Change is good: adapting strategies for archaeological prospection in a rapidly changing technological world

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Preparing for the future: A reappraisal of archaeo-geophysical surveying on Irish National Road Schemes 2001-2010

yesThis document reviews Legacy Data generated from 10 years’ worth of road scheme activity in Ireland to determine how archaeological geophysical surveys could be carried out on national roads in the future. The geophysical surveys were carried out by several different contractors across a range of challenging field conditions, geologies, weather and seasons. The research is based upon the results of linear schemes but also has validity for wider approaches. The findings of this research are based upon the compilation of all terrestrial archaeological geophysical surveys carried out on behalf of the National Roads Authority (NRA), a review of the success or otherwise of those surveys in comparison with ground-observed excavations and in combination with experimental surveys that tested previously held assumptions or knowledge to determine best practice methods for the future. The use and success of geophysical surveys in Ireland differ quite significantly from those in the UK, from where many of the methods of assessment were derived or adapted. Many of these differences can be attributed to geology. Ireland has a very high percentage of Carboniferous limestone geology, overlain mostly by tills and frequent occurrences of peat. These soils can reduce, to some extent, the effectiveness of magnetometer surveys; the most frequently used geophysical technique in Ireland. However, magnetometer data can be maximised in these cases by increasing the spatial resolution to produce effective results. An increase in spatial resolution is also effective generally, for enhancing the chances of identifying archaeological features by discriminating between archaeological and geological anomalies as well as increasing anomaly definition and visualisation of small and subtle archaeological features. Seasonal tests have determined that Irish soils are generally suitable for year round earth resistance assessments although some counties in the southeast of the country may experience very dry soils at the surface during some periods of the year. A variety of sampling strategies were used in the past, however it is now apparent that detailed assessments across the full length and width of a proposed road corridor are the most appropriate form of geophysical investigation. Magnetometer surveys are generally suitable for most Irish soils and geologies, although exceptions apply in areas of near-surface igneous deposits, deep peat and alluvial soils; however magnetometer surveys are not capable of identifying all types of archaeological features and other methods will be required for a full evaluation. Analysis of the Legacy Data has determined that in general the NRA archaeological geophysical surveys were historically used in a very positive way on road schemes. The range of features assessed or identified account for most types of archaeological sites in Ireland. These have provided a significant archive of case studies that will be of benefit to future archaeological geophysical research and will help to protect the globally dwindling archaeological resource that is threatened by development-led or commercially driven projects

A reappraisal of archaeological geophysical surveys on Irish road corridors 2001-2010. With particular reference to the influence of geological, seasonal and archaeological variables

Geophysical surveys in the Republic of Ireland and elsewhere rarely have the opportunity to receive direct, meaningful and quantitative feedback from ground observed excavations, despite their frequent occurrence as a subsequent phase of development-led archaeological projects. This research critically reappraises the largest and most coherent geophysical archive maintained by a single end-user over a ten year period. The geophysical archive has been collated from 170 reports on linear road schemes as a result of commercially-driven assessments in Ireland, to facilitate the biggest analysis of geophysical survey legacy data and subsequent detailed excavations. The analysis of the legacy data archive has reviewed and tested the influence of key variables that have, in some circumstances, affected the methods and outcomes of geophysical assessments in Ireland over the last 10 years. By understanding the impact of those key variables upon the legacy data - which include archaeological feature type, geology, sampling strategy and seasonality - appropriate and new ways to research linear corridors have been suggested that should be employed in future geophysical survey assessments for a range of environments and archaeological site types. The comprehensive analysis of geophysical surveys from the legacy data archive has created definitive statements regarding the validity of geophysical techniques in Ireland. Key failures that occurred in the past have been identified and a thorough investigation of new and novel techniques or methods of survey will facilitate a more robust approach to geophysical survey strategies in the future. The outcomes of this research are likely to have ramifications beyond the Irish road corridors from which the legacy data derives.National Roads Authority (NRA

Predators reduce extinction risk in noisy metapopulations

Background Spatial structure across fragmented landscapes can enhance regional population persistence by promoting local “rescue effects.” In small, vulnerable populations, where chance or random events between individuals may have disproportionately large effects on species interactions, such local processes are particularly important. However, existing theory often only describes the dynamics of metapopulations at regional scales, neglecting the role of multispecies population dynamics within habitat patches. Findings By coupling analysis across spatial scales we quantified the interaction between local scale population regulation, regional dispersal and noise processes in the dynamics of experimental host-parasitoid metapopulations. We find that increasing community complexity increases negative correlation between local population dynamics. A potential mechanism underpinning this finding was explored using a simple population dynamic model. Conclusions Our results suggest a paradox: parasitism, whilst clearly damaging to hosts at the individual level, reduces extinction risk at the population level

Computer Game Play Reduces Intrusive Memories of Experimental Trauma via Reconsolidation-Update Mechanisms.

Memory of a traumatic event becomes consolidated within hours. Intrusive memories can then flash back repeatedly into the mind's eye and cause distress. We investigated whether reconsolidation-the process during which memories become malleable when recalled-can be blocked using a cognitive task and whether such an approach can reduce these unbidden intrusions. We predicted that reconsolidation of a reactivated visual memory of experimental trauma could be disrupted by engaging in a visuospatial task that would compete for visual working memory resources. We showed that intrusive memories were virtually abolished by playing the computer game Tetris following a memory-reactivation task 24 hr after initial exposure to experimental trauma. Furthermore, both memory reactivation and playing Tetris were required to reduce subsequent intrusions (Experiment 2), consistent with reconsolidation-update mechanisms. A simple, noninvasive cognitive-task procedure administered after emotional memory has already consolidated (i.e., > 24 hours after exposure to experimental trauma) may prevent the recurrence of intrusive memories of those emotional events

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψm) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz+ rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz+ rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz+ communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of Bacteroidetes and Proteobacteria, including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψm) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome

Compound specific radiocarbon dating of essential and non-essential Amino acids:towards determination of dietary reservoir effects in humans

When humans consume foods from different radiocarbon reservoirs offset in age to the atmosphere, inaccuracies in the 14C date of bone collagen can occur. Mesolithic human skeletons from the Iron Gates section of the Lower Danube Valley have yielded reservoir offsets of up to ~500 yr. This has been demonstrated through direct dating of bulk collagen from human bones and the remains of ungulate bone projectile points that were found embedded in them (Cook et al. 2001). We present improvements to a novel HPLC method for the detection and separation of underivatized amino acids using a wateronly mobile phase free of organic or inorganic modifiers, ensuring very low carbon backgrounds. Our hypothesis is that direct 14C dating of single essential and non-essential amino acids might allow an improvement in the dating accuracy for reservoiraffected human bones. The method facilitates separation of less polar amino acids (mostly "essential"), currently not possible in the recently published protocol. We discuss methodological developments, demonstrate carbon backgrounds, and present analytical approaches to minimize their effects. We validate the precision and accuracy of the method by accelerator mass spectrometry (AMS) dating relatively modern and 14C-dead, known-age bone standards. Finally, we apply the method to the dating of single amino acids from bone samples with a proven ~500-yr carbon reservoir effect from Mesolithic burials at the Iron Gates sites. We investigate whether differences can be found in AMS dates for essential and non-essential amino acids since, although contemporaneous, these are expected to derive from dietary sources with differing 14C reservoirs. © 2013 by the Arizona Board of Regents on behalf of the University of Arizona

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

Motivation: Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script. Results: In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in