Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise

For some genes, notably essential genes, expression when expression is needed is vital hence low noise in expression is favourable. For others noise is necessary for coping with stochasticity or for providing dice-like mechanisms to control cell fate. But how is noise in gene expression modulated? We hypothesise that gene orientation may be crucial, as for divergently organized gene pairs expression of one gene could affect chromatin of a neighbour thereby reducing noise. Transcription of antisense non-coding RNA from a shared promoter is similarly argued to be a noise-reduction mechanism. Stochastic simulation models confirm the expectation. The model correctly predicts: that protein coding genes with bi-promoter architecture, including those with a ncRNA partner, have lower noise than other genes; divergent gene pairs uniquely have correlated expression noise; distance between promoters predicts noise; ncRNA divergent transcripts are associated with genes that a priori would be under selection for low noise; essential genes reside in divergent orientation more than expected; bi-promoter pairs are rare subtelomerically, cluster together and are enriched in essential gene clusters. We conclude that gene orientation and transcription of ncRNAs, even if unstable, are candidate modulators of noise levels

Controls on the distribution of cosmogenic 10Be across shore platforms

Quantifying rates of erosion on cliffed coasts across a range of timescales is vital for understanding the drivers and processes of coastal change and for assessing risks posed by future cliff retreat. Historical records cover at best the last 150 years; Cosmogenic radionuclides, such as 10Be could allow us to look further into past to assess coastal change at millenial timescales. CRNs accumulate in-situ near the Earth surface and have been used extensively to quantify erosion rates, burial dates and surface exposure ages in terrestrial landscapes over the last three decades. More recently, applications in rocky coast settings have quantified the timing of mass wasting events, determined long-term-averaged rates of cliff retreat and revealed the exposure history of shore platforms. In this contribution, we developed and explored a numerical model for the accumulation of 10Be on eroding shore platforms. In a series of numerical experiments, we investigated the influence of topographic and water shielding, dynamic platform erosion processes, the presence and variation in beach cover, and heterogeneous distribution of erosion on the distribution of 10Be across shore platforms. Results demonstrate that, taking into account relative sea level change and tides, the concentration of 10Be is sensitive to rates of cliff retreat. Factors such as topographic shielding and beach cover, act to reduce 10Be concentrations on the platform, and may result in overestimation of cliff retreat rates if not accounted for. The shape of the distribution of 10Be across a shore platform can potentially reveal whether cliff retreat rates are declining or accelerating through time. Measurement of 10Be in shore platforms has great potential to allow us to quantify long-term rates of cliff retreat and platform erosion

Erosion of rocky shore platforms by block detachment from layered stratigraphy

The majority of shore platforms form in rocks that are characterised by layered stratigraphy and pervasive jointing. Plucking of weathered, joint and bed bounded blocks is an important erosion process that existing models of platform development do not represent. Globally, measuring platform erosion rates have focused on microscale (< 1 mm) surface lowering rather than mesoscale (0.1‐1 m) block detachment, yet the latter appears to dominate the morphological development of discontinuity rich platforms. Given the sporadic nature of block detachment on platforms, observations of erosion from storm event to multi‐decadal timescales (and beyond) are required to quantify shore platform erosion rates. To this end, we collected aerial photography using an unmanned aerial vehicle to produce structure‐from‐motion‐derived digital elevation models and orthophotos. These were combined with historical aerial photographs to characterise and quantify the erosion of two actively eroding stratigraphic layers on a shore platform in Glamorgan, south Wales, UK, over 78‐years. We find that volumetric erosion rates vary over two orders of magnitude (0.1‐10 m3 yr‐1) and do not scale with the length of the record. Average rates over the full 78‐year record are 2‐5 m3 yr‐1. These rates are equivalent to 1.2‐5.3 mm yr‐1 surface lowering rates, an order of magnitude faster than previously published, both at our site and around the world in similar rock types. We show that meso‐scale platform erosion via block detachment processes is a dominant erosion process on shore platforms across seasonal to multi‐decadal timescales that have been hitherto under‐investigated

Sediment accumulation in embayments controlled by bathymetric slope and wave energy: Implications for beach formation and persistence

High energy, rocky coastlines often feature sandy beaches within headland‐bound embayments. Not all such embayments have beaches however, and beaches in embayments can be removed by storms and may subsequently reform. What dictates the presence or absence of an embayed beach and its resilience to storms? In this paper, we explore the effect of offshore slope and wind conditions on nearshore sediment transport within idealised embayments to give insight into nearshore sediment supplies. We use numerical simulations to show that sand can accumulate near shore if the offshore slope is >0.025 m/m, but only under persistent calm conditions. Our modelling also suggests that if sediment in an embayment with an offshore gradient steeper than 0.025 m/m is removed during a period of persistent stormy conditions, it will be unlikely to return in sub‐decadal timescales. In contrast, sediment located in embayments with shallower gradients can reform swiftly in both calm and stormy conditions. Our findings have wide implications for contemporary coastal engineering in the face of future global climate change, but also for Quaternary environmental reconstruction. Our simple method to predict beach stability based on slope can be used to interpret differing responses of embayments to periods of changing coastal storminess such as the medieval climate anomaly‐little ice age (MCA‐LIA) transition

Recent acceleration in coastal cliff retreat rates on the south coast of Great Britain

Rising sea levels and increased storminess are expected to accelerate the erosion of soft-cliff coastlines, threatening coastal infrastructure and livelihoods. To develop predictive models of future coastal change we need fundamentally to know how rapidly coasts have been eroding in the past, and to understand the driving mechanisms of coastal change. Direct observations of cliff retreat rarely extend beyond 150 y, during which humans have significantly modified the coastal system. Cliff retreat rates are unknown in prior centuries and millennia. In this study, we derived retreat rates of chalk cliffs on the south coast of Great Britain over millennial time scales by coupling high-precision cosmogenic radionuclide geochronology and rigorous numerical modeling. Measured 10Be concentrations on rocky coastal platforms were compared with simulations of coastal evolution using a Monte Carlo approach to determine the most likely history of cliff retreat. The 10Be concentrations are consistent with retreat rates of chalk cliffs that were relatively slow (2–6 cm⋅y−1) until a few hundred years ago. Historical observations reveal that retreat rates have subsequently accelerated by an order of magnitude (22–32 cm⋅y−1). We suggest that acceleration is the result of thinning of cliff-front beaches, exacerbated by regional storminess and anthropogenic modification of the coast

Exploring the sensitivities of crenulate-bay shorelines to wave climates using a new vector-based one-line model

We use a new exploratory model that simulates the evolution of sandy coastlines over decadal to centennial timescales to examine the behavior of crenulate-shaped bays forced by differing directional wave climates. The model represents the coastline as a vector in a Cartesian reference frame, and the shoreface evolves relative to its local orientation, allowing simulation of coasts with high planform-curvature. Shoreline change is driven by gradients in alongshore transport following newly developed algorithms that facilitate dealing with high planform-curvature coastlines. We simulated the evolution of bays from a straight coast between two fixed headlands with no external sediment inputs to an equilibrium condition (zero net alongshore sediment flux) under an ensemble of directional wave climate conditions. We find that planform bay relief increases with obliquity of the mean wave direction, and decreases with the spread of wave directions. Varying bay size over 2 orders of magnitude (0.1–16 km), the model predicts bay shape to be independent of bay size. The time taken for modeled bays to attain equilibrium was found to scale with the square of the distance between headlands, so that, all else being equal, small bays are likely to respond to and recover from perturbations more rapidly (over just a few years) compared to large bays (hundreds of years). Empirical expressions predicting bay shape may be misleading if used to predict their behavior over planning timescales

Complex coastlines responding to climate change: do shoreline shapes reflect present forcing or “remember” the distant past?

A range of planform morphologies emerge along sandy coastlines as a function of offshore wave climate. It has been implicitly assumed that the morphological response time is rapid compared to the timescales of wave climate change, meaning that coastal morphologies simply reflect the extant wave climate. This assumption has been explored by focussing on the response of two distinctive morphological coastlines – flying spits and cuspate capes – to changing wave climates, using a coastline evolution model. Results indicate that antecedent conditions are important in determining the evolution of morphologies, and that sandy coastlines can demonstrate hysteresis behaviour. In particular, antecedent morphology is particularly important in the evolution of flying spits, with characteristic timescales of morphological adjustment on the order of centuries for large spits. Characteristic timescales vary with the square of aspect ratios of capes and spits; for spits, these timescales are an order of magnitude longer than for capes (centuries vs. decades). When wave climates change more slowly than the relevant characteristic timescales, coastlines are able to adjust in a quasi-equilibrium manner. Our results have important implications for the management of sandy coastlines where decisions may be implicitly and incorrectly based on the assumption that present-day coastlines are in equilibrium with current conditions

Optix and cortex/ivory/mir-193 again: the repeated use of two mimicry hotspot loci

The extent to which evolution is repeatable has been a debated topic among evolutionary biologists. Although rewinding the tape of life perhaps would not lead to the same outcome every time, repeated evolution of analogous genes for similar functions has been extensively reported. Wing phenotypes of butterflies and moths have provided a wealth of examples of gene re-use, with certain ‘hotspot loci’ controlling wing patterns across diverse taxa. Here, we present an example of convergent evolution in the molecular genetic basis of Batesian wing mimicry in two Hypolimnas butterfly species. We show that mimicry is controlled by variation near cortex/ivory/mir-193, a known butterfly hotspot locus. By dissecting the genetic architecture of mimicry in Hypolimnas misippus and Hypolimnas bolina, we present evidence that distinct non-coding regions control the development of white pattern elements in the forewing and hindwing of the two species, suggesting independent evolution, and that no structural variation is found at the locus. Finally, we also show that orange coloration in H. bolina is associated with optix, a well-known patterning gene. Overall, our study once again implicates variation near the hotspot loci cortex/ivory/mir-193 and optix in butterfly wing mimicry and thereby highlights the repeatability of adaptive evolution

The effectiveness of beach mega-nourishment, assessed over three management epochs

Resilient coastal protection requires adaptive management strategies that build with nature to maintain long-term sustainability. With increasing pressures on shorelines from urbanisation, industrial growth, sea-level rise and changing storm climates soft approaches to coastal management are implemented to support natural habitats and maintain healthy coastal ecosystems. The impact of a beach mega-nourishment along a frontage of interactive natural and engineered systems that incorporate soft and hard defences is explored. A coastal evolution model is applied to simulate the impact of different hypothetical mega-nourishment interventions to assess their impacts’ over 3 shoreline management planning epochs: present-day (0–20 years), medium-term (20–50 years) and long-term (50–100 years). The impacts of the smaller interventions when appropriately positioned are found to be as effective as larger schemes, thus making them more cost-effective for present-day management. Over time the benefit from larger interventions becomes more noticeable, with multi-location schemes requiring a smaller initial nourishment to achieve at least the same benefit as that of a single-location scheme. While the longer-term impact of larger schemes reduces erosion across a frontage the short-term impact down drift of the scheme can lead to an increase in erosion as the natural sediment drift becomes interrupted. This research presents a transferable modelling tool to assess the impact of nourishment schemes for a variety of sedimentary shorelines and highlights both the positive and negative impact of beach mega-nourishment