Unifying spatial and social network analysis in disease ecology.

Social network analysis has achieved remarkable popularity in disease ecology, and is sometimes carried out without investigating spatial heterogeneity. Many investigations into sociality and disease may nevertheless be subject to cryptic spatial variation, so ignoring spatial processes can limit inference regarding disease dynamics. Disease analyses can gain breadth, power and reliability from incorporating both spatial and social behavioural data. However, the tools for collecting and analysing these data simultaneously can be complex and unintuitive, and it is often unclear when spatial variation must be accounted for. These difficulties contribute to the scarcity of simultaneous spatial-social network analyses in disease ecology thus far. Here, we detail scenarios in disease ecology that benefit from spatial-social analysis. We describe procedures for simultaneous collection of both spatial and social data, and we outline statistical approaches that can control for and estimate spatial-social covariance in disease ecology analyses. We hope disease researchers will expand social network analyses to more often include spatial components and questions. These measures will increase the scope of such analyses, allowing more accurate model estimates, better inference of transmission modes, susceptibility effects and contact scaling patterns, and ultimately more effective disease interventions.

Global effects of land use on local terrestrial biodiversity.

Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

Density dependence and persistence of Morogoro arenavirus transmission in a fluctuating population of its reservoir host.

A key aim in wildlife disease ecology is to understand how host and parasite characteristics influence parasite transmission and persistence. Variation in host population density can have strong impacts on transmission and outbreaks, and theory predicts particular transmission-density patterns depending on how parasites are transmitted between individuals. Here, we present the results of a study on the dynamics of Morogoro arenavirus in a population of multimammate mice (Mastomys natalensis). This widespread African rodent, which is also the reservoir host of Lassa arenavirus in West Africa, is known for its strong seasonal density fluctuations driven by food availability. We investigated to what degree virus transmission changes with host population density and how the virus might be able to persist during periods of low host density. A seven-year capture-mark-recapture study was conducted in Tanzania where rodents were trapped monthly and screened for the presence of antibodies against Morogoro virus. Observed seasonal seroprevalence patterns were compared with those generated by mathematical transmission models to test different hypotheses regarding the degree of density dependence and the role of chronically infected individuals. We observed that Morogoro virus seroprevalence correlates positively with host density with a lag of 1-4 months. Model results suggest that the observed seasonal seroprevalence dynamics can be best explained by a combination of vertical and horizontal transmission and that a small number of animals need to be infected chronically to ensure viral persistence. Transmission dynamics and viral persistence were best explained by the existence of both acutely and chronically infected individuals and by seasonally changing transmission rates. Due to the presence of chronically infected rodents, rodent control is unlikely to be a feasible approach for eliminating arenaviruses such as Lassa virus from Mastomys populations.

A global model of the response of tropical and sub-tropical forest biodiversity to anthropogenic pressures.

Habitat loss and degradation, driven largely by agricultural expansion and intensification, present the greatest immediate threat to biodiversity. Tropical forests harbour among the highest levels of terrestrial species diversity and are likely to experience rapid land-use change in the coming decades. Synthetic analyses of observed responses of species are useful for quantifying how land use affects biodiversity and for predicting outcomes under land-use scenarios. Previous applications of this approach have typically focused on individual taxonomic groups, analysing the average response of the whole community to changes in land use. Here, we incorporate quantitative remotely sensed data about habitats in, to our knowledge, the first worldwide synthetic analysis of how individual species in four major taxonomic groups--invertebrates, 'herptiles' (reptiles and amphibians), mammals and birds--respond to multiple human pressures in tropical and sub-tropical forests. We show significant independent impacts of land use, human vegetation offtake, forest cover and human population density on both occurrence and abundance of species, highlighting the value of analysing multiple explanatory variables simultaneously. Responses differ among the four groups considered, and--within birds and mammals--between habitat specialists and habitat generalists and between narrow-ranged and wide-ranged species.

Twenty-nine years of continuous monthly capture-mark-recapture data of multimammate mice (Mastomys natalensis) in Morogoro, Tanzania.

The multimammate mice (Mastomys natalensis) is the most-studied rodent species in sub-Saharan Africa, where it is an important pest species in agriculture and carrier of zoonotic diseases (e.g. Lassa virus). Here, we provide a unique dataset that consists of twenty-nine years of continuous monthly capture-mark-recapture entries on one 3 ha mosaic field (MOSA) in Morogoro, Tanzania. It is one of the most accurate and long-running capture-recapture time series on a small mammal species worldwide and unique to Africa. The database can be used by ecologists to test hypotheses on the population dynamics of small mammals (e.g. to test the effect of climate change), or to validate new algorithms on real long-term field data (e.g. new survival analyses techniques). It is also useful for both scientists and decision-makers who want to optimize rodent control strategies and predict outbreaks of multimammate mice.

Temperature driven hibernation site use in the Western barbastelle Barbastella barbastellus (Schreber, 1774).

In temperate regions, winter is characterized by cold temperatures and low food availability. Heterothermic animals can bridge this period by entering a state of torpor characterized by decreased body temperature and reduced metabolic rate. Hibernation site choice is crucial since temperature conditions in the hibernaculum will impact torpor. We analysed temperature-dependent hibernation site use of Barbastella barbastellus. Bats and temperature were monitored in an underground system (1999-2019) and standalone bunkers (2007-2019) in Western Poland. During the winter of 2017-2018 we analysed the thermal variability of the hibernacula. Seasonal variation is higher in bunkers and thus temperatures get colder in winter than in the underground system. On the other hand, short-term variability (thermal variability index) in the bunkers was lower than in the underground system. This makes bunkers a more stable environment to hibernate for cold dwelling bats in warm winters, when temperatures in the bunkers do not get below freezing. Bats use both the warm underground system and the colder bunkers. During the last decade, a continuous series of warm winters occurred and the population of barbastelle bats partly moved from the underground system to the bunkers. These present temperature increases broadened the range of potential hibernation sites for barbastelles. Our study indicates that long-term trends, seasonal variation and short-term variability in temperatures are all important and should be analysed to investigate hibernaculum use by bats. Our study shows that small hibernation sites may become more important in the future.

The metric matters when assessing diversity: Assessing lepidopteran species richness and diversity in two habitats under different disturbance regimes.

How we measure diversity can have important implications for understanding the impacts of anthropogenic pressure on ecosystem processes and functioning. Functional diversity quantifies the range and relative abundance of functional traits within a given community and, as such, may provide a more mechanistic understanding of ecosystems. Here, we use a novel approach to examine how lepidopteran richness and diversity, weighted by species abundance, differ between habitats under different disturbance regimes (highly disturbed non-native plantations and less disturbed broadleaf woodlands), both with and without constraining by similarity due to shared taxonomy or functional traits. Comparisons of diversity between the two habitats differed according to which metric was being used; while species richness was 58% greater in broadleaf woodlands, after accounting for species similarity due to shared functional traits, there was little difference between woodland types under two different disturbance regimes. Functional diversity varied within the landscape but was similar in paired broadleaf and plantation sites, suggesting that landscape rather than local factors drive biotic homogenization in plantation dominated landscapes. The higher richness in broadleaf sites appears to be driven by rare species, which share functional traits with more common species. Moth populations in disturbed, plantation sites represent a reduced subset of moth species compared to broadleaf sites, and may be more vulnerable to disturbance pressures such as clear-felling operations due to low community resilience.

Flexible foraging strategies in Pipistrellus pygmaeus in response to abundant but ephemeral prey.

There is growing recognition that with sympathetic management, plantation forests may contain more biodiversity than previously thought. However, the extent to which they may support bat populations is contentious. Many studies have demonstrated active avoidance of coniferous plantations and attributed this to the lack of available roost sites and low invertebrate density. In contrast, other work, carried out in plantation dominated landscapes have shown that certain bat species are able to exploit these areas. However, the extent to which bats use plantations for roosting and foraging, or simply move through the plantation matrix to access more favourable sites is unclear. We radio tracked female Pipistrellus pygmaeus over two summers to establish the extent to which individual bats use Sitka Spruce plantations in southern Scotland for foraging and roosting and assess the implications for felling operations on bats. Maternity roosts identified (n = 17) were in all in buildings and most were large (> 500 individuals). We found no evidence of bats roosting in mature Sitka Spruce crop trees, although several bats used roosts in old or dead beech and oak trees as an alternative to their main maternity roost. Home ranges were much larger (mean 9.6 ± 3.12 km2) than those reported from other studies (0.6-1.6 km2), and it is likely that roost availability rather than food abundance constrains P. pygmaeus use of Sitka Spruce plantations. At the landscape scale, most individuals selected coniferous habitats over other habitat types, covering large distances to access plantation areas, whilst at a local scale bats used forest tracks to access water, felled stands or patches of broadleaf cover within the plantation. Sitka Spruce plantations support a high abundance of Culicoides impuctatus, the Highland midge which may act as a reliable and plentiful food source for females during lactation, an energetically expensive period. The use of felled stands for foraging by bats has implications for forest management as wind turbines, following small-scale felling operations, are increasingly being installed in plantations; wind turbines have been associated with high bat mortality in some countries. Decisions about siting wind turbines in upland plantations should consider the likelihood of increased bat activity post felling.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project.

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts.

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.