The distribution of pelagic sound scattering layers across the southwest Indian Ocean

Ship of Opportunity Data were sourced from the Integrated Marine Observing System (IMOS)—an initiative of the Australian Government being conducted as part of the National Collaborative Research Infrastructure Strategy and the Super Science Initiative. Other acoustic data were collected as part of the Southwest Indian Ocean Seamounts Project (http://www.iucn.org/marine/seamounts) which was supported supported by the EAF Nansen Project, the Food and Agriculture Organization of the United Nations, the Global Environment Facility, the International Union for the Conservation of Nature, the Natural Environment Research Council (Grant NE/F005504/1), the Leverhulme Trust (Grant F00390C) and the Total Foundation. We thank the Masters, officers, crews and science parties of cruises DFN 2009-410 and JCO66/67 for their assistance during echosounder calibration and data acquisition, and two anonymous reviewers for their comments. PHBS was supported by the German National Academic Foundation, a Cusanuswerk doctoral fellowship, and a Lesley & Charles Hilton-Brown Scholarship.Shallow and deep scattering layers (SLs) were surveyed with split-beam echosounders across the southwest Indian Ocean (SWIO) to investigate their vertical and geographical distribution. Cluster analysis was employed to objectively classify vertical backscatter profiles. Correlations between backscatter and environmental covariates were modelled using generalized additive mixed models (GAMMs) with spatial error structures. Structurally distinct SL regimes were found across the Subantarctic Front. GAMMs indicated a close relationship between sea surface temperature and mean volume backscatter, with significantly elevated backscatter in the subtropical convergence zone. The heterogeneous distribution of scattering layer biota reflects the biogeographic zonation of the survey area and is likely to have implications for predator foraging and carbon cycling in the Indian Ocean.PostprintPeer reviewe

The heart of a dragon: 3D anatomical reconstruction of the ‘scaly-foot gastropod’ (Mollusca: Gastropoda: Neomphalina) reveals its extraordinary circulatory system

Introduction The ‘scaly-foot gastropod’ (Chrysomallon squamiferum Chen et al., 2015) from deep-sea hydrothermal vent ecosystems of the Indian Ocean is an active mobile gastropod occurring in locally high densities, and it is distinctive for the dermal scales covering the exterior surface of its foot. These iron-sulfide coated sclerites, and its nutritional dependence on endosymbiotic bacteria, are both noted as adaptations to the extreme environment in the flow of hydrogen sulfide. We present evidence for other adaptations of the ‘scaly-foot gastropod’ to life in an extreme environment, investigated through dissection and 3D tomographic reconstruction of the internal anatomy. Results Our anatomical investigations of juvenile and adult specimens reveal a large unganglionated nervous system, a simple and reduced digestive system, and that the animal is a simultaneous hermaphrodite. We show that Chrysomallon squamiferum relies on endosymbiotic bacteria throughout post-larval life. Of particular interest is the circulatory system: Chrysomallon has a very large ctenidium supported by extensive blood sinuses filled with haemocoel. The ctenidium provides oxygen for the host but the circulatory system is enlarged beyond the scope of other similar vent gastropods. At the posterior of the ctenidium is a remarkably large and well-developed heart. Based on the volume of the auricle and ventricle, the heart complex represents approximately 4 % of the body volume. This proportionally giant heart primarily sucks blood through the ctenidium and supplies the highly vascularised oesophageal gland. Thus we infer the elaborate cardiovascular system most likely evolved to oxygenate the endosymbionts in an oxygen poor environment and/or to supply hydrogen sulfide to the endosymbionts. Conclusions This study exemplifies how understanding the autecology of an organism can be enhanced by detailed investigation of internal anatomy. This gastropod is a large and active species that is abundant in its hydrothermal vent field ecosystem. Yet all of its remarkable features—protective dermal sclerites, circulatory system, high fecundity—can be viewed as adaptations beneficial to its endosymbiont microbes. We interpret these results to show that, as a result of specialisation to resolve energetic needs in an extreme chemosynthetic environment, this dramatic dragon-like species has become a carrying vessel for its bacteria

How the mollusc got its scales: convergent evolution of the molluscan scleritome

Radiation of dramatically disparate forms among the phylum Mollusca remains a key question in metazoan evolution, and requires careful evaluation of homology of hard parts throughout the deep fossil record. Enigmatic early Cambrian taxa such as Halkieria and Wiwaxia (in the clade Halwaxiida) have been proposed to represent stem-group aculiferan molluscs (Caudofoveata + Solenogastres + Polyplacophora), as complex scleritomes were considered to be unique to aculiferans among extant molluscs. The ‘scaly-foot gastropod’ (Neomphalina: Peltospiridae) from hydrothermal vents of the Indian Ocean, however, also carries dermal sclerites and thus challenges this inferred homology. Despite superficial similarities to various mollusc sclerites, the scaly-foot gastropod sclerites are secreted in layers covering outpockets of epithelium and are largely proteinaceous, while chiton (Polyplacophora: Chitonida) sclerites are secreted to fill an invaginated cuticular chamber and are largely calcareous. Marked differences in the underlying epithelium of the scaly-foot gastropod sclerites and operculum suggest that the sclerites do not originate from multiplication of the operculum. This convergence in different classes highlights the ability of molluscs to adapt mineralized dermal structures, as supported by the extensive early fossil record of molluscs with scleritomes. Sclerites of halwaxiids are morphologically variable, undermining the assumed affinity of specific taxa with chitons, or the larger putative clade Aculifera. Comparisons with independently derived similar structures in living molluscs are essential for determining homology among fossils and their position with respect to the enigmatic evolution of molluscan shell forms in deep time

Primnoidae (Cnidaria: Octocorallia) of the SW Indian Ocean: new species, genus revisions and systematics

The Indian Ocean is one of the least-studied areas of the world’s largest biome, the deep sea. On an expedition to five seamounts along the SW Indian Ocean Ridge in 2011, thousands of specimens from deep-sea habitats were procured. We propose five new species of Primnoidae, a predominantly deep-sea octocoral family. The new species include three from the genus Narella, and one new species each from Primnoa and Primnoeides; the latter genus is revised and we propose Digitogorgia as its junior synonym. We support the new species placement within Primnoidae through taxonomic descriptions and the most comprehensive molecular phylogenetic analysis of any deep-sea coral family (81 species across 29 genera). We also present a rare example of polar submergence (from the Antarctic shelf into deeper waters)

The HANDE-QMC project: open-source stochastic quantum chemistry from the ground state up

Building on the success of Quantum Monte Carlo techniques such as diffusion Monte Carlo, alternative stochastic approaches to solve electronic structure problems have emerged over the last decade. The full configuration interaction quantum Monte Carlo (FCIQMC) method allows one to systematically approach the exact solution of such problems, for cases where very high accuracy is desired. The introduction of FCIQMC has subsequently led to the development of coupled cluster Monte Carlo (CCMC) and density matrix quantum Monte Carlo (DMQMC), allowing stochastic sampling of the coupled cluster wave function and the exact thermal density matrix, respectively. In this article we describe the HANDE-QMC code, an open-source implementation of FCIQMC, CCMC and DMQMC, including initiator and semi-stochastic adaptations. We describe our code and demonstrate its use on three example systems; a molecule (nitric oxide), a model solid (the uniform electron gas), and a real solid (diamond). An illustrative tutorial is also included

De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development

Bosma arhinia microphthalmia syndrome (BAMS) is an extremely rare and striking condition characterized by complete absence of the nose with or without ocular defects. We report here that missense mutations in the epigenetic regulator SMCHD1 mapping to the extended ATPase domain of the encoded protein cause BAMS in all 14 cases studied. All mutations were de novo where parental DNA was available. Biochemical tests and in vivo assays in Xenopus laevis embryos suggest that these mutations may behave as gain-of-function alleles. This finding is in contrast to the loss-of-function mutations in SMCHD1 that have been associated with facioscapulohumeral muscular dystrophy (FSHD) type 2. Our results establish SMCHD1 as a key player in nasal development and provide biochemical insight into its enzymatic function that may be exploited for development of therapeutics for FSHD

A diffusion based shifting algorithm for incompressible smoothed particle hydrodynamics: Validation with cases involving slamming bodies and cylinder exit.

When simulating an incompressible fluid, traditional weakly compressible SPH techniques have disadvantages includ- ing noisy pressure predictions and high computational costs. As an alternative, incompressible SPH simulations can be achieved by employing a projection method to enforce a divergence free velocity field. Such techniques are receiving considerable interest in the literature due to the potential for noise free pressure predictions, with acceptable computational costs. The method does however suffer from stability issues when particles bunch together or are stretched apart from one another, which is generally the case if particles are restricted to following streamlines, as is dictated by the Navier-Stokes equations. To overcome this issue, particles can be shifted away from one another, across streamlines, according to some algorithm whose job it is to determine a suitable displacement vector. The primitive variables are then corrected to account for their change in position via interpolation.Here, we follow on from earlier work in the authors’ group and employ Ficks’s law to shift the particles. We present validation cases involving cylinder and wedge slamming into initially calm water. We also consider cylinder exit from initially calm water. These cases are particularly relevant to the design of ships and wave energy extraction devices. The results we present show effectively noise free pressures and very high accuracy. To our knowledge, this is the first time such accuracy has been achieved via SPH techniques for such complex cases

Landscapes in transition: an analysis of sustainable policy initiatives and emerging corporate commitments in the palm oil industry

The recent Southeast Asian haze crisis has generated intense public scrutiny over the rate, methods and types of landscape change in the tropics. Debate has centred on the environmental impacts of large-scale agricultural expansion, particularly the associated loss of high carbon stock forest and forests of high conservation value. Focusing on palm oil—a versatile food crop and source of bioenergy—this paper analyses national, international and corporate policy initiatives in order to clarify the current and future direction of oil palm expansion in Malaysia and Indonesia. The policies of ‘zero burn’, ‘no deforestation’ and ‘no planting on peatlands’ are given particular emphasis in the paper. The landscape implications of corporate commitments are analysed to determine the amount of land, land types and geographies that could be affected in the future. The paper concludes by identifying key questions related to the further study of sustainable land use policy and practice

Cutting through the smoke: the diversity of microorganisms in deep-sea hydrothermal plumes

There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes. The microbial data were sequenced on an Illumina MiSeq platform for the 16SrRNA gene. A substantial amount of vent-specific putative chemosynthetic microorganisms were found, particularly in samples from focused hydrothermal venting. Common vent-specific organisms from both vent fields were the genera Arcobacter, Caminibacter and Sulfurimonas from the Epsilonproteobacteria and the SUP05 group from the Gammaproteobacteria. There were no major differences in microbial composition between SWIR and ESR for focused plume samples. However, within the ESR the diffuse flow and focused samples differed significantly in microbial community composition and relative abundance. For Epsilonproteobacteria, we found evidence of niche-specificity to hydrothermal vent environments. This taxon decreased in abundance by three orders of magnitude from the vent orifice to background water. Epsilonproteobacteria distribution followed a distance–decay relationship as vent-effluents mixed with the surrounding seawater. This study demonstrates strong habitat affinity of vent microorganisms on a metre scale with distinct environmental selection