Extraction of tidal channel networks from airborne scanning laser altimetry and aerial photography

The study of the morphodynamics of tidal channel networks is important because of their role in tidal propagation and the evolution of salt-marshes and tidal flats. Channel dimensions range from tens of metres wide and metres deep near the low water mark to only 20-30cm wide and 20cm deep for the smallest channels on the marshes. The conventional method of measuring the networks is cumbersome, involving manual digitising of aerial photographs. This paper describes a semi-automatic knowledge-based network extraction method that is being implemented to work using airborne scanning laser altimetry (and later aerial photography). The channels exhibit a width variation of several orders of magnitude, making an approach based on multi-scale line detection difficult. The processing therefore uses multi-scale edge detection to detect channel edges, then associates adjacent anti-parallel edges together to form channels using a distance-with-destination transform. Breaks in the networks are repaired by extending channel ends in the direction of their ends to join with nearby channels, using domain knowledge that flow paths should proceed downhill and that any network fragment should be joined to a nearby fragment so as to connect eventually to the open sea.

Deglaciation of the Caucasus Mountains, Russia/Georgia, in the 21st century observed with ASTER satellite imagery and aerial photograpy

Changes in the map area of 498 glaciers located on the Main Caucasus ridge (MCR) and on Mt. Elbrus in the Greater Caucasus Mountains (Russia and Georgia) were assessed using multispectral ASTER and panchromatic Landsat imagery with 15 m spatial resolution in 1999/2001 and 2010/2012. Changes in recession rates of glacier snouts between 1987–2001 and 2001–2010 were investigated using aerial photography and ASTER imagery for a sub-sample of 44 glaciers. In total, glacier area decreased by 4.7 ± 2.1% or 19.2 ± 8.7 km2 from 407.3 ± 5.4 km2 to 388.1 ± 5.2 km2. Glaciers located in the central and western MCR lost 13.4 ± 7.3 km2 (4.7 ± 2.5%) in total or 8.5 km2 (5.0 ± 2.4%) and 4.9 km2 (4.1 ± 2.7%) respectively. Glaciers on Mt. Elbrus, although located at higher elevations, lost 5.8 ± 1.4 km2 (4.9 ± 1.2%) of their total area. The recession rates of valley glacier termini increased between 1987–2000/01 and 2000/01–2010 (2000 for the western MCR and 2001 for the central MCR and Mt.~Elbrus) from 3.8 ± 0.8, 3.2 ± 0.9 and 8.3 ± 0.8 m yr−1 to 11.9 ± 1.1, 8.7 ± 1.1 and 14.1 ± 1.1 m yr−1 in the central and western MCR and on Mt. Elbrus respectively. The highest rate of increase in glacier termini retreat was registered on the southern slope of the central MCR where it has tripled. A positive trend in summer temperatures forced glacier recession, and strong positive temperature anomalies in 1998, 2006, and 2010 contributed to the enhanced loss of ice. An increase in accumulation season precipitation observed in the northern MCR since the mid-1980s has not compensated for the effects of summer warming while the negative precipitation anomalies, observed on the southern slope of the central MCR in the 1990s, resulted in stronger glacier wastage.

Changes in the extent of glaciers in the Eastern Terskey Alatoo, the Central Tien-Shan, in response to climatic fluctuations in between the end of the 19th and the beginning of the 21st century

Changes in the extent of glaciers and rates of glacier termini retreat in the eastern Terskey-Alatoo Range, the Tien Shan Mountains, Central Asia have been evaluated using the remote sensing techniques. Changes in the extent of 335 glaciers between the end of the Little Ice Age (LIA; mid-19th century), 1990 and 2003 have been estimated through the delineation of glacier outlines and the LIA moraine positions on the Landsat TM and ASTER imagery for 1990 and 2003 respectively. By 2003, the glacier surface area had decreased by 19% of the LIA value, which constitutes a 76 km(2) reduction in glacier surface area. Mapping of 109 glaciers using the 1965 1:25,000 maps revealed that glacier surface area decreased by 12.6% of the 1965 value between 1965 and 2003. Detailed mapping of 10 glaciers using historical maps and aerial photographs from the 1943-1977 period, has enabled glacier extent variations over the 20th century to be identified with a higher temporal resolution. Glacial retreat was slow in the early 20th century but increased considerably between 1943 and 1956 and then again after 1977. The post-1990 period has been marked by the most rapid glacier retreat since the end of the LIA. The observed changes in the extent of glaciers are in line with the observed climatic warming. The regional weather stations have revealed a strong climatic warming during the ablation season since the 1950s at a rate of 0.02-0.03 degrees Ca-1. At the higher elevations in the study area represented by the Tien Shan meteorological station, the summer warming was accompanied by negative anomalies in annual precipitation in the 1990s enhancing glacier retreat. However, trends in precipitation in the post-1997 period cannot be evaluated due to the change in observational practices at this station. Neither station in the study area exhibits significant long-term trends in precipitation. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Glacier shrinkage and climatic change in the Russian Altai from the mid-20th century: An assessment using remote sensing and PRECIS regional climate model

This paper examines changes in the surface area of glaciers in the North and South Chuya Ridges, Altai Mountains in 1952-2004 and their links with regional climatic variations. The glacier surface areas for 2004 were derived from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) imagery. Data from the World Glacier Inventory (WGI)dating to 1952 and aerial photographs from 1952 were used to estimate the changes. 256 glaciers with a combined area of 253±5.1 km2 have been identified in the region in 2004. Estimation of changes in extent of 126 glaciers with the individual areas not less than 0.5 km2 in 1952 revealed a 19.7±5.8% reduction. The observed glacier retreat is primarily driven by an increase in summer temperatures since the 1980s when air temperatures were increasing at a rate of 0.10 - 0.13oC a-1 at the glacier tongue elevation. The regional climate projections for A2 and B2 CO2 emission scenarios developed using PRECIS regional climate model indicate that summer temperatures will increase in the Altai in 2071-2100 by 6-7oC and 3-5oC respectively in comparison with 1961-1990 while annual precipitation will increase by 15% and 5%. The length of the ablation season will extend from June-August to the late April – early October. The projected increases in precipitation will not compensate for the projected warming and glaciers will continue to retreat in the 21st century under both B2 and A2 scenarios.

Ecology of sponge assemblages (Porifera) in the Wakatobi region, south-east Sulawesi, Indonesia: richness and abundance

The influence of sedimentation, depth and substratum angle on sponge assemblages in the Wakatobi region, south-eastern Sulawesi, Indonesia was considered. Sponge assemblages were sampled from two reef localities. The first reef (Sampela) was highly impacted by high sedimentation rates with fine sediment particles that settle slowly, while the second (Hoga) experienced only fast settling coarse sediment with lower overall sedimentation rates. Sponge assemblages were sampled (area occupied and numbers) on the reef fiat (0 m) and at 5 (reef crest), 10 and 15 m (15 m at Hoga only). Some significant (P < 0.001) differences were observed in the area occupied and the number of sponge patches between surface angles and sites. Significantly lower (t > 4.61, df = 9, P < 0.001) sponge numbers, percentage cover and richness were associated with the reef flat at both sites compared with all other depths at each site, with the exception of abundance of sponges on the reef flat at Sampela, which was much greater than at any other depth sampled. Species richness increased with depth at both sites but differences between surface angles were only recorded at Sampela, with higher species richness being found on vertical, inclined and horizontal surfaces respectively A total of 100 sponge species (total area sampled 52.5 m(2)) was reported from the two sites, with 58 species found at Sampela and 71 species at Hoga (41% of species shared). Multi-dimensional scaling (MDS) indicated differences in assemblage structure between sites and most depth intervals, but not substratum angles. A number of biological (e.g. competition and predation) and physical (e.g. sedimentation and aerial exposure) factors were considered to control sponge abundance and richness. Unexpectedly a significant (F-1,F-169 = 148.98, P < 0.001) positive linear relationship was found between sponge density and area occupied. In areas of high sponge coverage, the number of patches was also high, possibly due to fragmentation of large sponges produced as a result of predation and physical disturbance. The MDS results were also the same whether sponge numbers or percentage cover estimates were used, suggesting that although these different approaches yield different sorts of information, the same assemblage structure can be identified.

Autocyclic erosion in tidal marshes

A common mode whereby destruction of coastal lowlands occurs is frontal erosion. The edge cliffing, nonetheless, is also an inherent aspect of salt marsh development in many northwest European tidal marshes. Quite a few geomorphologists in the earlier half of the past century recognized such edge erosion as a definite repetitive stage within an autocyclic mode of marsh growth. A shift in research priorities during the past decades (primarily because of coastal management concerns, however) has resulted in an enhanced focus on sediment-flux measurement campaigns on salt marshes. This, somewhat "object-oriented" strategy hindered any further development of the once-established autocyclic growth concept, which virtually has gone into oblivion in recent times. This work makes an attempt to resurrect the notion of autocyclicity by employing its premises to address edge erosion in tidal marshes. Through a review of intertidal morphosedimentology the underlying framework for autocyclicity is envisaged. The phenomenon is demonstrated in the Holocene salt marsh plain of Moricambe basin in NW England that displays several distinct phases of marsh retreat in the form of abandoned clifflets. The suite of abandoned shorelines and terraces has been identified in detailed field mapping that followed analysis of topographic maps and aerial photographs. Vertical trends in marsh plain sediments are recorded in trenches for signs of past marsh front movements. The characteristic sea level history of the area offers an opportunity to differentiate the morphodynamic variability induced in the autocyclic growth of the marsh plain in scenarios of rising and falling sea level and the accompanied change in sediment budget. The ideas gathered are incorporated to construct a conceptual model that links temporal extent of marsh erosion to inner tidal flat sediment budget and sea level tendency. The review leads to recognition of the necessity of adopting an holistic approach in the morphodynamic investigations where marshes should be treated as a component within the "marsh-mudflat system" as each element apparently modulates evolution of the other, with an eventual linkage to subtidal channels. (C) 2009 Elsevier B.V. All rights reserved.

Using remotely sensed data to support flood modelling

Recent severe flooding in the UK has highlighted the need for better information on flood risk, increasing the pressure on engineers to enhance the capabilities of computer models for flood prediction. This paper evaluates the benefits to be gained from the use of remotely sensed data to support flood modelling. The remotely sensed data available can be used either to produce high-resolution digital terrain models (DTMs) (light detection and ranging (Lidar) data), or to generate accurate inundation mapping of past flood events (airborne synthetic aperture radar (SAR) data and aerial photography). The paper reports on the modelling of real flood events that occurred at two UK sites on the rivers Severn and Ouse. At these sites a combination of remotely sensed data and recorded hydrographs was available. It is concluded first that light detection and ranging Lidar generated DTMs support the generation of considerably better models and enhance the visualisation of model results and second that flood outlines obtained from airborne SAR or aerial images help develop an appreciation of the hydraulic behaviour of important model components, and facilitate model validation. The need for further research is highlighted by a number of limitations, namely: the difficulties in obtaining an adequate representation of hydraulically important features such as embankment crests and walls; uncertainties in the validation data; and difficulties in extracting flood outlines from airborne SAR images in urban areas.

TRY: a global database of plant traits

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Assessing the reliability of probabilistic flood inundation model predictions

An ability to quantify the reliability of probabilistic flood inundation predictions is a requirement not only for guiding model development but also for their successful application. Probabilistic flood inundation predictions are usually produced by choosing a method of weighting the model parameter space, but previous study suggests that this choice leads to clear differences in inundation probabilities. This study aims to address the evaluation of the reliability of these probabilistic predictions. However, a lack of an adequate number of observations of flood inundation for a catchment limits the application of conventional methods of evaluating predictive reliability. Consequently, attempts have been made to assess the reliability of probabilistic predictions using multiple observations from a single flood event. Here, a LISFLOOD-FP hydraulic model of an extreme (>1 in 1000 years) flood event in Cockermouth, UK, is constructed and calibrated using multiple performance measures from both peak flood wrack mark data and aerial photography captured post-peak. These measures are used in weighting the parameter space to produce multiple probabilistic predictions for the event. Two methods of assessing the reliability of these probabilistic predictions using limited observations are utilized; an existing method assessing the binary pattern of flooding, and a method developed in this paper to assess predictions of water surface elevation. This study finds that the water surface elevation method has both a better diagnostic and discriminatory ability, but this result is likely to be sensitive to the unknown uncertainties in the upstream boundary condition

Extraction of tidal channel networks from aerial photographs alone and combined with laser altimetry

Tidal channel networks play an important role in the intertidal zone, exerting substantial control over the hydrodynamics and sediment transport of the region and hence over the evolution of the salt marshes and tidal flats. The study of the morphodynamics of tidal channels is currently an active area of research, and a number of theories have been proposed which require for their validation measurement of channels over extensive areas. Remotely sensed data provide a suitable means for such channel mapping. The paper describes a technique that may be adapted to extract tidal channels from either aerial photographs or LiDAR data separately, or from both types of data used together in a fusion approach. Application of the technique to channel extraction from LiDAR data has been described previously. However, aerial photographs of intertidal zones are much more commonly available than LiDAR data, and most LiDAR flights now involve acquisition of multispectral images to complement the LiDAR data. In view of this, the paper investigates the use of multispectral data for semiautomatic identification of tidal channels, firstly from only aerial photographs or linescanner data, and secondly from fused linescanner and LiDAR data sets. A multi-level, knowledge-based approach is employed. The algorithm based on aerial photography can achieve a useful channel extraction, though may fail to detect some of the smaller channels, partly because the spectral response of parts of the non-channel areas may be similar to that of the channels. The algorithm for channel extraction from fused LiDAR and spectral data gives an increased accuracy, though only slightly higher than that obtained using LiDAR data alone. The results illustrate the difficulty of developing a fully automated method, and justify the semi-automatic approach adopted.

HAWAIIAN SKIRT: an F-box gene that regulates organ fusion and growth in arabidopsis

A fast neutron-mutagenized population of Arabidopsis ( Arabidopsis thaliana) Columbia-0 wild-type plants was screened for floral phenotypes and a novel mutant, termed hawaiian skirt ( hws), was identified that failed to shed its reproductive organs. The mutation is the consequence of a 28 bp deletion that introduces a premature amber termination codon into the open reading frame of a putative F-box protein ( At3g61590). The most striking anatomical characteristic of hws plants is seen in flowers where individual sepals are fused along the lower part of their margins. Crossing of the abscission marker, Pro(PGAZAT):beta-glucuronidase, into the mutant reveals that while floral organs are retained it is not the consequence of a failure of abscission zone cells to differentiate. Anatomical analysis indicates that the fusion of sepal margins precludes shedding even though abscission, albeit delayed, does occur. Spatial and temporal characterization, using Pro(HWS):beta-glucuronidase or Pro(HWS):green fluorescent protein fusions, has identified HWS expression to be restricted to the stele and lateral root cap, cotyledonary margins, tip of the stigma, pollen, abscission zones, and developing seeds. Comparative phenotypic analyses performed on the hws mutant, Columbia-0 wild type, and Pro(35S):HWS ectopically expressing lines has revealed that loss of HWS results in greater growth of both aerial and below-ground organs while overexpressing the gene brings about a converse effect. These observations are consistent with HWS playing an important role in regulating plant growth and development.

Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages

Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging.