A heterogeneity test for fine-scale genetic structure

For organisms with limited vagility and/or occupying patchy habitats, we often encounter nonrandom patterns of genetic affinity over relatively small spatial scales, labelled fine-scale genetic structure. Both the extent and decay rate of that pattern can be expected to depend on numerous interesting demographic, ecological, historical, and mating system factors, and it would be useful to be able to compare different situations. There is, however, no heterogeneity test currently available for fine-scale genetic structure that would provide us with any guidance on whether the differences we encounter are statistically credible. Here, we develop a general nonparametric heterogeneity test, elaborating on standard autocorrelation methods for pairs of individuals. We first develop a 'pooled within-population' correlogram, where the distance classes (lags) can be defined as functions of distance. Using that pooled correlogram as our null-hypothesis reference frame, we then develop a heterogeneity test of the autocorrelations among different populations, lag-by-lag. From these single-lag tests, we construct an analogous test of heterogeneity for multilag correlograms. We illustrate with a pair of biological examples, one involving the Australian bush rat, the other involving toadshade trillium. The Australian bush rat has limited vagility, and sometimes occupies patchy habitat. We show that the autocorrelation pattern diverges somewhat between continuous and patchy habitat types. For toadshade trillium, clonal replication in Piedmont populations substantially increases autocorrelation for short lags, but clonal replication is less pronounced in mountain populations. Removal of clonal replicates reduces the autocorrelation for short lags and reverses the sign of the difference between mountain and Piedmont correlograms

Channel incision into a submarine landslide on a Carboniferous basin margin, San Juan, Argentina: Evidence for the role of knickpoints

Emplacement of submarine landslides, or mass-transport deposits, can radically reshape the physiography of continental margins, and strongly influence subsequent sedimentary processes and dispersal patterns. Typically, progressive healing of the complicated relief generated by the submarine landslide occurs prior to progradation of sedimentary systems. However, subsurface and seabed examples show that submarine channels can incise directly into submarine landslides. Here, the evolution of a unique exhumed example of two adjacent, and partially contemporaneous, submarine channel-fills is documented. The channels show deep incision (>75 m), and steep lateral margins (up to 70°), cut into a >200 m thick submarine landslide. The stepped basal erosion surface, and multiple terrace surfaces, are mantled by clasts (gravels to cobbles) reflecting periods of bedload-derived sedimentation, punctuated by phases of downcutting and sediment bypass. The formation of multiple terrace surfaces in a low aspect ratio confinement is consistent with the episodic migration of knickpoints during entrenchment on the dip slope of the underlying submarine landslide. Overlying sandstone-rich channel-fills mark a change to aggradation. Laterally stacked channel bodies coincide with steps in the original large-scale erosion surface, recording widening of the conduit; this is followed by tabular, highly aggradational fill. The upper fill, above a younger erosional surface, shows an abrupt change to partially confined tabular sandstones with normally graded caps, interpreted as lobe fringe deposits, which formed due to down-dip confinement, followed by prograding lobe deposits. Overlying this, an up-dip avulsion induced lobe switching and back-stepping, and subsequent failure of a sandstone body up-dip led to emplacement of a sandstone-rich submarine landslide within the conduit. Collectively, this outcrop represents episodic knickpoint-generated incision, and later infill, of a slope adjusting to equilibrium. The depositional signature of knickpoints is very different from existing models, but is probably reflective of other highly erosional settings undergoing large-scale slope adjustment.Fil: Allen, Charlotte. University of Leeds; Reino UnidoFil: Gomis Cartesio, Luz E.. No especifíca;Fil: Hodgson, David M.. University of Leeds; Reino UnidoFil: Peakall, Jeff. University of Leeds; Reino UnidoFil: Milana, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; Argentin

Flow dynamics and mixing processes in hydraulic jump arrays: Implications for channel-lobe transition zones

A detailed field investigation of a saline gravity current in the southwest Black Sea has enabled the first complete analysis of three-dimensional flow structure and dynamics of a series of linked hydraulic jumps in stratified, density-driven, flows. These field observations were collected using an acoustic Doppler current profiler mounted on an autonomous underwater vehicle, and reveal that internal mixing processes in hydraulic jumps, including flow expansion and recirculation, provide a previously unrecognised mechanism for grain-size sorting and segregation in stratified density-driven flows. Field observations suggest a newly identified type of hydraulic jump, that is a stratified low Froude number (< 1.5–2) subaqueous hydraulic jump, with an enhanced ability to transport sediment downstream of the jump, in comparison to hydraulic jumps in other subaerial and submarine flows. These novel field data underpin a new process-based conceptual model of channel lobe transition zones (CLTZs) that explains the scattered offset nature of scours within such settings, the temporal variations in infill and erosion between adjacent scours, how bed shear stresses are maintained across the CLTZ, and why the locus of deposition is so far downstream of the scour zone

Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others

The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.PES was supported by the USDA National Institute of Food and Agriculture Hatch Project 1005333, and the New Jersey Agricultural Experiment Station, Hatch project NJ17160; SCB was supported by Australian Research Council Future Fellowship FT130100043. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Longitudinal flow evolution and turbulence structure of dynamically similar, sustained, saline density and turbidity currents

Experimental results are presented concerning flow evolution and turbulence structure of sustained saline and turbidity flows generated on 0°, 3°, 6°, and 9° sloping ramps that terminate abruptly onto a horizontal floor. Two-component velocity and current density were measured with an ultrasonic Doppler velocity profiler and siphon sampler on the slope, just beyond the slope break and downstream on the horizontal floor. Three main factors influence longitudinal flow evolution and turbulence structure: sediment transport and sedimentation, slope angle, and the presence of a slope break. These controls interact differently depending on flow type. Sediment transport is accompanied by an inertial fluid reaction that enhances Reynolds stresses in turbidity flows. Thus turbidity flows mix more vigorously than equivalent saline density flows. For saline flows, turbulent kinetic energy is dependent on slope, and rapid deceleration occurs on the horizontal floor. For turbidity flows, normalized turbulent kinetic energy increases downstream, and mean streamwise deceleration is reduced compared with saline flows. The slope break causes mean bed-normal velocity of turbidity flows to become negative and have a gentler gradient compared with other locations. A reduction of peak Reynolds normal stress in the bed-normal direction is accompanied by an increase in turbulent accelerations across the rest of the flow thickness. Thus the presence of particles acts to increase Reynolds normal stresses independently of gradients of mean velocity, and sediment transport increases across the break in slope. The experiments illustrate that saline density currents may not be good dynamic analogues for natural turbidity currents

Self-recognition in corals facilitates deep-sea habitat engineering

The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting coralline algae bind together substrates and dead coral framework to make continuous reef structures, but beyond the photic zone, the cold-water coral Lophelia pertusa also forms large biogenic reefs, facilitated by skeletal fusion. Skeletal fusion in tropical corals can occur in closely related or juvenile individuals as a result of non-aggressive skeletal overgrowth or allogeneic tissue fusion, but contact reactions in many species result in mortality if there is no ‘self-recognition’ on a broad species level. This study reveals areas of ‘flawless’ skeletal fusion in Lophelia pertusa, potentially facilitated by allogeneic tissue fusion, are identified as having small aragonitic crystals or low levels of crystal organisation, and strong molecular bonding. Regardless of the mechanism, the recognition of ‘self’ between adjacent L. pertusa colonies leads to no observable mortality, facilitates ecosystem engineering and reduces aggression-related energetic expenditure in an environment where energy conservation is crucial. The potential for self-recognition at a species level, and subsequent skeletal fusion in framework-forming cold-water corals is an important first step in understanding their significance as ecological engineers in deep-seas worldwide

Evolution from syn-rift carbonates to early post-rift deep-marine intraslope lobes: The role of rift basin physiography on sedimentation patterns

The stratigraphic architecture of Early Jurassic strata exposed along a >10 km long transect in the Chachil Graben, an exhumed marine rift depocentre in the Neuquén Basin (Argentina), provides insights into the sedimentological and stratigraphic expression of the syn-rift to post-rift transition. A change from syn-rift intrabasinal carbonate to post-rift extrabasinal siliciclastic sedimentation is recorded, as well as variations in sediment supply and dispersal patterns across rift-related topography. The late syn-rift was marked by a transgression and development of a shallow-marine carbonate system, including carbonate platform deposits perched on fault-block highs and periplatform deposits accumulated in fault-block lows, which overlies continental volcano-sedimentary syn-rift deposits. Differential subsidence and basin deepening induced retrogradation of the carbonate system, which was progressively drowned and overlain by organic-rich calcareous mudstone that draped across rift structures at the onset of the early post-rift. The first extrabasinal siliciclastic influx led to progradation of an early post-rift intraslope lobe complex into the graben, which is associated with kilometre-scale clastic injectites. The depositional architecture, facies distribution and pinch-out style of intraslope lobes record the effects of an inherited compaction hinge, which acted as an oblique counterslope to sediment gravity flows. The occurrence of combined-flow bedforms, widespread erosion, and limited facies segregation across lobes bearing different hybrid event bed types, is in sharp contrast to sedimentological characteristics of existing intraslope lobe models. Documentation of the syn-rift to post-rift transition stratigraphy permitted identification of changes in thickness and facies resulting from the passive infill of inherited topography with early post-rift differential compaction. This architecture contrasts markedly with those developed during syn-rift normal faulting. Furthermore, the influence of local inherited topography on the development of early post-rift lobes is key to improve subsurface prediction of sandstone distribution and quality during assessment of hydrocarbon reservoirs and carbon storage sites

Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels

Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels’ species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants