The relative importance of nitrogen deposition and climate change in driving plant diversity decline in roadside grasslands.

Nitrogen deposition and climate change have been identified as major threats to the biodiversity of semi-natural grasslands. Their relative contribution to recent biodiversity loss is however not fully understood, and may depend on local site conditions such as soil type, which hampers efforts to prevent further decline. We used data from >900 permanent plots in semi-natural grasslands in Dutch roadsides to investigate whether trends in plant diversity and community composition (2004-2020) could be explained by: (1) nitrogen deposition (NH and NO) and climate change (winter degree days and summer drought), (2) the interactive effect of nitrogen deposition and climate change, and (3) the interactive effect of nitrogen deposition and climate change with soil type.

From data to a validated score-based LR system: A practitioner's guide.

Likelihood ratios (LRs) are a useful measure of evidential strength. In forensic casework consisting of a flow of cases with essentially the same question and the same analysis method, it is feasible to construct an 'LR system', that is, an automated procedure that has the observations as input and an LR as output. This paper is aimed at practitioners interested in building their own LR systems.

Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts.

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring.

Automated interpretation of comparison scores for firearm toolmarks on cartridge case primers.

An automated approach for evaluating the strength of the evidence of firearm toolmark comparison results is presented for a common source scenario. First, comparison scores are derived describing the similarity of marks typically encountered on the primer of fired cartridge cases: aperture shear striations as well as breechface and firing pin impressions. Subsequently, these scores are interpreted using reference distributions of comparison scores obtained for representative known matching (KM) and known non-matching (KNM) ballistic samples in a common source, score-based likelihood ratio (LR) system.

DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures.

Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory.

Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana.

The phenotypes of plants can be influenced by the environmental conditions experienced by their parents. However, there is still much uncertainty about how common and how predictable such parental environmental effects really are. We carried out a comprehensive experimental test for parental effects, subjecting plants of multiple Arabidopsis thaliana genotypes to 24 different biotic or abiotic stresses, or combinations thereof, and comparing their offspring phenotypes in a common environment.

Healthcare utilization and maternal and child mortality during the COVID-19 pandemic in 18 low- and middle-income countries: An interrupted time-series analysis with mathematical modeling of administrative data.

Background: The Coronavirus Disease 2019 (COVID-19) pandemic has had wide-reaching direct and indirect impacts on population health. In low- and middle-income countries, these impacts can halt progress toward reducing maternal and child mortality. This study estimates changes in health services utilization during the pandemic and the associated consequences for maternal, neonatal, and child mortality.

A strawman with machine learning for a brain: A response to Biedermann (2022) the strange persistence of (source) "identification" claims in forensic literature.

We agree wholeheartedly with Biedermann (2022) FSI Synergy article 100222 in its criticism of research publications that treat forensic inference in source attribution as an "identification" or "individualization" task. We disagree, however, with its criticism of the use of machine learning for forensic inference. The argument it makes is a strawman argument.

epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.

Several reduced-representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost- and time-efficient and the computational workflow is designed in a user-friendly and reproducible manner.

From facial images of different quality to score based LR.

A simple method is proposed to assess the quality of a trace facial image in the context of the facial recognition system used using the similarity scores with low quality different-source facial images, defined as the Confusion Score (CS). Methods are proposed to calculate the probability of finding the correct facial image in a database using low quality images for investigational purposes using the CS, as well as calculation of the Likelihood Ratio (LR) for comparison of low quality trace facial images with good quality reference facial images, based on the assessed CS of the trace image. Improvement of performance of an LR-system using training datasets stratified on CS over the use of pooled data is demonstrated.

Directional turnover towards larger-ranged plants over time and across habitats.

Species turnover is ubiquitous. However, it remains unknown whether certain types of species are consistently gained or lost across different habitats. Here, we analysed the trajectories of 1827 plant species over time intervals of up to 78 years at 141 sites across mountain summits, forests, and lowland grasslands in Europe.

Disruptions in maternal and child health service utilization during COVID-19: analysis from eight sub-Saharan African countries.

The coronavirus-19 pandemic and its secondary effects threaten the continuity of essential health services delivery, which may lead to worsened population health and a protracted public health crisis. We quantify such disruptions, focusing on maternal and child health, in eight sub-Saharan countries. Service volumes are extracted from administrative systems for 63 954 facilities in eight countries: Cameroon, Democratic Republic of Congo, Liberia, Malawi, Mali, Nigeria, Sierra Leone and Somalia.

Measuring calibration of likelihood-ratio systems: A comparison of four metrics, including a new metric devPAV.

Numerical likelihood-ratio (LR) systems aim to calculate evidential strength for forensic evidence evaluation. Calibration of such LR-systems is essential: one does not want to over- or understate the strength of the evidence. Metrics that measure calibration differ in sensitivity to errors in calibration of such systems.

Artificial intelligence and thermodynamics help solving arson cases.

In arson cases, evidence such as DNA or fingerprints is often destroyed. One of the most important evidence modalities left is relating fire accelerants to a suspect. When gasoline is used as accelerant, the aim is to find a strong indication that a gasoline sample from a fire scene is related to a sample of a suspect.

A method for forensic gasoline comparison in fire debris samples: A numerical likelihood ratio system.

In many arson cases gasoline is used as a means to start the fire. In this paper results are presented for a likelihood-ratio (LR) system aimed at comparing gasoline traces from fire debris to a reference gasoline. The LR-system is able to deal with disturbing effects caused by burning and exposure to surroundings: pyrolysis products, preferential adsorption and evaporation.

Why calibrating LR-systems is best practice. A reaction to "The evaluation of evidence for microspectrophotometry data using functional data analysis", in FSI 305.

In their paper "The evaluation of evidence for microspectrophotometry data using functional data analysis", in FSI 305, Aitken et al. present a likelihood-ratio (LR) system for their data. We show the values generated by this system cannot be interpreted as LRs: they are ill-calibrated and should be interpreted as discriminating scores.

Epigenetic Approaches in Non-Model Plants.

Reduced representation bisulfite sequencing is an emerging methodology for evolutionary and ecological genomics and epigenomics research because it provides a cost-effective, high-resolution tool for exploration and comparative analysis of DNA methylation and genetic variation. Here we describe how digestion of genomic plant DNA with restriction enzymes, subsequent bisulfite conversion of unmethylated cytosines, and final DNA sequencing allow for the examination of genome-wide genetic and epigenetic variation in plants without the need for a reference genome. We explain how the use of several combinations of barcoded adapters for the creation of highly multiplexed libraries allows the inclusion of up to 144 different samples/individuals in only one sequencing lane.

Combining evidence in complex cases - a practical approach to interdisciplinary casework.

Activity level evaluations, although still a major challenge for many disciplines, bring a wealth of possibilities for a more formal approach to the evaluation of interdisciplinary forensic evidence. This paper proposes a practical methodology for combining evidence from different disciplines within the likelihood ratio framework. Evidence schemes introduced in this paper make the process of combining evidence more insightful and intuitive thereby assisting experts in their interdisciplinairy evaluation and in explaining this process to the courts.

Evidence for rapid evolution in a grassland biodiversity experiment.

In long-term grassland experiments, positive biodiversity effects on plant productivity commonly increase with time. Subsequent glasshouse experiments showed that these strengthened positive biodiversity effects persist not only in the local environment but also when plants are transferred into a common environment. Thus, we hypothesized that community diversity had acted as a selective agent, resulting in the emergence of plant monoculture and mixture types with differing genetic composition.

A practical tool for assessing ecosystem services enhancement and degradation associated with invasive alien species.

Current approaches for assessing the effects of invasive alien species (IAS) are biased toward the negative effects of these species, resulting in an incomplete picture of their real effects. This can result in an inefficient IAS management. We address this issue by describing the INvasive Species Effects Assessment Tool (INSEAT) that enables expert elicitation for rapidly assessing the ecological consequences of IAS using the ecosystem services (ES) framework.

Decision support for using mobile Rapid DNA analysis at the crime scene.

Mobile Rapid DNA technology is close to being incorporated into crime scene investigations, with the potential to identify a perpetrator within hours. However, the use of these techniques entails the risk of losing the sample and potential evidence, because the device not only consumes the inserted sample, it is also is less sensitive than traditional technologies used in forensic laboratories. Scene of Crime Officers (SoCOs) therefore will face a 'time/success rate trade-off' issue when making a decision to apply this technology.

Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea.

Background: Temperature is one of the most important abiotic factors limiting plant growth and productivity. Many plants exhibit cold acclimation to prepare for the likelihood of freezing as temperatures decrease towards 0 °C. The physiological mechanisms associated with enabling increased tolerance to sub-zero temperatures vary between species and genotypes.

Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection.

Background: Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data.