Disentangling Niche Theory and Beta Diversity Change.

AbstractBeta diversity describes the differences in species composition among communities. Changes in beta diversity over time are thought to be due to selection based on species' niche characteristics. For example, theory predicts that selection that favors habitat specialists will increase beta diversity. In practice, ecologists struggle to predict how beta diversity changes. To remedy this problem, we propose a novel solution that formally measures selection's effects on beta diversity. Using the Price equation, we show how change in beta diversity over time can be partitioned into fundamental mechanisms including selection among species, variable selection among communities, drift, and immigration. A key finding of our approach is that a species' short-term impact on beta diversity cannot be predicted using information on its long-term environmental requirements (i.e., its niche). We illustrate how our approach can be used to partition causes of diversity change in a montane tropical forest before and after an intense hurricane. Previous work in this system highlighted the resistance of habitat specialists and the recruitment of light-demanding species but was unable to quantify the importance of these effects on beta diversity. Using our approach, we show that changes in beta diversity were consistent with ecological drift. We use these results to highlight the opportunities presented by a synthesis of beta diversity and formal models of selection.

Estimating the global distribution of field size using crowdsourcing.

There is an increasing evidence that smallholder farms contribute substantially to food production globally, yet spatially explicit data on agricultural field sizes are currently lacking. Automated field size delineation using remote sensing or the estimation of average farm size at subnational level using census data are two approaches that have been used. However, both have limitations, for example, automatic field size delineation using remote sensing has not yet been implemented at a global scale while the spatial resolution is very coarse when using census data. This paper demonstrates a unique approach to quantifying and mapping agricultural field size globally using crowdsourcing. A campaign was run in June 2017, where participants were asked to visually interpret very high resolution satellite imagery from Google Maps and Bing using the Geo-Wiki application. During the campaign, participants collected field size data for 130 K unique locations around the globe. Using this sample, we have produced the most accurate global field size map to date and estimated the percentage of different field sizes, ranging from very small to very large, in agricultural areas at global, continental, and national levels. The results show that smallholder farms occupy up to 40% of agricultural areas globally, which means that, potentially, there are many more smallholder farms in comparison with the two different current global estimates of 12% and 24%. The global field size map and the crowdsourced data set are openly available and can be used for integrated assessment modeling, comparative studies of agricultural dynamics across different contexts, for training and validation of remote sensing field size delineation, and potential contributions to the Sustainable Development Goal of Ending hunger, achieve food security and improved nutrition and promote sustainable agriculture.

Evaluating statistical model performance in water quality prediction.

Exposure to contaminated water while swimming or boating or participating in other recreational activities can cause gastrointestinal and respiratory disease. It is not uncommon for water bodies to experience rapid fluctuations in water quality, and it is therefore vital to be able to predict them accurately and in time so as to minimise population's exposure to pathogenic organisms. E. coli is commonly used as an indicator to measure water quality in freshwater, and higher counts of E. coli are associated with increased risk to illness. In this case study, we compare the performance of a wide range of statistical models in prediction of water quality via E. coli levels for the weekly data collected over the summer months from 2006 to 2014 at the recreational site on the Oreti river in Wallacetown, New Zealand. The models include naive model, multiple linear regression, dynamic regression, regression tree, Markov chain, classification tree, random forests, multinomial logistic regression, discriminant analysis and Bayesian network. The results show that Bayesian network was superior to all the other models. Overall, it had a leave-one-out and k-fold cross validation error rate of 21%, while predicting the majority of instances of E. coli levels classified as unsafe by the Microbiological Water Quality Guidelines for Marine and Freshwater Recreational Areas 2003, New Zealand. Because Bayesian networks are also flexible in handling missing data and outliers and allow for continuous updating in real time, we have found them to be a promising tool, and in the future, plan to extend the analysis beyond the current case study site.

Nesting Ecology of a Small Montane Population of the Nigerian/Cameroon Chimpanzee (Pan troglodytes ellioti) in Nigeria.

Understanding nest site choice by chimpanzees has implications for ecology, anthropology, and in the collection of census data, yet it remains controversial. Here we provide the first information on environmental factors affecting nest site choice in a montane population of the rare and relatively understudied Nigerian/Cameroon chimpanzee (Pan troglodytes ellioti) in Ngel Nyaki Forest Reserve, Nigeria. The forest is small, isolated, and visited by researchers, community members, and hunters. We also tested the hypothesis that people (researchers) walking along forest trails collecting data on a regular basis since 2005 will have changed nesting behaviour in the vicinity of the trails. Along the trails searched for nests, the chimpanzees used a subset of 35 (28.5%) of all available tree species. The top 5 nest tree species represented 16% of all non-nest tree species. The nest trees were on steeper than average slopes and the trees themselves were shorter and had a smaller DBH (diameter at breast height) than trees without nests. We found no evidence to suggest a change in nesting behaviour along trails compared with off trails; however, the average nest height today is considerably higher than it was in 2004, which may indicate a change in behaviour across the whole forest.

Mapping global cropland and field size.

A new 1 km global IIASA-IFPRI cropland percentage map for the baseline year 2005 has been developed which integrates a number of individual cropland maps at global to regional to national scales. The individual map products include existing global land cover maps such as GlobCover 2005 and MODIS v.5, regional maps such as AFRICOVER and national maps from mapping agencies and other organizations. The different products are ranked at the national level using crowdsourced data from Geo-Wiki to create a map that reflects the likelihood of cropland. Calibration with national and subnational crop statistics was then undertaken to distribute the cropland within each country and subnational unit. The new IIASA-IFPRI cropland product has been validated using very high-resolution satellite imagery via Geo-Wiki and has an overall accuracy of 82.4%. It has also been compared with the EarthStat cropland product and shows a lower root mean square error on an independent data set collected from Geo-Wiki. The first ever global field size map was produced at the same resolution as the IIASA-IFPRI cropland map based on interpolation of field size data collected via a Geo-Wiki crowdsourcing campaign. A validation exercise of the global field size map revealed satisfactory agreement with control data, particularly given the relatively modest size of the field size data set used to create the map. Both are critical inputs to global agricultural monitoring in the frame of GEOGLAM and will serve the global land modelling and integrated assessment community, in particular for improving land use models that require baseline cropland information. These products are freely available for downloading from the http://cropland.geo-wiki.org website.

Blunted hypothalamic-pituitary-adrenal axis and insulin response to psychosocial stress in young adults born preterm at very low birth weight.

BACKGROUND: Young adults born preterm at very low birth weight (VLBW, ≤1500 g) have higher levels of cardiovascular risk factors, including impaired glucose regulation, than their term-born peers. This could be mediated through altered hypothalamic-pituitary-adrenal axis (HPAA) response to stress. OBJECTIVE: To compare HPAA, glucose and insulin responses provoked by psychosocial stress in VLBW subjects versus a comparison group of term-born controls. DESIGN AND PARTICIPANTS: We studied 54 unimpaired young adults, aged 19-27 years, born at VLBW and a comparison group of 40 adults born at term, group-matched for age, sex and birth hospital, from one regional centre in southern Finland. The participants underwent a standardized psychosocial stress test (Trier Social Stress Test, TSST). MEASUREMENTS: In conjunction with TSST, we measured salivary cortisol, plasma ACTH, cortisol, glucose and insulin. Data were analysed with mixed-effects model and multiple linear regression analyses. RESULTS: Baseline concentrations for cortisol, ACTH, insulin and glucose were similar in VLBW and comparison groups. During TSST, analysed with mixed-effects model, overall concentrations of plasma cortisol were 17·2% lower (95% CI; 3·5 to 28·9) in the VLBW group. The VLBW group also had lower salivary (P = 0·04) and plasma cortisol (P = 0·02) responses to TSST. Insulin and glucose concentrations correlated with changes in cortisol concentrations. Accordingly, VLBW subjects had 26·5% lower increment in insulin (95% CI; 9·8-40·1). Analyses were adjusted for age, sex, body mass index, hormonal contraception, menstrual cycle phase, time of day and parental education. CONCLUSIONS: VLBW adults have lower HPAA responses to psychosocial stress than term-born controls. This is accompanied by a lower insulin response.

Efficacy and safety of a mineral and vitamin treatment on symptoms of antenatal depression: 12-week fully blinded randomised placebo-controlled trial (NUTRIMUM).

BACKGROUND: Broad-spectrum micronutrients (minerals and vitamins) have shown benefit for treatment of depressive symptoms. AIMS: To determine whether additional micronutrients reduce symptoms of antenatal depression. METHOD: Eighty-eight medication-free pregnant women at 12-24 weeks gestation, who scored ≥13 on the Edinburgh Postnatal Depression Scale (EPDS), were randomised 1:1 to micronutrients or active placebo (containing iodine and riboflavin), for 12 weeks. Micronutrient doses were generally between recommended dietary allowance and tolerable upper level. Primary outcomes (EPDS and Clinical Global Impression - Improvement Scale (CGI-I)) were analysed with constrained longitudinal data analysis. RESULTS: Seventeen (19%) women dropped out, with no group differences, and four (4.5%) gave birth before trial completion. Both groups improved on the EPDS, with no group differences (P = 0.1018); 77.3% taking micronutrients and 72.7% taking placebos were considered recovered. However, the micronutrient group demonstrated significantly greater improvement, based on CGI-I clinician ratings, over time (P = 0.0196). The micronutrient group had significantly greater improvement on sleep and global assessment of functioning, and were more likely to identify themselves as 'much' to 'very much' improved (68.8%) compared with placebo (38.5%) (odds ratio 3.52, P = 0.011; number needed to treat: 3). There were no significant group differences on treatment-emergent adverse events, including suicidal ideation. Homocysteine decreased significantly more in the micronutrient group. Presence of personality difficulties, history of psychiatric medication use and higher social support tended to increase micronutrient response compared with placebo. CONCLUSIONS: This study highlights the benefits of active monitoring on antenatal depression, with added efficacy for overall functioning when taking micronutrients, with no evidence of harm. Trial replication with larger samples and clinically diagnosed depression are needed.

The regional association of rising type 2 diabetes incidence with magnesium in drinking water among young adults.

The incidence of type 2 diabetes is increasing among Finnish young adults. A slightly increased risk in men was found in the north-east and western part of the country. The higher risk areas in women were found in the western coastal area and in eastern Finland. The present register-based study aimed to evaluate the regional association of the incidence of type 2 diabetes among young adults with the concentration of magnesium in local ground water. The association was evaluated using Bayesian modeling of geo-referenced data aggregated into a regular 10 km × 10 km grid cells. No marked association was found, although suggestive findings were detected for magnesium in well water and diabetes in young adult women. The results of this register-based study did not completely rule out the association of well water magnesium with the geographical variation of type 2 diabetes. The incidence of type 2 diabetes was much higher among individuals aged 40 or over. These suggestive findings indicate that the association between magnesium and type 2 diabetes would also be worth examining among individuals over 40 years of age.

Modelling the emergence dynamics of the western corn rootworm beetle (Diabrotica virgifera virgifera).

The western corn rootworm is an invasive species to Europe and is a major agricultural pest that causes widespread economic and yield losses to maize producers. The Gompertz curve was originally used to model human population mortality. It is a sigmoidal curve where the beginning and end of a period shows the slowest time for growth, and adequately describes observed dynamics of many phenomena. We propose the use of the Gompertz function in a Bayesian Hierarchical framework to model the emergence dynamics of the western corn rootworm beetle. The proposed model includes the use of climatic variables to assess how weather can influence the observed dynamics. We apply the model to Austrian monitoring data collected in 2004-2015.

How many people need to classify the same image? A method for optimizing volunteer contributions in binary geographical classifications.

Involving members of the public in image classification tasks that can be tricky to automate is increasingly recognized as a way to complete large amounts of these tasks and promote citizen involvement in science. While this labor is usually provided for free, it is still limited, making it important for researchers to use volunteer contributions as efficiently as possible. Using volunteer labor efficiently becomes complicated when individual tasks are assigned to multiple volunteers to increase confidence that the correct classification has been reached. In this paper, we develop a system to decide when enough information has been accumulated to confidently declare an image to be classified and remove it from circulation. We use a Bayesian approach to estimate the posterior distribution of the mean rating in a binary image classification task. Tasks are removed from circulation when user-defined certainty thresholds are reached. We demonstrate this process using a set of over 4.5 million unique classifications by 2783 volunteers of over 190,000 images assessed for the presence/absence of cropland. If the system outlined here had been implemented in the original data collection campaign, it would have eliminated the need for 59.4% of volunteer ratings. Had this effort been applied to new tasks, it would have allowed an estimated 2.46 times as many images to have been classified with the same amount of labor, demonstrating the power of this method to make more efficient use of limited volunteer contributions. To simplify implementation of this method by other investigators, we provide cutoff value combinations for one set of confidence levels.

Estimating global economic well-being with unlit settlements.

It is well established that nighttime radiance, measured from satellites, correlates with economic prosperity across the globe. In developing countries, areas with low levels of detected radiance generally indicate limited development - with unlit areas typically being disregarded. Here we combine satellite nighttime lights and the world settlement footprint for the year 2015 to show that 19% of the total settlement footprint of the planet had no detectable artificial radiance associated with it. The majority of unlit settlement footprints are found in Africa (39%), rising to 65% if we consider only rural settlement areas, along with numerous countries in the Middle East and Asia. Significant areas of unlit settlements are also located in some developed countries. For 49 countries spread across Africa, Asia and the Americas we are able to predict and map the wealth class obtained from ~2,400,000 geo-located households based upon the percent of unlit settlements, with an overall accuracy of 87%.

Soil cadmium mobilisation by dissolved organic matter from soil amendments.

Dissolved organic matter (DOM) release from Cd contaminated soils been linked to mobilisation of the metal as Cd-DOM complexes and this may be exacerbated by organic matter-rich soil amendments. The quantity and quality of the DOM can determine the proportion of dissolved Cd that partitions to mobile complexes and their stability and, thus, the potential for Cd transport from contaminated soils. The aim of this work was to examine differences in Cd mobilisation from soils to which different types of soil amendments/conditioners have been applied and the importance of DOM characteristics in determining the extent to which this can happen. Three soils were spiked with Cd to 2 mg kg-1, allowed to equilibrate and then treated with compost and peat. These soils and an untreated subsample of each soil were then adjusted to three different pHs: 5.6, 6.4 and 7.4, using lime. The amount of Cd mobilised from each soil was tested using a column leaching experiment. Ultrafiltration and speciation modelling were used to determine amounts of Cd as DOM-complexed, "truly" dissolved (<5 kDa) and colloidal species, while DOM quality was assessed using UV-Vis and fluorescence spectroscopy. Most colloidal Cd was mobilised from the compost treated soils (50%-60%), followed by the peat treated soils (20-44%). The relationships between colloidal Cd, DOC concentration and soil pH, together with the spectroscopic and modelling results showed that structural properties of DOM are an important factor in mobilising Cd from contaminated soils.

Urinary neopterin and total neopterin measurements allow monitoring of oxidative stress and inflammation levels of knee and hip arthroplasty patients.

Knee and hip arthroplasty are common surgeries within an aging population. Some data has suggested that knee arthroplasty is more traumatic to the body than hip arthroplasty due to the increased complexity and load bearing nature of the joint. Here, we compare the stress of the two surgeries by measuring urinary neopterin and total neopterin as biomarkers of oxidative stress and inflammation. Urinary neopterin and total neopterin (neopterin + 7,8-dihydroneopterin) levels were analysed in 28 knee and 22 hip arthroplasty patients pre- and post-operatively to determine oxidative stress and inflammation levels. Total neopterin was 31.1% higher with knee arthroplasty (p<0.05). Urinary neopterin was 32.8% higher in the knee arthroplasty group versus hips. The increase in neopterin and total neopterin following a post-surgical decrease in levels was significant in both groups. Levels of neopterin and total neopterin were varied between patients, but all increased following surgery and subsided by day 28. The increased levels of urinary neopterin and total neopterin from knee arthroplasty indicate that knee osteoarthritis and arthroplasty is a more significant trauma to the body than hip osteoarthritis and arthroplasty surgery. This is also shown by faster inflammatory resolution following hip arthroplasty.

Russian forest sequesters substantially more carbon than previously reported.

Since the collapse of the Soviet Union and transition to a new forest inventory system, Russia has reported almost no change in growing stock (+ 1.8%) and biomass (+ 0.6%). Yet remote sensing products indicate increased vegetation productivity, tree cover and above-ground biomass. Here, we challenge these statistics with a combination of recent National Forest Inventory and remote sensing data to provide an alternative estimate of the growing stock of Russian forests and to assess the relative changes in post-Soviet Russia. Our estimate for the year 2014 is 111 ± 1.3 × 109 m3, or 39% higher than the value in the State Forest Register. Using the last Soviet Union report as a reference, Russian forests have accumulated 1163 × 106 m3 yr-1 of growing stock between 1988-2014, which balances the net forest stock losses in tropical countries. Our estimate of the growing stock of managed forests is 94.2 × 109 m3, which corresponds to sequestration of 354 Tg C yr-1 in live biomass over 1988-2014, or 47% higher than reported in the National Greenhouse Gases Inventory.

Expressing uncertainty in Human-Robot interaction.

Most people struggle to understand probability which is an issue for Human-Robot Interaction (HRI) researchers who need to communicate risks and uncertainties to the participants in their studies, the media and policy makers. Previous work showed that even the use of numerical values to express probabilities does not guarantee an accurate understanding by laypeople. We therefore investigate if words can be used to communicate probability, such as "likely" and "almost certainly not". We embedded these phrases in the context of the usage of autonomous vehicles. The results show that the association of phrases to percentages is not random and there is a preferred order of phrases. The association is, however, not as consistent as hoped for. Hence, it would be advisable to complement the use of words with numerical expression of uncertainty. This study provides an empirically verified list of probabilities phrases that HRI researchers can use to complement the numerical values.

Perinatal risk factors in young adult-onset type 1 and type 2 diabetes - a population-based case-control study.

OBJECTIVE: To examine the effects of the size of the mother and the newborn, including placental weight and gestational age at delivery, on the risk for young adult-onset type 1 diabetes (T1DM) and type 2 diabetes (T2DM). DESIGN: Case-control study. SETTING: Finland. POPULATION: Subjects with T1DM and T2DM aged 15-39 at diagnosis between the years 1992 and 1996. The number of case-control pairs was 858 for T1DM and 355 for T2DM. METHODS: Diabetic subjects were identified from the Finnish national healthcare registers and reports from diabetes nurses. Control subjects were obtained from the population register. Data on perinatal factors were obtained from the original healthcare records. The odds ratios (ORs) for both types of diabetes were estimated using conditional logistic regression. RESULTS: The risk for early-onset T2DM decreased with increasing birthweight until 4.2 kg (OR 0.49 (95% confidence interval 0.37-0.66) per 1 kg), but with birthweight above 4.2 kg the risk increased (OR 4.8 (1.3-17.6) per 1 kg). The risk for T2DM decreased also with increasing birth length (OR 0.88 (0.81-0.95) per 1 cm), body mass index at birth (OR 0.81 (0.73-0.90) per 1 kg/m2), and placental weight (OR 0.77 (0.61-0.98) per 100 g). The latter was not significant when adjusted for birthweight. The examined perinatal factors did not affect the risk for T1DM in young adults. CONCLUSIONS: Birth size significantly affects the risk for T2DM diagnosed in young adulthood but no evidence was found of an association between late-onset T1DM and perinatal factors.

Spatio-temporal analysis of differences in campylobacteriosis incidence between urban and rural areas in the Southern District Health Board, New Zealand.

The objective of this paper is to investigate differences in campylobacteriosis incidence between urban and rural areas in the Southern District Health Board of New Zealand between 2000 and 2015. The data were analysed using a Bayesian change-point model to evaluate how campylobacteriosis incidence changed over time and to see whether the dynamics differed between rural and urban areas. A conditional auto regressive error term was introduced to account for any spatial effects. The results of our analysis showed that campylobacteriosis incidence increased between 2000 and 2005, decreased between 2006 and 2008 then stabilised from 2009 onward. In addition we found that the changes in incidence were greater in urban areas than in rural ones.

Long seed dispersal distances by an inquisitive flightless rail (Gallirallus australis) are reduced by interaction with humans.

Human presence is becoming increasingly ubiquitous, but the influence this has on the seed dispersal services performed by frugivorous animals is largely unknown. The New Zealand weka (Gallirallus australis) is an inquisitive flightless rail that frequently congregates in areas of high human use. Weka are important seed dispersers, yet the seed dispersal services they provide are still poorly understood. We estimated seed dispersal distances of weka for two plant species (Prumnopitys ferruginea and Elaeocarpus dentatus) and tested how human interaction affected these dispersal distances. We estimated weka seed dispersal distances by combining GPS data from 39 weka over three sites with weka seed retention time data in a mechanistic model. The mean seed retention times were extremely long (38-125 h). Weka were highly effective dispersers, dispersing 93-96% of seeds away from parent canopies, and 1% of seeds over 1 km. However, we found evidence of a significant human impact on the seed dispersal distances of weka, with birds occupying areas of high human use performing 34.8-40.9% shorter distances than their more remote counterparts. This represents an example of cryptic function loss, where although weka are still present in the ecosystem, their seed dispersal services are impaired by human interaction.

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI.

Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved are not fully understood. Here, we combine genome-wide association studies with modeling of longitudinal growth traits to study the genetics of infant and child growth, followed by functional, pathway, genetic correlation, risk score, and colocalization analyses to determine how developmental timings, molecular pathways, and genetic determinants of these traits overlap with those of adult health. We found a robust overlap between the genetics of child and adult body mass index (BMI), with variants associated with adult BMI acting as early as 4 to 6 years old. However, we demonstrated a completely distinct genetic makeup for peak BMI during infancy, influenced by variation at the LEPR/LEPROT locus. These findings suggest that different genetic factors control infant and child BMI. In light of the obesity epidemic, these findings are important to inform the timing and targets of prevention strategies.

Geographical variation of medicated parkinsonism in Finland during 1995 to 2000.

We performed a nation-wide study on geographical variation in the incidence and prevalence of medicated parkinsonism among the Finns aged > or =30 years using Bayesian spatial conditional autoregressive models. Registry of reimbursed medication for parkinsonism and a prescription database of purchase of these drugs were used to identify the study subjects. They were located by the map coordinates of the place of residence and aggregated into regular 100 km(2) grid cells. A total of 7,190 incident and 10,616 prevalent cases were found. The age-adjusted annual incidence was 32.6/100,000 (95% HDR 31.8-33.4) during the years 1995 to 2000 and prevalence was 268/100,000 (95% HDR 263-274) in 2000. The male to female ratio was 1.45 (95% HDR 1.39-1.51) in incidence and 1.54 (95% HDR 1.47-1.61) in prevalence. There was strong evidence for geographic variation in incidence and prevalence. A zone with high incidence and prevalence was identified in the eastern and central part of Finland. There was no evidence for difference in incidence and prevalence between urban and rural areas. The marked (more than two-fold) geographic variation can hardly be caused solely by practices of the registration and collection of data on diagnosis or by methodological issues, but rather suggests to geographic variation in protective and predisposing factors of Parkinsonism in Finland.