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Failure to adapt migration timing to changes in environmental conditions along migration routes and at breeding locations can result in mismatches across trophic levels, as occurs between the brood parasitic common cuckoo Cuculus canorus and its hosts. Using satellite tracking data from 87 male cuckoos across 11 years, we evaluate why the cuckoo has not advanced its arrival to the UK. Across years, breeding ground arrival was primarily determined by timing of departure from stopover in West Africa before northward crossing of the Sahara. Together with high population synchrony and low apparent endogenous control of this event, this suggests that a seasonal ecological constraint operating here limits overall variation in breeding grounds arrival, although this event was itself influenced by carry-over from timing of arrival into tropical Africa. Between-year variation within individuals was, in contrast, mostly determined by northward migration through Europe, likely due to weather conditions. We find evidence of increased mortality risk for a) early birds following migration periods positively impacting breeding grounds arrival, and b) late birds, possibly suffering energy limitation, after departure from the breeding grounds. These results help identify areas where demands of responding to global change can potentially be alleviated by improving stopover quality.

Acknowledgements: We would like to acknowledge the help of UEA Master’s students Rhianna Wren, Evan Burdett, Abigail Hunns and Ashis Datta who assisted with the review and identification of relevant papers., Funder: BTO Donations and Memberships, Funder: Penchant Foundation, Funder: Kenneth Trouth Gift in Will, Large-scale declines in terrestrial insects have been reported over much of Europe and across the world, however, population change assessments of other key invertebrate groups, such as soil invertebrates, have been largely neglected through a lack of available monitoring data. This study collates historic data from previously published studies to assess whether it is possible to infer previously undocumented long-term changes in soil invertebrate abundance. Earthworm and tipulid data were collated from over 100 studies across the UK, spanning almost 100 years. Analyses suggested long-term declines in earthworm abundance of between 1.6 to 2.1% per annum, equivalent to a 33% to 41% decline over 25 years. These appeared greatest in broadleaved woodlands and farmland habitats, and were greater in pasture than arable farmland. Significant differences in earthworm abundance between habitats varied between models but appeared to be highest in urban greenspaces and agricultural pasture. More limited data were available on tipulid abundance, which showed no significant change over time or variation between enclosed farmland and unenclosed habitats. Declines in earthworm populations could be contributing to overall declines in ecosystem function and biodiversity as they are vital for a range of ecosystem services and are keystone prey for many vertebrate species. If robust, our results identify a previously undetected biodiversity decline that would be a significant conservation and economic issue in the UK, and if replicated elsewhere, internationally. We highlight the need for long-term and large-scale soil invertebrate monitoring, which potentially could be carried out by citizen/community scientists.

Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage-drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. The exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage-drag in recombination 'cold' regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis-specific DNA double-strand breaks, catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11-1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11-1 homoeologues of hexaploid wheat. Characterization of progeny lines shows plants deficient in all six SPO11-1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild-type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that the transformation of wheat mutants carrying six edited copies of SPO11-1 with the TaSPO11-1B gene, restores synapsis, CO formation, and fertility and hence opens a route to modifying recombination in this agronomically important crop.

Meiosis recombines genetic variation and influences eukaryote genome evolution. During meiosis, DNA double-strand breaks (DSBs) enter interhomolog repair to yield crossovers and noncrossovers. DSB repair occurs as replicated sister chromatids are connected to a polymerized axis. Cohesin rings containing the REC8 kleisin subunit bind sister chromatids and anchor chromosomes to the axis. Here, we report the genomic landscape of REC8 using chromatin immunoprecipitation sequencing (ChIP-seq) in Arabidopsis (Arabidopsis thaliana). REC8 associates with regions of high nucleosome occupancy in multiple chromatin states, including histone methylation at H3K4 (expressed genes), H3K27 (silent genes), and H3K9 (silent transposons). REC8 enrichment is associated with suppression of meiotic DSBs and crossovers at the chromosome and fine scales. As REC8 enrichment is greatest in transposon-dense heterochromatin, we repeated ChIP-seq in kyp suvh5 suvh6 H3K9me2 mutants. Surprisingly, REC8 enrichment is maintained in kyp suvh5 suvh6 heterochromatin and no defects in centromeric cohesion were observed. REC8 occupancy within genes anti-correlates with transcription and is reduced in COPIA transposons that reactivate expression in kyp suvh5 suvh6. Abnormal axis structures form in rec8 that recruit DSB-associated protein foci and undergo synapsis, which is followed by chromosome fragmentation. Therefore, REC8 occupancy correlates with multiple chromatin states and is required to organize meiotic chromosome architecture and interhomolog recombination.

The electricity gas and heat networks are finding it necessary to increase their ad hoc interactions as they develop their contribution to the net zero1 targets for green house gases for the UK and Scotland. The organisations involved in the “Getting to Net Zero” working group are all directly engaged in the energy sector encountering day-to-day challenges around how to include “getting to net zero” in their operations. The working group met to consider the progress of networks to date in addressing net zero and to identify immediate actions that would remove barriers to progress. This snap shot report summarises the working group findings.

Supplemental material, JHSPY_Supplemental_Table_1_ for A Prospective Pilot Study of Vascular Assessment of the Upper Extremity With Laser Angiography by Helen G. Hui-Chou, Madhuli Y. Thakkar, Kenneth R. Means and James P. Higgins in HAND

Tick infestation increased with temperature and vegetation height, and was negatively correlated with Golden Plover Pluvialis apricaria chick survival, but not growth rates. To examine the factors associated with tick loads on Golden Plover chicks and whether tick loads correlated with the growth rate or short-term survival probability. Twenty-one chicks from eight broods were radio-tagged and recaptured at 4-day intervals to measure tick loads, growth rate and determine survival probability between recaptures. All broods and 90% of chicks (19/21) had ticks present during at least one recapture, and ticks were present on 81% (70/86) of all recaptures. Mean tick load per capture was 9.2 (range 0–45) which was 13 times higher than the only previous comparable study on wader chicks. Tick loads were highest in warmer weather and when chicks moved through areas with taller average field layer vegetation. Tick loads were also correlated with chick age and date. The chick growth rate was highest in warmer weather and at mid-altitudes (400–450 m) but showed no significant correlation with tick load. The probability of a chick surviving between recaptures was positively correlated with chick body condition and negatively correlated with tick load. This study, albeit from one site and with small sample size, recorded high tick loads on Golden Plover chicks. Although unrelated to growth rates, ticks were negatively correlated with chick survival. Further work to identify the mechanism(s) underpinning associations between tick load and survival is required. Prior to considering whether tick control is an effective and justified management for wader conservation, research should first establish whether chick mortality from ticks limits Golden Plover and other wader populations on moorland.

Supplemental material, Supplemental_figures for A Prospective Pilot Study of Vascular Assessment of the Upper Extremity With Laser Angiography by Helen G. Hui-Chou, Madhuli Y. Thakkar, Kenneth R. Means and James P. Higgins in HAND

Supplemental material, JHSPY_Supplemental_Table_2 for A Prospective Pilot Study of Vascular Assessment of the Upper Extremity With Laser Angiography by Helen G. Hui-Chou, Madhuli Y. Thakkar, Kenneth R. Means and James P. Higgins in HAND

Figure S1. Transmission electron microscopy images of ultra-thin sections of Chinese Spring wheat anthers varying in length from 0.5 to 1.4 mm. Scale bar = 50 μm. (PDF 570 kb)

Comparison of model predictions to the IUCN Red List assessment of species vulnerability to the threat of renewable energy.

Rationale for species traits selection for species included in the meta analysis.

Mitigation of anthropogenic climate change involves deployments of renewable energy worldwide, including wind farms, which can pose a significant collision risk to volant animals. Most studies into the collision risk of species with wind turbines, however, have taken place in industrialized countries. Potential effects for many locations and species therefore remain unclear. To redress this gap, we conducted a systematic literature review of recorded collisions of birds and bats with wind turbines within developed countries. We related collision rate to species-level traits and turbine characteristics to quantify the potential vulnerability of 9538 bird and 888 bat species globally. Avian collision rate was affected by migratory strategy, dispersal distance and habitat associations and bat collision rates were influenced by dispersal distance. For birds and bats, larger turbine capacity (megawatts) increased collision rates, however, deploying a smaller number of large turbines with greater energy output, reduced total collision risk per unit energy output, although bat mortality increased again with the largest turbines. Areas with high concentrations of vulnerable species were also identified, including migration corridors. Our results can therefore guide wind farm design and location to reduce the risk of large-scale animal mortality. This is the first quantitative global assessment of the relative collision vulnerability of species groups with wind turbines, providing valuable guidance for minimizing potentially serious negative impacts on biodiversity.

Beta coefficients from MCMCglmm models for birds and bats.

Supplementary figure for the location of onshore wind farms included in this study.

Summary of model predictions of collisions per turbine per year for families of birds and bats.

Table S1: Names of the 238 species included in the analysis; Table S2: Full list of potential climate variables; Table S3: Extreme years along the first three axes of the principal components analysis; Table S4: Number of species, broken down by taxon, experiencing extreme population changes in each year; Figure S1: Relationships between climate and species' population crashes; Figure S2: Relationships between climate and species' population explosions.

Supplementary methods detailing classification of study quality for studies included in the meta analysis.

Additional information on data manipulation and statistical analyses.

Capsule Black Grouse declines across Scotland were greatest on less heterogeneous moorland, at low to intermediate altitudes and, more weakly, around post-thicket woodland. Aims To examine correlates of change in abundance of Black Grouse across Scotland. Methods Changes in abundance within 5-km squares between national surveys in 1995/96 and 2005 were modelled in relation to measures of habitat cover and woodland age derived from satellite imagery. Results Populations across Scotland were most stable where unenclosed moorland comprised rough grassland, intermediate heather cover and at higher altitude. Declines tended to be greatest in squares which had transitioned from pre-thicket to closed-canopy woodland. Conclusion Moorland will be most beneficial where it is heterogeneous in composition, and the role of woodland maturation in driving regional declines has support, albeit more weakly, at a national scale.

Species distribution models (SDMs) are important tools for forecasting the potential impacts of future environmental changes but debate remains over the most robust modelling approaches for making projections. Suggested improvements in SDMs vary from algorithmic development through to more mechanistic modelling approaches. Here, we focus on the improvements that can be gained by conditioning SDMs on more detailed data. Specifically, we use breeding bird data from across Europe to compare the relative performances of SDMs trained on presence-absence data and those trained on abundance data. SDMs trained on presence-absence data, with a poor to slight fit according to Cohen's kappa, show an average improvement in model performance of 0.32 (se ±0.12) when trained on abundance data. Even those species for which models trained on presence-absence data are classified as good to excellent show a mean improvement in Cohen's kappa score of 0.05 (se ±0.01) when corresponding SDMs are trained on abundance data. This improved explanatory power is most pronounced for species of high prevalence. Our results illustrate that even using coarse scale abundance data, large improvements in our ability to predict species distributions can be achieved. Furthermore, predictions from abundance models provide a greater depth of information with regard to population dynamics than their presence-absence model counterparts. Currently, despite the existence of a wide variety of abundance data sets, species distribution modellers continue to rely almost exclusively on presence-absence data to train and test SDMs. Given our findings, we advocate that, where available, abundance data rather than presence-absence data can be used to more accurately predict the ecological consequences of environmental change. Additionally, our findings highlight the importance of informative baseline data sets. We therefore recommend the move towards increased collection of abundance data, even if only coarse numerical scales of recording are possible.

Current specifications for Jet A limit the amount of FAME contamination to 5 ppm (5 mg/Kg). The focus of this work was to evaluate the thermal stability impact to Jet A due to FAME contamination at levels up to 400 ppm (400 mg/Kg), the goal being to provide data that supports increasing the level of allowable FAME contamination in Jet A from 5 ppm to 100 ppm. Testing was performed by the U.S. Air Force at the Air Force Research Laboratory, Fuels and Energy Branch using the Advanced Reduced Scale Fuel System Simulator (ARSFSS). Results of testing showed that at 400 ppm contamination, there was no definitely discernible negative impact on thermal stability due to FAME contamination.

2017-05-01

Duchenne muscular dystrophy is one of the most common lethal monogenic disorders and is caused by dystrophin deficiency. The disease is transmitted as an X-linked recessive trait; however, recent biochemical and clinical studies have shown that many girls and women with a primary myopathy have an underlying dystrophinopathy, despite a negative family history for Duchenne dystrophy. These isolated female dystrophinopathy patients carried ambiguous diagnoses with presumed autosomal recessive inheritance (limb-girdle muscular dystrophy) prior to biochemical detection of dystrophin abnormalities in their muscle biopsy. It has been assumed that these female dystrophinopathy patients are heterozygous carriers who show preferential inactivation of the X chromosome harboring the normal dystrophin gene, although this has been shown for only a few X:autosome translocations and for two cases of discordant monozygotic twin female carriers. Here we study X-inactivation patterns of 13 female dystrophinopathy patients--10 isolated cases and 3 cases with a positive family history for Duchenne dystrophy in males. We show that all cases have skewed X-inactivation patterns in peripheral blood DNA. Of the nine isolated cases informative in our assay, eight showed inheritance of the dystrophin gene mutation from the paternal germ line. Only a single case showed maternal inheritance. The 10-fold higher incidence of paternal transmission of dystrophin gene mutations in these cases is at 30-fold variance with Bayesian predictions and gene mutation rates. Thus, our results suggest some mechanistic interaction between new dystrophin gene mutations, paternal inheritance, and skewed X inactivation. Our results provide both empirical risk data and a molecular diagnostic test method, which permit genetic counseling and prenatal diagnosis of this new category of patients.

This is our ninth annual horizon scan to identify emerging issues that we believe could affect global biological diversity, natural capital and ecosystem services, and conservation efforts. Our diverse and international team, with expertise in horizon scanning, science communication, as well as conservation science, practice, and policy, reviewed 117 potential issues. We identified the 15 that may have the greatest positive or negative effects but are not yet well recognised by the global conservation community. Themes among these topics include new mechanisms driving the emergence and geographic expansion of diseases, innovative biotechnologies, reassessments of global change, and the development of strategic infrastructure to facilitate global economic priorities.

Includes supplemental Information in PDF format including Supplemental Notes S1-S9, Supplemental Figures S1-S9 and Supplemental Tables S1-S7. (PDF 6178 kb)

Includes supplemental Information in PDF format including Supplemental Notes S1-S9, Supplemental Figures S1-S9 and Supplemental Tables S1-S7. (PDF 6178 kb)

FANCM suppresses crossovers in plants by unwinding recombination intermediates. In wheat, crossovers are skewed toward the chromosome ends, thus limiting generation of novel allelic combinations. Here, we observe that FANCM maintains the obligate crossover in tetraploid and hexaploid wheat, thus ensuring that every chromosome pair exhibits at least one crossover, by localizing class I crossover protein HEI10 at pachytene. FANCM also suppresses class II crossovers that increased 2.6-fold in fancm msh5 quadruple mutants. These data are consistent with a role for FANCM in second-end capture of class I designated crossover sites, whilst FANCM is also required to promote formation of non-crossovers. In hexaploid wheat, genetic mapping reveals that crossovers increase by 31% in fancm compared to wild type, indicating that fancm could be an effective tool to accelerate breeding. Crossover rate differences in fancm correlate with wild type crossover distributions, suggesting that chromatin may influence the recombination landscape in similar ways in both wild type and fancm.

Mitigation of anthropogenic climate change involves deployments of renewable energy worldwide, including wind farms, which can pose a significant collision risk to volant animals. Most studies into the collision risk between species and wind turbines, however, have taken place in industrialized countries. Potential effects for many locations and species therefore remain unclear. To redress this gap, we conducted a systematic literature review of recorded collisions between birds and bats and wind turbines within developed countries. We related collision rate to species-level traits and turbine characteristics to quantify the potential vulnerability of 9538 bird and 888 bat species globally. Avian collision rate was affected by migratory strategy, dispersal distance and habitat associations, and bat collision rates were influenced by dispersal distance. For birds and bats, larger turbine capacity (megawatts) increased collision rates; however, deploying a smaller number of large turbines with greater energy output reduced total collision risk per unit energy output, although bat mortality increased again with the largest turbines. Areas with high concentrations of vulnerable species were also identified, including migration corridors. Our results can therefore guide wind farm design and location to reduce the risk of large-scale animal mortality. This is the first quantitative global assessment of the relative collision vulnerability of species groups with wind turbines, providing valuable guidance for minimizing potentially serious negative impacts on biodiversity.