis sororia. We grew each species over 12 weeks under low nutrients and three low water regimes differentiated by timing: continuous, pulsed, and mixed treatments (switched from continuous to pulsed and back to continuous). Over time, we measured germination rates, time to germination (first and second generations), height, root biomass, vegetative biomass, and reproductive biomass. Contrary to our expectations that the pulsed watering regime would favor the invader, water-supply treatments had little significant effect on plant growth. We did find inherent advantages in a suite of early colonization traits that likely favor African lovegrass over the natives including faster germination speed, earlier flowering times, faster growth rates and from 2 weeks onward it was taller. African lovegrass also showed similar growth allocation strategies to the native grasses in terms of biomass levels belowground, but produced more vegetative biomass than kangaroo grass. Overall our results suggest that even under low resource conditions invasive plant species like African lovegrass can grow similarly to native grasses, and for some key colonization traits, like germination rate, perform better than natives.

Isolation and functional characterisation of banana phytoene synthase genes as potential cisgenes

Carotenoids occur in all photosynthetic organisms where they protect photosystems from auto-oxidation, participate in photosynthetic energy-transfer and are secondary metabolites. Of the more than 600 known plant carotenoids, few can be converted into vitamin A by humans and so these pro-vitamin A carotenoids (pVAC) are important in human nutrition. Phytoene synthase (PSY) is a key enzyme in the biosynthetic pathway of pVACs and plays a central role in regulating pVAC accumulation in the edible portion of crop plants. Bananas are a major commercial crop and serve as a staple crop for more than 30 million people. There is natural variation in fruit pVAC content across different banana cultivars, but this is not well understood. Therefore, we isolated PSY genes from banana cultivars with relatively high (cv. Asupina) and low (cv. Cavendish) pVAC content. We provide evidence that PSY in banana is encoded by two paralogs (PSY1 and PSY2), each with a similar gene structure to homologous genes in other monocots. Further, we demonstrate that PSY2 is more highly expressed in fruit pulp compared to leaf. Functional analysis of PSY1 and PSY2 in rice callus and E. coli demonstrate that both genes encode functional enzymes, and that Asupina PSYs have approximately twice the enzymatic activity of the corresponding Cavendish PSYs. These results suggest that differences in PSY enzyme activity contribute significantly to the differences in Asupina and Cavendish fruit pVAC content. Importantly, Asupina PSY genes could potentially be used to generate new cisgenic or intragenic banana cultivars with enhanced pVAC content.

Development and characterisation of tri- and tetra-nucleotide polymorphic microsatellite markers for skipjack tuna (Katsuwonus pelamis)

Skipjack tuna (katsuwonus pelamis) (SJT) is the largest tuna fishery in all the major oceans around the world, and the largest marine fishery in Sri Lanka. Knowledge of genetic population structure and effective population size of SJT in the Indian Ocean and other major oceans, however, is still lacking for better management practices and conservation strategies. We developed microsatellite genetic markers using SJT around Sri Lanka in the Indian Ocean, and characterise one tri- and seven tetra-nucleotide microsatellite loci isolated from enriched genomic libraries from SJT, to provide tools for addressing both conservation and fisheries management questions. An analysis of these eight microsatellite markers in two populations of SJT from eastern Sri Lanka (n = 44) and the Maldives Islands (n = 53) showed that all eight microsatellites were polymorphic with an average number of alleles per locus of 11.80 (range 5-27). Expected heterozygosities at marker loci ranged from 0.450 to 0.961. These markers are being used currently to characterise population structure and extent of natural gene flow in SJT populations from the eastern and western Indian Ocean. No significant linkage disequilibrium was detected among any loci pairs.

Response to comments on "Productivity is a poor predictor of plant species richness"

Pan et al. claim that our results actually support a strong linear positive relationship between productivity and richness, whereas Fridley et al. contend that the data support a strong humped relationship. These responses illustrate how preoccupation with bivariate patterns distracts from a deeper understanding of the multivariate mechanisms that control these important ecosystem properties.

Discriminating stromatolite formation modes using rare earth element geochemistry: Trapping and binding versus in situ precipitation of stromatolites from the Neoproterozoic Bitter Springs Formation, Northern Territory, Australia

Stromatolites consist primarily of trapped and bound ambient sediment and/or authigenic mineral precipitates, but discrimination of the two constituents is difficult where stromatolites have a fine texture. We used laser ablation-inductively coupled plasma-mass spectrometry to measure trace element (rare earth element – REE, Y and Th) concentrations in both stromatolites (domical and branched) and closely associated particulate carbonate sediment in interspaces (spaces between columns or branches) from bioherms within the Neoproterozoic Bitter Springs Formation, central Australia. Our high resolution sampling allows discrimination of shale-normalised REE patterns between carbonate in stromatolites and immediately adjacent, fine-grained ambient particulate carbonate sediment from interspaces. Whereas all samples show similar negative La and Ce anomalies, positive Gd anomalies and chondritic Y/Ho ratios, the stromatolites and non-stromatolite sediment are distinguishable on the basis of consistently elevated light REEs (LREEs) in the stromatolitic laminae and relatively depleted LREEs in the particulate sediment samples. Additionally, concentrations of the lithophile element Th are higher in ambient sediment samples than in stromatolites, consistent with accumulation of some fine siliciclastic detrital material in the ambient sediment but a near absence in the stromatolites. These findings are consistent with the stromatolites consisting dominantly of in situ carbonate precipitates rather than trapped and bound ambient sediment. Hence, high resolution trace element (REE + Y, Th) geochemistry can discriminate fine-grained carbonates in these stromatolites from coeval non-stromatolitic carbonate sediment and demonstrates that the sampled stromatolites formed primarily from in situ precipitation, presumably within microbial mats/biofilms, rather than by trapping and binding of ambient sediment. Identification of the source of fine carbonate in stromatolites is significant, because if it is not too heavily contaminated by trapped ambient sediment, it may contain geochemical biosignatures and/or direct evidence of the local water chemistry in which the precipitates formed.

Undrained sediment loading key to long-runout submarine mass movements : evidence from the Caribbean Volcanic Arc

Long undersea debris runout can be facilitated by a boundary layer formed by weak marine sediments under a moving slide mass. Undrained loading of such offshore sediment results in a profound drop of basal shear resistance, compared to subaerial shear resistance, enabling long undersea runout. Thus large long-runout submarine landslides are not truly enigmatic (Voight and Elsworth 1992, 1997), but are understandable in terms of conventional geotechnical principles. A corollary is that remoulded undrained strength, and not friction angle, should be used for basal resistance in numerical simulations. This hypothesis is testable via drilling and examining the structure at the soles of undersea debris avalanches for indications of incorporation of sheared marine sediments, by tests of soil properties, and by simulations. Such considerations of emplacement process are an aim of ongoing research in the Lesser Antilles (Caribbean Sea), where multiple offshore debris avalanche and dome-collapse debris deposits have been identified since 1999 on swath bathymetric surveys collected in five oceanographic cruises. This paper reviews the prehistoric and historic collapses that have occurred offshore of Antilles arc islands and summarizes ongoing research on emplacement processes.

Evidence for carbonate platform failure during rapid sea-level rise; ca 14 000 year old bioclastic flow deposits in the Lesser Antilles

Bioclastic flow deposits offshore from the Soufrie`re Hills volcano on Montserrat in the Lesser Antilles were deposited by the largest volume sediment flows near this active volcano in the last 26 kyr. The volume of these deposits exceeds that of the largest historic volcanic dome collapse in the world, which occurred on Montserrat in 2003. These flows were most probably generated by a large submarine slope failure of the carbonate shelf comprising the south west flank of Antigua or the east flank of Redonda; adjacent islands that are not volcanically active. The bioclastic flow deposits are relatively coarse-grained and either ungraded or poorly graded, and were deposited by non cohesive debris flow and high density turbidity currents. The bioclastic deposit often comprises multiple sub-units that cannot be correlated between core sites; some located just 2 km apart. Multiple sub-units in the bioclastic deposit result from either flow reflection, stacking of multiple debris flow lobes, and/or multi-stage collapse of the initial landslide. This study provides unusually precise constraints on the age of this mass flow event that occurred at ca 14 ka. Few large submarine landslides have been well dated, but the slope failures that have been dated are commonly associated with periods of rapid sea-level change.

Eruption of Soufrière Hills (1995–2009) from an offshore perspective : insights from repeated swath bathymetry surveys

This contribution provides an analysis of the 1995–2009 eruptive period of Soufrière Hills volcano (Montserrat) from a unique offshore perspective. The methodology is based on five repeated swath bathymetric surveys. The difference between the 2009 and 1999 bathymetry suggests that at least 395 Mm3 of material has entered the sea. This proximal deposit reaches 95 m thick and extends ∼7km from shore. However, the difference map does not include either the finer distal part of the submarine deposit or the submarine part of the delta close to the shoreline. We took both contributions into account by using additional information such as that from marine sediment cores. By March 2009, at least 65% of the material erupted throughout the eruption has been deposited into the sea. This work provides an excellent basis for assessing the future activity of the Soufrière Hills volcano (including potential collapse), and other volcanoes on small islands.

Anatomy of a submarine pyroclastic flow and associated turbidity current : July 2003 dome collapse, Soufrière Hills volcano, Montserrat, West Indies

The 12 to 13 July 2003 andesite lava dome collapse at the Soufrière Hills volcano, Montserrat, provides the first opportunity to document comprehensively both the sub-aerial and submarine sequence of events for an eruption. Numerous pyroclastic flows entered the ocean during the collapse, depositing approximately 90% of the total material into the submarine environment. During peak collapse conditions, as the main flow penetrated the air–ocean interface, phreatic explosions were observed and a surge cloud decoupled from the main flow body to travel 2 to 3 km over the ocean surface before settling. The bulk of the flow was submerged and rapidly mixed with sea water forming a water-saturated mass flow. Efficient sorting and physical differentiation occurred within the flow before initial deposition at 500 m water depth. The coarsest components (∼60% of the total volume) were deposited proximally from a dense granular flow, while the finer components (∼40%) were efficiently elutriated into the overlying part of the flow, which evolved into a far-reaching turbidity current.

Submarine pyroclastic deposits formed at the Soufrière Hills volcano, Montserrat (1995–2003) : what happens when pyroclastic flows enter the ocean?

The Soufrière Hills volcano, Montserrat, West Indies, has undergone a series of dome growth and collapse events since the eruption began in 1995. Over 90% of the pyroclastic material produced has been deposited into the ocean. Sampling of these submarine deposits reveals that the pyroclastic flows mix rapidly and violently with the water as they enter the sea. The coarse components (pebbles to boulders) are deposited proximally from dense basal slurries to form steep-sided, near-linear ridges that intercalate to form a submarine fan. The finer ash-grade components are mixed into the overlying water column to form turbidity currents that flow over distances >30 km from the source. The total volume of pyroclastic material off the east coast of Montserrat exceeds 280 × 106 m3, with 65% deposited in proximal lobes and 35% deposited as distal turbidites.

Reconstructing the event stratigraphy from the complex structural - stratigraphic architecture of an Archaean volcanic – intrusive – sedimentary succession : the Boorara Domain, Eastern Goldfields Superterrane, Western Australia

Two main deformational phases are recognised in the Archaean Boorara Domain of the Kalgoorlie Terrane, Eastern Goldfields Superterrane, Yilgarn Craton, Western Australia, primarily involving southover- north thrust faulting that repeated and thickened the stratigraphy, followed by east northeast – west-southwest shortening that resulted in macroscale folding of the greenstone lithologies. The domain preserves mid-greenschist facies metamorphic grade, with an increase to lower amphibolite metamorphic grade towards the north of the region. As a result of the deformation and metamorphism, individual stratigraphic horizons are difficult to trace continuously throughout the entire domain. Volcanological and sedimentological textures and structures, primary lithological contacts, petrography and geochemistry have been used to correlate lithofacies between faultbounded structural blocks. The correlated stratigraphic sequence for the Boorara Domain comprises quartzo-feldspathic turbidite packages, overlain by high-Mg tholeiitic basalt (lower basalt), coherent and clastic dacite facies, intrusive and extrusive komatiite units, an overlying komatiitic basalt unit (upper basalt), and at the stratigraphic top of the sequence, volcaniclastic quartz-rich turbidites. Reconstruction of the stratigraphy and consideration of emplacement dynamics has allowed reconstruction of the emplacement history and setting of the preserved sequence. This involves a felsic, mafic and ultramafic magmatic system emplaced as high-level intrusions, with localised emergent volcanic centres, into a submarine basin in which active sedimentation was occurring.

Tephrochronology of marine sediments around the Island of Montserrat, Lesser Antilles volcanic arc

The recent history of the Soufrière Hills Volcano, Montserrat, Lesser Antilles volcanic arc, is reconstructed using data obtained from recently drilled submarine cores.Tephra layers in these cores preserve a record of the volcanic history of Montserrat back to ~250 ka on the basis of micropaleontology and stable isotope stratigraphy. Stratigraphic relationships identified in the cores collected in 2002 and 2005 document the fate of both pyroclastic flows entering the ocean to the east of Montserrat and carbonate-rich turbidites sourced from the carbonate platformssurrounding the islands of the Lesser Antilles. Using oxygen isotope stratigraphy, micropalaeontological analysis and Carbon-14 dating, it can be shown that three significant volcanic events, including the on-going eruption, have occurred over the last 12 ka. Preceding this was a time of volcanic quiescence, with three carbonate-rich turbidite events being documented in many of the cores. Our data suggest that these events occurred during Marine Isotope Stage 2, following the Last Glacial Maximum (LGM) and onset of post-glacial sea level rise.

Submarine deposition of volcaniclastic material from the 1995-2005 eruptions of Soufriere Hills volcano, Montserrat

Soufrière Hills volcano, Montserrat, has been erupting since 1995. During the current eruption, a large part of the material produced by the volcano has been transported into the sea, modifying the morphology of the submarine flanks of the volcano. We present a unique set of swath bathymetric data collected offshore from Montserrat in 1999, 2002 and 2005. From 1999 to 2002, pyroclastic flows associated with numerous dome collapses entered the sea to produce 100 Mm3 deposit. From 2002 to 2005, the 290 Mm3 submarine deposit is mainly from the 12–13 July 2003 collapse. These data allow us to estimate that, by May 2005, at least 482 Mm3 of material had been deposited on the sea floor since 1995. We compare on-land characteristics and volumes of dome collapse events with the submarine deposits and propose a new analysis of their emplacement on the submarine flanks of the volcano. The deposition mechanism shows a slope dependence, with the maximum thickness of deposit before the break in the slope, probably because of the type of the dense granular flow involved. We conclude that from 1995 to 2005 more than 75% of the erupted volume entered the sea.