A nestbox trial for British marsh tits Poecile palustris

Two experimental nestbox trials were attempted, which aimed to maximise uptake by Marsh Tits in British woodland. Nestboxes which more closely approximated the dimensions of natural cavities were used more frequently than standard nestboxes, but the overall uptake was low. We conclude that nestboxes are an inefficient method of monitoring Marsh Tits, at least in the British context, and researchers should concentrate efforts on locating and monitoring natural nest sites

Parid foraging choices in urban habitat and their consequences for fitness

Urban environments are habitat mosaics, often with an abundance of exotic flora, and represent complex problems for foraging arboreal birds. In this study, we used compositional analysis to test how Blue Tits Cyanistes caeruleus and Great Tits Parus major used heterogeneous urban habitat, with the aim of establishing whether breeding birds were selective in the habitat they used when foraging and particularly how they responded to non-native trees and shrubs. We also tested whether they showed foraging preferences for certain plant taxa, such as oak Quercus, which are important to their breeding performance in native woodland. Additionally, we used mixed models to test the impact these different habitat types had on breeding success (expressed as mean nestling mass). Blue Tits foraged significantly more in native than non-native deciduous trees during incubation and when feeding fledglings, and significantly more in deciduous than in evergreen plants throughout the breeding season. Great Tits used deciduous trees more than expected by chance when feeding nestlings, and a positive relationship was found between availability of deciduous trees and mean nestling mass. Overall, the breeding performance of both species was poor and highly variable. Positive relationships were found between mean nestling mass and the abundance of Quercus for Great Tits, but not for Blue Tits. Our study shows the importance of native vegetation in the complex habitat matrix found in urban environments. The capacity of some, but not all, species to locate and benefit from isolated patches of native trees suggests that species vary in their response to urbanisation and this has implications for urban ecosystem function

Asking sensitive questions using the Unmatched Count Technique: Applications and guidelines for conservation

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordData accessibility: All data used in the analyses are freely available in the University of Oxford research archive at this link: https://ora.ox.ac.uk/objects/uuid:556a8a97-2d3d-4bf2-8fc1-359ce9786986. Data were gathered from 101 English language publications that empirically tested the UCT method. For each paper, information on 17 variables was collected, including the context (e.g. discipline, behaviour studied, rationale for using UCT, location), details of survey administration (e.g. whether a pilot study was conducted, whether design assumptions were checked), type of analysis, and comparisons to other methods (e.g. direct questions). Full data collection protocol and citations for all 101 reviewed publications are included in Appendix III and IV.1.Researchers and practitioners are increasingly using methods from the social sciences to address complex conservation challenges. This brings benefits but also the responsibility to understand the suitability and limitations of these methods in different contexts. After years of use in other disciplines, the Unmatched Count Technique (UCT) has recently been adopted by conservation scientists to investigate illegal and socially undesirable human behaviours. Here we provide guidance for practitioners and researchers on how to apply UCT effectively, and outline situations where it will be most and least appropriate. 2.We reviewed 101 publications in refereed journals that used UCT to draw conclusions on its use to date and provide recommendations on when and how to use the method effectively in conservation. In particular, we explored: type of studies undertaken (e.g. disciplines; behaviour being studied; rationale for using UCT); survey administration (e.g. sample size, pilot studies, administration mode); UCT outcomes (e.g. type of analyses, estimates, comparison with other methods); and type of recommendations. 3.We show that UCT has been used across multiple disciplines and contexts, with 10 studies that focus on conservation and natural resource use. The UCT has been used to investigate topics falling into five categories: socially undesirable behaviours, socially undesirable views, illegal or non‐compliant behaviours, socially desirable behaviours; and personal topics (e.g. being HIV positive). It has been used in 51 countries and is suitable to several situations, but limitations do exist, and the method does not always improve reporting of sensitive topics. 4.We provide best‐practice guidance to researchers and practitioners considering using UCT. We highlight that alternate methods should be considered if sample sizes are likely to be small, the behaviour in question is likely to be extremely rare, or if the behaviour is not particularly sensitive. UCT can be a useful tool for estimating the extent of non‐compliance within a conservation context, but as with all scientific investigation, careful study design, robust sampling and consistent implementation are required in order for it to be effective.Oxford Martin Programme on the Illegal Wildlife TradeNational Environment Research Council (NERC)Darwin Initiativ

Report 49: Growth, population distribution and immune escape of Omicron in England

To estimate the growth of the Omicron variant of concern (1) and its immune escape (2–9) characteristics, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England excluding those with a history of recent international travel. We undertook separate analyses according to two case definitions. For the first definition, we included all cases with a definitive negative S-gene Target Failure (SGTF) result and specimen dates between 29/11/2021 and 11/12/2021 inclusive. For the second definition, we included cases with a positive genotype result and specimen date between 23/11/2021 and 11/12/2021 inclusive. We chose a later start date for the SGTF definition to ensure greater specificity of SGTF for Omicron. We used logistic and Poisson regression to identify factors associated with testing positive for Omicron compared to non-Omicron (mostly Delta) cases. We explored the following predictors: day, region, symptomatic status, sex, ethnicity, age band and vaccination status. Our results suggest rapid growth of the frequency of the Omicron variant relative to Delta, with the exponential growth rate of its frequency estimated to be 0.34/day (95% CI: 0.33-0.35) [2.0 day doubling time] over the study period from both SGTF and genotype data. The distribution of Omicron by age, region and ethnicity currently differs markedly from Delta, with 18–29-year-olds, residents in the London region, and those of African ethnicity having significantly higher rates of infection with Omicron relative to Delta. Hospitalisation and asymptomatic infection indicators were not significantly associated with Omicron infection, suggesting at most limited changes in severity compared with Delta. To estimate the impact of Omicron on vaccine effectiveness (VE) for symptomatic infection we used conditional Poisson regression to estimate the hazard ratio of being an Omicron case (using SGTF definition) compared with Delta, restricting our analysis to symptomatic cases and matching by day, region, 10-year age band, sex and ethnicity. We found a significant increased risk of an Omicron case compared to Delta for those with vaccine status AZ 2+weeks post-dose 2 (PD2) , Pfizer 2+w PD2, AZ 2+w post-dose 3 (PD3) and PF 2+w PD3 vaccine states with hazard ratios of 1.86 (95%CI: 1.67-2.08), 2.68 (95%CI: 2.54-2.83), 4.32 (95%CI: 3.84-4.85) and 4.07 (95%CI: 3.66-4.51), respectively, where PD3 states are categorised by the dose 1/2 vaccine used. Depending on the Delta VE estimates used (10), these estimates translate into Omicron VE estimates of between 0% and 20% PD2 and between 55% and 80% PD3 against Omicron, consistent with other estimates (11). Similar estimates were obtained using genotype data, albeit with greater uncertainty. To assess the impact of Omicron on reinfection rates we relied on genotype data, since SGTF is associated with a higher observed rate of reinfection, likely due to reinfections typically having higher Ct values than primary infections and therefore being subject to a higher rate of random PCR target failure. Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date and using conditional Poisson regression to predict reinfection status, Omicron was associated with a 5.41 (95% CI: 4.87-6.00) fold higher risk of reinfection compared with Delta. This suggests relatively low remaining levels of immunity from prior infection

Winter habitat selection by marsh tits Poecile palustris in a British woodland

Capsule: Radio-tracking and remote sensing showed Marsh Tits selected for English Oak Quercus robur trees within large winter home-ranges. Aims: To investigate winter habitat selection by Marsh Tits in a British wood, testing for preferences in tree species and woodland structure. Methods: Thirteen Marsh Tits were radio-tracked during the winter, and home-ranges were derived. Lidar and hyperspectral data were used to compare the vegetation structure and tree species composition of entire home-ranges and the core areas of intensive use within. Instantaneous sampling observations provided further information for tree species utilization. Results: The mean home-range was very large (39 ha, n=13). There were no significant differences in mean tree height, canopy closure, understorey height, or shrub volume between full home-ranges and the core areas of use. Core areas contained a significantly greater proportion of English Oak relative to availability in the full home-ranges. Instantaneous sampling confirmed that English Oak was used significantly more than other trees. Conclusion: Selection for English Oak during winter contrasted with previous studies of breeding territories, indicating that habitat usage varies seasonally and demonstrating the need for habitat selection studies throughout the year. Large home-ranges help to explain the Marsh Tit’s sensitivity to habitat fragmentation

Using consumer preferences to characterize the trade of wild‐collected ornamental orchids in China

Over-exploitation of wildlife for trade threatens taxa globally. Interest in demand-side approaches to address this problem has grown but understanding of how consumer preferences shape demand remains limited. To quantify the role of consumer preferences for wild orchids in China’s horticultural market, we used conjoint analysis to determine which attributes are preferred by orchid owners and non-owners in two socio-economically contrasting areas of South China. Across all respondents, price was the most important attribute followed by flower colour. Whilst Xishuangbanna participants exhibited a slight preference for wild over cultivated plants, origin (wild/cultivated) was of minimal importance. We also measured awareness of orchid import regulations. Most did not recognise the CITES logo, and knowledge of import laws was significantly lower in Hong Kong than in Xishuangbanna. Our findings suggest that trade in wild ornamental orchids in South China is supply-driven, and strengthened regulations might be effective in reducing over-exploitation

Towards forest condition assessment: evaluating small-footprint full-waveform airborne laser scanning data for deriving forest structural and compositional metrics

Spatial data on forest structure, composition, regeneration and deadwood are required for informed assessment of forest condition and subsequent management decisions. Here, we estimate 27 forest metrics from small-footprint full-waveform airborne laser scanning (ALS) data using a random forest (RF) and automated variable selection (Boruta) approach. Modelling was conducted using leaf-off (April) and leaf-on (July) ALS data, both separately and combined. Field data from semi-natural deciduous and managed conifer plantation forests were used to generate the RF models. Based on NRMSE and NBias, overall model accuracies were good, with only two of the best 27 models having an NRMSE > 30% and/or NBias > 15% (Standing deadwood decay class and Number of sapling species). With the exception of the Simpson index of diversity for native trees, both NRMSE and NBias varied by less than ±4.5% points between leaf-on only, leaf-off only and combined leaf-on/leaf-off models per forest metric. However, whilst model performance was similar between ALS datasets, model composition was often very dissimilar in terms of input variables. RF models using leaf-on data showed a dominance of height variables, whilst leaf-off models had a dominance of width variables, reiterating that leaf-on and leaf-off ALS datasets capture different aspects of the forest and that structure and composition across the full vertical profile are highly inter-connected and therefore can be predicted equally well in different ways. A subset of 17 forest metrics was subsequently used to assess favourable conservation status (FCS), as a measure of forest condition. The most accurate RF models relevant to the 17 FCS indicator metrics were used to predict each forest metric across the field site and thresholds defining favourable conditions were applied. Binomial logistic regression was implemented to evaluate predicative accuracy probability relative to the thresholds, which varied from 0.73–0.98 area under the curve (AUC), where 11 of 17 metrics were >0.8. This enabled an index of forest condition (FCS) based on structure, composition, regeneration and deadwood to be mapped across the field site with reasonable certainty. The FCS map closely and consistently corresponded to forest types and stand boundaries, indicating that ALS data offer a feasible approach for forest condition mapping and monitoring to advance forest ecological understanding and improve conservation efforts

Wildlife-friendly farming increases crop yield: evidence for ecological intensification

Ecological intensification has been promoted as a means to achieve environmentally sustainable increases in crop yields by enhancing ecosystem functions that regulate and support production. There is, however, little direct evidence of yield benefits from ecological intensification on commercial farms growing globally important foodstuffs (grains, oilseeds and pulses). We replicated two treatments removing 3 or 8% of land at the field edge from production to create wildlife habitat in 50–60 ha patches over a 900 ha commercial arable farm in central England, and compared these to a business as usual control (no land removed). In the control fields, crop yields were reduced by as much as 38% at the field edge. Habitat creation in these lower yielding areas led to increased yield in the cropped areas of the fields, and this positive effect became more pronounced over 6 years. As a consequence, yields at the field scale were maintained—and, indeed, enhanced for some crops—despite the loss of cropland for habitat creation. These results suggested that over a 5-year crop rotation, there would be no adverse impact on overall yield in terms of monetary value or nutritional energy. This study provides a clear demonstration that wildlife-friendly management which supports ecosystem services is compatible with, and can even increase, crop yields

Social structure of coal tits Periparus ater in temperate deciduous forest

Analysis of the impacts of social structure on the behaviour and life history of birds is a rapidly developing area of ornithology. Such studies commonly focus on the Paridae (tits and chickadees) as a model group, but detailed assessment of the basic social structure is lacking for many parids, particularly in the non-breeding season. Such baseline information is essential for understanding the organisation of bird populations, including associations between individuals within social and spatial networks. We assessed the non-breeding (autumn-winter) and spring (i.e. breeding season) social structure of Coal Tits Periparus ater in broadleaved forest in southern Britain. Coal Tits were found to be resident and sedentary in this habitat, with birds remaining close to their spring territories during the non-breeding season and associating in small groups averaging 3-4 individuals. Associations were variable, however, with no evidence of stable flock membership, group territoriality or strong pair bonds during autumn-winter. The non-breeding social structure did not change between years of high and low population density, being most similar to a 'basic flock' organisation. This differed from that expected of a food-hoarding parid and contradicted some earlier classifications, highlighting the potential plasticity of social behaviour between bird populations. Such variation can inform the understanding of the evolution of avian social structures and associated behavioural traits, such as food hoarding, and aid the interpretation of intraand inter-specific differences in behaviour

Report 50: Hospitalisation risk for Omicron cases in England

To assess differences in the risk of hospitalisation between the Omicron variant of concern (1) and the Delta variant, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England with last test specimen dates between 1st and 14th December inclusive. Variant was defined using a combination of S-gene Target Failure (SGTF) and genetic data. Case data were linked by National Health service (NHS) number to the National Immunisation Management System (NIMS) database, the NHS Emergency Care (ECDS) and Secondary Use Services (SUS) hospital episode datasets. Hospital attendance was defined as any record of attendance at a hospital by a case in the 14 days following their last positive PCR test, up to and including the day of attendance. A secondary analysis examined the subset of attendances with a length of stay of one or more days. We used stratified conditional Poisson regression to predict hospitalisation status, with demographic strata defined by age, sex, ethnicity, region, specimen date, index of multiple deprivation and in some analyses, vaccination status. Predictor variables were variant (Omicron or Delta), reinfection status and vaccination status. Overall, we find evidence of a reduction in the risk of hospitalisation for Omicron relative to Delta infections, averaging over all cases in the study period. The extent of reduction is sensitive to the inclusion criteria used for cases and hospitalisation, being in the range 20-25% when using any attendance at hospital as the endpoint, and 40-45% when using hospitalisation lasting 1 day or longer or hospitalisations with the ECDS discharge field recorded as “admitted” as the endpoint (Table 1). These reductions must be balanced against the larger risk of infection with Omicron, due to the reduction in protection provided by both vaccination and natural infection. A previous infection reduces the risk of any hospitalisation by approximately 50% (Table 2) and the risk of a hospital stay of 1+ days by 61% (95%CI:55-65%) (before adjustments for under ascertainment of reinfections). High historical infection attack rates and observed reinfection rates with Omicron mean it is necessary to correct hazard ratio estimates to accurately quantify intrinsic differences in severity between Omicron and Delta and to assess the protection afforded by past infection. The resulting adjustments are moderate (typically less than an increase of 0.2 in the hazard ratio for Omicron vs Delta and a reduction of approximately 0.1 in the hazard ratio for reinfections vs primary infections) but significant for evaluating severity overall. Using a hospital stay of 1+ days as the endpoint, the adjusted estimate of the relative risk of reinfections versus primary cases is 0.31, a 69% reduction in hospitalisation risk (Table 2). Stratifying hospitalisation risk by vaccination state reveals a more complex overall picture, albeit consistent with the unstratified analysis. This showed an apparent difference between those who received AstraZenca (AZ) vaccine versus Pfizer or Moderna (PF/MD) for their primary series (doses 1 and 2). Hazard ratios for hospital attendance with Omicron for PF/MD are similar to those seen for Delta in those vaccination categories, while Omicron hazard ratios are generally lower than for Delta for the AZ vaccination categories. Given the limited samples sizes to date, we caution about over-interpreting these trends, but they are compatible with previous findings that while protection afforded against mild infection from AZ was substantially reduced with the emergency of Delta, protection against more severe outcomes was sustained (2,3). We emphasise that these are estimates which condition upon infection; net vaccine effectiveness against hospital attendance may not vary between the vaccines, given that PF/MD maintain higher effectiveness against symptomatic infection with Omicron than AZ (4). Our estimates will assist in refining mathematical models of potential healthcare demand associated with the unfolding European Omicron wave. The hazard ratios provided in Table 3 can be translated into estimates of vaccine effectiveness (VE) against hospitalisation, given estimates of VE against infection (4). In broad terms, our estimates suggest that individuals who have received at least 2 vaccine doses remain substantially protected against hospitalisation, even if protection against infection has been largely lost against the Omicron variant (4,5)