A neglected aspect of human-elephant conflict: fence damage by elephants in the Trans Mara, Kenya

Human–elephant conflict (HEC) is one of the most complex issues for elephant conservation today and is on the increase. Incidents involving elephants can have severe consequences for people who co-exist with them, creating negative attitudes. While there has been a great deal of research on crop raiding, other forms of conflict including fence damage are poorly documented, but could still give rise to significant costs for households. In this study, we investigated the frequency, severity and patterns of fence damage caused by elephants in communities of the Trans Mara District, Kenya in 2014–2015 and compared these to patterns of crop raiding. In total there were 792 incidents involving fence damage only, 517 incidents involving crop and fence damage, and 72 incidents involving only crop damage. While the majority of fence damage incidents occurred between 18:00 and 06:00, some damage continued until 09:00. Fence damage occurred in every month of the study period and peaked when the frequency of crop damage decreased, highlighting the year-round nature of HEC in this region. The persistent occurrence of HEC in the Trans Mara, on both a daily and an annual timescale, becomes much more apparent when incidents of fence damage are considered as well as crop raiding. Such constant conflict could have significant implications for effects on human wellbeing and consequently, on local attitudes towards elephants and conservation efforts. This research highlights the need for more attention to be paid to the patterns and perceptions of all types of HEC, not just crop raiding, across elephant ranges in order to plan effective mitigation strategies

De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia

Background Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century. In recent years there has been a resurgence of interest in sainfoin due to its potential beneficial nutraceutical and environmental attributes. However, genomic resources are scarce, thus hampering progress in genetic analysis and improvement. To address this we have used next generation RNA sequencing technology to obtain the first transcriptome of sainfoin. We used the library to identify gene-based simple sequence repeats (SSRs) and potential single nucleotide polymorphisms (SNPs). Results One genotype from each of five sainfoin accessions was sequenced. Paired-end (PE) sequences were generated from cDNA libraries of RNA extracted from 7 day old seedlings. A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. A total of 63 transcripts were annotated as involved in the tannin biosynthesis pathway. We identified 3786 potential SSRs. SNPs were identified by mapping the reads of the individual assemblies against the combined assembly. After stringent filtering a total of 77,000 putative SNPs were identified. A phylogenetic analysis of single copy number genes showed that sainfoin was most closely related to red clover and Medicago truncatula, while Lotus japonicus, bean and soybean are more distant relatives. Conclusions This work describes the first transcriptome assembly in sainfoin. The 92 K transcripts provide a rich source of SNP and SSR polymorphisms for future use in genetic studies of this crop. Annotation of genes involved in the condensed tannin biosynthesis pathway has provided the basis for further studies of the genetic control of this important trait in sainfoin

Evaluation of striped bass stocks in Virginia, monitoring and tagging studies, 2005-2009 Annual report, 1 September 2008 - 31 August 2009

This report presents the results of striped bass (Morone saxatilis) tagging and monitoring activities in Virginia during the period 1 September 2008 through 31 August 2009. It includes an assessment of the biological characteristics of striped bass taken from the 2009 spring spawning run, estimates of annual survival and fishing mortality based on annual spring tagging, and the results of the study that documents the prevalence of mycobacterial infections of striped bass in Chesapeake Bay. The information contained in this report is required by the Atlantic States Marine Fisheries Commission and is used to implement a coordinated management plan for striped bass in Virginia, and along the eastern seaboard

Carbon-13 cross-polarization magic-angle spinning nuclear magnetic resonance (CPMAS NMR) for measuring proanthocyanidin content and procyanidin to prodelphinidin ratio in sainfoin (Onobrychis viciifolia) tissues

A procedure based on 13C CPMAS NMR was developed to study procyanidins (PCs) and prodelphinidins (PDs) directly in milled sainfoin plant tissues. Blackcurrant and Tilia samples enabled reference spectra of purified proanthocyanidin (PA) fractions, crude extracts and milled plant tissues, with characteristic resonances at 155, 144 and 132 ppm. PC/PD ratios were estimated from the I132/I155 intensity ratio and differed by 2.5 to 5.9% compared to thiolysis data. Normalization to the 155 ppm signal intensity from reference spectra enabled analysis of PA contents with an error of ca 8 g PAs/100 g plant tissue. The procedure estimates the lignin contribution and allows for a correction of the PA content. In six sainfoin accessions, estimated PA contents, were 1.6- to 20.8-fold higher than the thiolysis and 1.4- to 2.6-fold higher than the HCl-butanol-acetone results. Method differences may reflect the presence of unextractable, possibly high molecular weight PAs in sainfoin

Evaluation of striped bass stocks in Virginia, monitoring and tagging studies, 2004-2008 Annual report, 1 September 2007 - 31 September 2008

This report presents the results of striped bass (Morone saxatilis) tagging and monitoring activities in Virginia during the period 1 September 2007 through 31 August 2008. It includes an assessment of the biological characteristics of striped bass taken from the 2008 spring spawning run, estimates of annual survival and fishing mortality based on annual spring tagging, and the results of the study that documents the prevalence of mycobacterial infections of striped bass in Chesapeake Bay. The information contained in this report is required by the Atlantic States Marine Fisheries Commission and is used to implement a coordinated management plan for striped bass in Virginia, and along the eastern seaboar

From regional pulse vaccination to global disease eradication: insights from a mathematical model of Poliomyelitis

Mass-vaccination campaigns are an important strategy in the global fight against poliomyelitis and measles. The large-scale logistics required for these mass immunisation campaigns magnifies the need for research into the effectiveness and optimal deployment of pulse vaccination. In order to better understand this control strategy, we propose a mathematical model accounting for the disease dynamics in connected regions, incorporating seasonality, environmental reservoirs and independent periodic pulse vaccination schedules in each region. The effective reproduction number, $R_e$, is defined and proved to be a global threshold for persistence of the disease. Analytical and numerical calculations show the importance of synchronising the pulse vaccinations in connected regions and the timing of the pulses with respect to the pathogen circulation seasonality. Our results indicate that it may be crucial for mass-vaccination programs, such as national immunisation days, to be synchronised across different regions. In addition, simulations show that a migration imbalance can increase $R_e$ and alter how pulse vaccination should be optimally distributed among the patches, similar to results found with constant-rate vaccination. Furthermore, contrary to the case of constant-rate vaccination, the fraction of environmental transmission affects the value of $R_e$ when pulse vaccination is present.Comment: Added section 6.1, made other revisions, changed titl

Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

Background: Understanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm. Results: The evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture. Conclusions: The discovery of population structure, combined with knowledge of associated phenotypes and environmental adaptations, enables a rational approach to identification of landraces that might be used as sources of germplasm for breeding programs. The population structure also enables hypotheses concerning the prehistoric spread and development of agriculture to be addressed

Elephant pathway use in a human‐dominated landscape

Habitat loss and fragmentation are two of the biggest threats facing wildlife today. Understanding the role of wildlife pathways in connecting resource areas is key for maintaining landscape connectivity, reducing the impacts of habitat loss and helping address human–wildlife conflict. In this study, we used sign surveys and camera trapping to understand the fine scale movement of elephants moving between a protected area and agricultural zone in the Masai Mara, Kenya. We used generalised linear models to determine factors driving high frequency of pathway use by elephants. Our results showed strong seasonal trends in pathway use, with peaks coinciding with the dry season. However, no correlations between rainfall and pathway use were found. Temporal patterns of pathway use indicate that elephants use risk avoidance strategies by moving between the two areas at times of low human disturbance. Spatial analysis revealed that the most frequently used pathways were closer to farms, saltlicks and forest and those that had a higher percentage of forest cover. Our models also showed a positive relationship between pathway use and the number of elephant crop raiding incidents, highlighting that pathways can play a role in human–elephant conflict. As habitat loss continues, pathways may become more important for linking resources. However, they are also likely to facilitate movement into farmland. The results from this study provide an opportunity for planned management activities to ensure connectivity and to mitigated conflict

The three-peat challenge : business as usual, responsible agriculture, and conservation and restoration as management trajectories in global peatlands

FundingThis work was supported by the Natural Environment Research Council [grant numbers NE/X015238/1; NE/ V006444/1; NE/V018760/1], the Royal Geographical Society (RBEA 02.21), the Royal Society (RGS\R2\202229), and Growing Health (BB/X010953/1) BBSRC Institute Strategic Programme.Peer reviewedPublisher PD

PROTOCOL: Exploring the effect of case management in homelessness per components: A systematic review of effectiveness and implementation, with meta-analysis and thematic synthesis

This is the protocol for a Campbell review. The objectives are as follows: To carry out a mixed methods review to summarise current evidence relating to the components of case-management interventions for people experiencing homelessness