Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology

Given the diversity and ecological importance of Fungi, there is a lack of population genetic research on these organisms. The reason for this can be explained in part by their cryptic nature and difficulty in identifying genets. In addition the difficulty (relative to plants and animals) in developing molecular markers for fungal population genetics contributes to the lack of research in this area. This study examines the ability of restriction-site associated DNA (RAD) sequencing to generate SNPs in Laccaria bicolor. Eighteen samples of morphologically identified L. bicolor from the United States and Europe were selected for this project. The RAD sequencing method produced anywhere from 290 000 to more than 3 000 000 reads. Mapping these reads to the genome of L. bicolor resulted in 84 000-940 000 unique reads from individual samples. Results indicate that incorporation of non-L. bicolor taxa into the analysis resulted in a precipitous drop in shared loci among samples, suggests the potential of these methods to identify cryptic species. F-statistics were easily calculated, although an observable "noise" was detected when using the "All Loci" treatment versus filtering loci to those present in at least 50% of the individuals. The data were analyzed with tests of Hardy-Weinburg equilibrium, population genetic statistics (FIS and FST), and population structure analysis using the program Structure. The results provide encouraging feedback regarding the potential utility of these methods and their data for population genetic analysis. We were unable to draw conclusions of life history of L. bicolor populations from this dataset, given the small sample size. The results of this study indicate the potential of these methods to address population genetics and general life history questions in the Agaricales. Further research is necessary to explore the specific application of these methods in the Agaricales or other fungal groups

Marble use and reuse at Pompeii and Herculaneum:the evidence from the bars

The marble-clad surfaces of the numerous bars or shops (so-calledthermopolia) of Pompeii and Herculaneum are a vast and hitherto untapped source of information about marble use beyond the confines of public building and élite houses. Four field seasons of survey work have documented 49 bars at Pompeii and eight at Herculaneum with over 8,000 pieces of stone, mainly marble. This paper discusses the results of this project: first, the types of stone used on these bars and how they were displayed; second, what their quantities and distribution, within these cities and on individual bars, reveal about the pervasiveness of the wider pan-Mediterranean marble trade; third, what we can say about where these materials came from and how they were acquired, and what this in turn reveals about the economics of reuse of architectural materials in the Vesuvian cities.</jats:p

Concordant cues in faces and voices: testing the backup signal hypothesis

Information from faces and voices combines to provide multimodal signals about a person. Faces and voices may offer redundant, overlapping (backup signals), or complementary information (multiple messages). This article reports two experiments which investigated the extent to which faces and voices deliver concordant information about dimensions of fitness and quality. In Experiment 1, participants rated faces and voices on scales for masculinity/femininity, age, health, height, and weight. The results showed that people make similar judgments from faces and voices, with particularly strong correlations for masculinity/femininity, health, and height. If, as these results suggest, faces and voices constitute backup signals for various dimensions, it is hypothetically possible that people would be able to accurately match novel faces and voices for identity. However, previous investigations into novel face–voice matching offer contradictory results. In Experiment 2, participants saw a face and heard a voice and were required to decide whether the face and voice belonged to the same person. Matching accuracy was significantly above chance level, suggesting that judgments made independently from faces and voices are sufficiently similar that people can match the two. Both sets of results were analyzed using multilevel modeling and are interpreted as being consistent with the backup signal hypothesis

Is Current Irrigation Sustainable in the United States? An Integrated Assessment of Climate Change Impact on Water Resources and Irrigated Crop Yields

While the impact of climate change on crop yields has been extensively studied, the quantification of water shortages on irrigated crop yields has been regarded as more challenging due to the complexity of the water resources management system. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling (IGSM) framework, an integrated assessment model that links a model of the global economy to an Earth system model. While accounting for uncertainty in climate change, we assess the effects of climate and socio-economic changes on the competition for water resources between industrial, energy, domestic and irrigation; the implications for water availability for irrigation; and the subsequent impacts on crop yields in the US by 2050. We find that climate and socio-economic changes will increase water shortages and strongly reduce irrigated crop yields in specific regions (mostly in the Southwest), or for specific crops (i.e. cotton and forage). While the most affected regions are usually not major crop growers, the heterogeneous response of crop yield to global change and water stress suggests that some level of adaptation can be expected, such as the relocation of cropland area to regions where irrigation is more sustainable. Finally, GHG mitigation has the potential to alleviate the effect of water stress on irrigated crop yields—enough to offset the reduced CO2 fertilization effect compared to an unconstrained GHG emission scenario.This work was partially funded by the U.S. Environmental Protection Agency’s Climate Change Division, under Cooperative Agreement No. XA-83600001 and by the U.S. Department of Energy, Office of Biological and Environmental Research, under grant DE-FG02-94ER61937. The Joint Program on the Science and Policy of Global Change is funded by a number of federal agencies and a consortium of 40 industrial and foundation sponsors. (For the complete list see http://globalchange.mit.edu/sponsors/current.html)

A Framework for Analysis of the Uncertainty of Socioeconomic Growth and Climate Change on the Risk of Water Stress: a Case Study in Asia

The sustainability of future water resources is of paramount importance and is affected by many factors, including population, wealth and climate. Inherent in how these factors change in the future is the uncertainty of their prediction. In this study, we integrate a large ensemble of scenarios—internally consistent across economics, emissions, climate, and population—to develop a risk portfolio of water stress over a large portion of Asia that includes China, India, and Mainland Southeast Asia. We isolate the effects of socioeconomic growth from the effects of climate change in order to identify the primary drivers of stress on water resources. We find that water needs related to socioeconomic changes, which are currently small, are likely to increase considerably in the future, often overshadowing the effect of climate change on levels of water stress. As a result, there is a high risk of severe water stress in densely populated watersheds by 2050, compared to recent history. If socio-economic growth is unconstrained by global actions to limit greenhouse gas concentrations, water-stressed populations may increase from about 800 million to 1.7 billion in this region.The Joint Program on the Science and Policy of Global Change is funded by a consortium of industrial and foundation sponsors. For the complete list see http://globalchange.mit.edu/sponsors/all

Testing the assumptions of linear prediction analysis in normal vowels

This paper develops an improved surrogate data test to show experimental evidence, for all the simple vowels of US English, for both male and female speakers, that Gaussian linear prediction analysis, a ubiquitous technique in current speech technologies, cannot be used to extract all the dynamical structure of real speech time series. The test provides robust evidence undermining the validity of these linear techniques, supporting the assumptions of either dynamical nonlinearity and/or non-Gaussianity common to more recent, complex, efforts at dynamical modelling speech time series. However, an additional finding is that the classical assumptions cannot be ruled out entirely, and plausible evidence is given to explain the success of the linear Gaussian theory as a weak approximation to the true, nonlinear/non-Gaussian dynamics. This supports the use of appropriate hybrid linear/nonlinear/non-Gaussian modelling. With a calibrated calculation of statistic and particular choice of experimental protocol, some of the known systematic problems of the method of surrogate data testing are circumvented to obtain results to support the conclusions to a high level of significance

Statistical properties of linear prediction analysis underlying the challenge of formant bandwidth estimation

Formant bandwidth estimation is often observed to be more challenging than the estimation of formant center frequencies due to the presence of multiple glottal pulses within a period and short closed-phase durations. This study explores inherently different statistical properties between linear prediction (LP)–based estimates of formant frequencies and their corresponding bandwidths that may be explained in part by the statistical bounds on the variances of estimated LP coefficients. A theoretical analysis of the Cramér-Rao bounds on LP estimator variance indicates that the accuracy of bandwidth estimation is approximately twice as low as that of center frequency estimation. Monte Carlo simulations of all-pole vowels with stochastic and mixed-source excitation demonstrate that the distributions of estimated LP coefficients exhibit expectedly different variances for each coefficient. Transforming the LP coefficients to formant parameters results in variances of bandwidth estimates being typically larger than the variances of respective center frequency estimates, depending on vowel type and fundamental frequency. These results provide additional evidence underlying the challenge of formant bandwidth estimation due to inherent statistical properties of LP-based speech analysi

High gradient experiments on NLCTA accelerator structures

This paper presents new results of high-gradient studies performed on a 1.8 m traveling-wave accelerator section with detuned high-order deflecting modes. This structure was designed initially for studies of detuned structures and will be installed in the Next Linear Collider Test Accelerator (NLCTA). The paper describes the test set-up in the Accelerator Structure Test Area (ASTA) including electron gun, prebuncher, pre-accelerator, spectrometer, Faraday cups, 200 MW SLED-II power compression system, Magic-T type phase shifters and attenuators. Rf processing, detailed dark current analysis, radiation problems, and beam acceleration measurements are discussed

Scenarios of Global Change: Integrated Assessment of Climate Impacts

Using the MIT Integrated Global System Modeling (IGSM) framework, we assess the climate impacts of emission scenarios exhibiting global mean surface temperatures ranging between 2.4°C and 4.3°C above pre-industrial by 2100. We compare the outcomes from these forward-looking scenarios against the common goal described by the target-driven scenario of 2°C. Without further policy measures, the agreement at COP-21 in Paris is projected to result in a 3.5°C increase in global temperature in 2100 relative to pre-industrial levels. Scenarios developed by Shell International (called Mountains and Oceans) exhibit a substantial movement towards temperature stabilization, as they result in increases of only 2.4–2.7°C by 2100. Valuable components of these scenarios include a substantial shift to renewable energy and deployment of carbon capture and storage (CCS). These scenarios are successful in mitigating a large portion of water stress impacts and air pollution damages. They also significantly mitigate increases in ocean acidity. These projections show the significant value of policies that do not quite reach 2°C stabilization, but fall substantially close to that target by the end of the century. The challenge of meeting the Paris Agreement’s aspiration to limit warming to 1.5°C is monumental, yet may be desirable if societies see the 2°C impacts, described here, as running too much risk.The MIT Joint Program on the Science and Policy of Global Change is supported by the U.S. Department of Energy, Office of Science under grants DEFG02-94ER61937, DE-FG02-08ER64597, DE-FG02-93ER61677, DE-SC0003906, DE-SC0007114, XEU-0-9920-01; the U.S. Department of Energy, Oak Ridge National Laboratory under Subcontract 4000109855; the U.S. Environmental Protection Agency under grants XA-83240101, PIv83412601-0, RD-83427901-0, XA-83505101-0, XA-83600001-1, and subcontract UTA12-000624; the U.S. National Science Foundation under grants AGS-0944121, EFRI-0835414, IIS-1028163, ECCSv1128147, ARC- 1203526, EF-1137306, AGS-1216707, and SES-0825915; the U.S. National Aeronautics and Space Administration under grants NNX06AC30A, NNX07AI49G, NNX11AN72G and Sub Agreement No. 08-SFWS-209365.MIT; the U.S. Federal Aviation Administration under grants 06-C-NE-MIT, 09-C-NEMIT, Agmt. No. 4103-30368; the U.S. Department of Transportation under grant DTRT57-10-C-10015; the Electric Power Research Institute under grant EP-P32616/C15124, EP-P8154/C4106; the U.S. Department of Agriculture under grant 58-6000-2-0099, 58-0111-9-001; and a consortium of industrial and foundation sponsors (for the complete list see: globalchange.mit.edu/sponsors/all). Shell participated actively in this study, supplying all the background data behind their scenarios. MIT remain responsible for 32 all analysis and conclusions. Shell provided a gift of USD 250,000 to the MIT Joint Program, to defray costs related to this research. Martin Haigh represents the Scenarios Team at Shell International Ltd. The paper also benefited from comments from David Hone