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We deposited the codes for running the microclimate model and endotherm model used in the study. We made customized versions of micro_terra (for using downloaded climate data) and endo_devel (for changing sequence of thermoregulation strategies and using Fortran for speed)from NicheMapR, which were also deposited.

Wet markets have been implicated in multiple zoonotic outbreaks, including COVID-19. They are also a conduit for legal and illegal trade in wildlife, which threatens thousands of species. Yet wet markets supply food to millions of people around the world, and differ drastically in their physical composition, the goods they sell, and the subsequent risks they pose. As such, policy makers need to know how to target their actions to efficiently safeguard human health and biodiversity without depriving people of ready access to food. Here, we propose a taxonomy of wet markets, oriented around the presence of live or dead animals, and whether those animals are domesticated or wild (either captive-reared or wild-caught). We assess the dimensions and levels of risk that different types of wet markets pose to people and to biodiversity. We identify six key risk factors of wet markets that can affect human health: (1) presence of high disease-risk animal taxa, (2) presence of live animals, (3) hygiene conditions, (4) market size, (5) animal density and interspecies mixing, and (6) the length and breadth of animal supply chains. We also identify key factors informing risk to biodiversity. Finally, we recommend targeted, risk-adjusted policies to more efficiently and humanely address the dangers posed by wet markets.

A key component of nature’s contribution to people is aesthetic value.1,2 Charismatic species rally public support and bolster conservation efforts.3,4 However, an insidious aspect to humanity’s valuation of nature is that high value also drives wildlife trade,5,6 which can spearhead the demise of prized species.7–9 Here, we explore the antagonistic roles of aesthetic value in biodiversity conservation by using novel metrics of color to evaluate the aesthetics of the most speciose radiation of birds: passerines (i.e., the perching birds). We identify global color hotspots for passerines and highlight the breadth of color in the global bird trade. The tropics emerge as an epicentre of color, encompassing 91% and 65% of the world’s most diverse and most uniquely colored passerine assemblages, respectively. We show that the pet trade, which currently affects 30% of passerines (1,408/5,266), traverses the avian phylogeny and targets clusters of related species that are uniquely colored. We identify an additional 478 species at risk of future trade based on their coloration and phylogenetic relationship to currently traded species—together totaling 1,886 species traded, a 34% increase. By modeling future extinctions based on species’ current threat status, we predict localized losses of color diversity and uniqueness in many avian communities, undermining their aesthetic value and muting nature’s color palette. Given the distribution of color and the association of unique colors with threat and trade, proactive regulation of the bird trade is crucial to conserving charismatic biodiversity, alongside recognition and celebration of color hotspots.

1. Variation in temperature at a fine spatial scale creates critically important microclimates for many organisms. Quantifying thermal heterogeneity at this scale is challenging and, until recently, has been largely restricted to the use of dataloggers to record air temperature. Thermography is becoming an increasingly viable alternative. A single photo from a thermal imaging camera contains thousands of spatially explicit surface temperature measurements, making thermal cameras ideal for rapidly assessing temperature variation at fine scale. 2. Here, we present an R package – ThermStats – for processing thermal images and other gridded temperature data. The package addresses current constraints on applying thermography in ecology, by speeding up and simplifying the extraction of data from thermal images, and by facilitating the calculation of different metrics of thermal heterogeneity. The metrics capture both the frequency distribution and spatial patterns of temperature, and the package functions are designed to accommodate different sampling strategies and data in either matrix or raster format. 3. We demonstrate how ThermStats can be used to capture temperature variation at fine spatial scales in structurally complex habitat, such as tropical rainforest. Using thermal images collected in the field (~0.5 cm2 resolution), we found that thermal hetereogeneity varied little between primary and logged forest, but did vary with time of day. Comparing temperature extremes in a microclimate layer estimated from LIght Detection And Ranging (LIDAR) data (2,500 m2 resolution), we found that both hot and cold extremes were hotter inside oil palm plantations than in the neighbouring forest. 4. Our package simplifies the processing of thermal data, and our metrics capture key spatiotemporal temperature trends that underpin physiological, behavioural and demographic responses to environmental change. As such, ThermStats can advance a wide range of studies requiring fine-scale surface temperature data for microclimate investigations.

Range shifts are a crucial mechanism enabling species to avoid extinction under climate change1,2. The majority of terrestrial biodiversity is concentrated in the tropics3, including species considered most vulnerable to climate warming4, but extensive and ongoing deforestation of tropical forests is likely to impede range shifts5,6. We conduct a global assessment of the potential for tropical species to reach analogous future climates—‘climate connectivity’—and empirically test how this has changed in response to deforestation between 2000 and 2012. We find that over 62% of tropical forest area (~10 million km2) is already incapable of facilitating range shifts to analogous future climates. In just 12 years, continued deforestation has caused a loss of climate connectivity for over 27% of surviving tropical forest, with accelerating declines in connectivity as forest loss increased. On average, if species’ ranges shift as far down climate gradients as permitted by existing forest connectivity, by 2070 they would still experience 0.77 °C of warming under the least severe climate warming scenario and up to 2.6 °C warming for the most severe scenario. Limiting further forest loss and focusing the global restoration agenda towards creating climate corridors are global priorities for improving resilience of tropical forest biotas under climate change. Physically connected habitats are required for terrestrial species to shift their liveable ranges as the tropics warm. The authors show that over half of tropical forest area is currently unable to provide such climate connectivity, and that loss of connectivity is accelerating with deforestation.

Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes. ispartof: GLOBAL CHANGE BIOLOGY vol:26 issue:11 pages:6616-6629 ispartof: location:England status: published

In Focus: Bladon, A. J., Lewis, M., Bladon, E. K., Buckton, S. J., Corbett, S., Ewing, S. R., … Turner, E. C. (2020). How butterflies keep their cool: Physical and ecological traits influence thermoregulatory ability and population trends. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13319 Threatened with rising average temperatures and the new normal of climate extremes, species that cannot keep pace with climate change must adapt where they are, or face extinction. The ranges of many British butterflies have indeed extended northwards as the climate has warmed, but this option is increasingly restricted by the expansion and intensification of urban and agricultural lands. On a day-to-day basis, butterflies can thermoregulate using behaviours such as adjusting their wing positioning or moving into suitable microclimates. The extent to which these two options buffer individuals from free-air temperature, however, is not well known. Nor is the extent to which the different mechanisms are exploited by different species, and whether that has had any bearing on species' population trends over the time-scale of recent climate change. Using a simple and easily replicated approach, Bladon et al. (2020) were able to quantify intra- and interspecific variation in buffering ability, and species' relative reliance on the two thermoregulatory mechanisms of wing adjustment versus microclimate selection. The authors report marked variation in buffering capacity, correlated with wing size, wing colouration and taxonomic family. Species also differed in their thermoregulatory behaviours, with some - such as the Ringlet Aphantopus hyperantus and Large Skipper Ochlodes sylvanus-achieving impressive buffering through wing positioning. Others, like the Brown Argus Aricia agestis and Small Heath Coenonympha pamphilus, were more reliant on microclimate selection, and these were the species most likely to have shown declining population trends over the past 40 years. The study underscores the importance of individual thermoregulatory behaviours for understanding species' vulnerability to climate change. In combination with much improved methods for measuring and modelling climate at biologically relevant scales, the approach of Bladon et al. (2020) can and should be extended to identify the places and species most at risk, and the steps that conservation practitioners can take to maximise resilience to climate change. Much attention has been given to improving habitat connectivity to facilitate range shifts, but we should also consider how microclimate availability can be enhanced to allow species to manage when they cannot move.

Logging and habitat fragmentation impact tropical forest ecosystems in numerous ways, perhaps the most striking of which is by altering the temperature, humidity, and light environment of the forest—its microclimate. Because local-scale microclimatic conditions directly influence the physiology, demography and behavior of most species, many of the impacts of land-use intensification on the biodiversity and ecosystem functioning of tropical forests have been attributed to changes in microclimate. However, the actual pathways through which altered microclimatic conditions reshape the ecology of these human-modified ecosystems remain largely unexplored. To bridge this knowledge gap, here we outline an agenda for future microclimate research in human-modified tropical ecosystems. We focus specifically on three main themes: the role of microclimate in shaping (i) species distributions, (ii) species interactions, and (iii) ecosystem functioning in tropical forests. In doing so we aim to highlight how a renewed focus on microclimate can help us not only better understand the ecology of human-modified tropical ecosystems, but also guide efforts to manage and protect them. Published version

Temperature is a core component of a species' fundamental niche. At the fine scale over which most organisms experience climate (mm to ha), temperature depends upon the amount of radiation reaching the Earth's surface, which is principally governed by vegetation. Tropical regions have undergone widespread and extreme changes to vegetation, particularly through the degradation and conversion of rainforests. As most terrestrial biodiversity is in the tropics, and many of these species possess narrow thermal limits, it is important to identify local thermal impacts of rainforest degradation and conversion. We collected pantropical, site‐level (

Background and AimsSouthern Arabia is a global biodiversity hotspot with a high proportion of endemic desert-adapted plants. Here we examine evidence for a Pleistocene climate refugium in the southern Central Desert of Oman, and its role in driving biogeographical patterns of endemism.MethodsDistribution data for seven narrow-range endemic plants were collected systematically across 195 quadrats, together with incidental and historic records. Important environmental variables relevant to arid coastal areas, including night-time fog and cloud cover, were developed for the study area. Environmental niche models using presence/absence data were built and tuned for each species, and spatial overlap was examined.Key ResultsA region of the Jiddat Al Arkad reported independent high model suitability for all species. Examination of environmental data across southern Oman indicates that the Jiddat Al Arkad displays a regionally unique climate with higher intra-annual stability, due in part to the influence of the southern monsoon. Despite this, the relative importance of environmental variables was highly differentiated among species, suggesting that characteristic variables such as coastal fog are not major cross-species predictors at this scale.ConclusionsThe co-occurrence of a high number of endemic study species within a narrow monsoon-influenced region is indicative of a refugium with low climate change velocity. Combined with climate analysis, our findings provide strong evidence for a southern Arabian Pleistocene refugium in Oman’s Central Desert. We suggest that this refugium has acted as an isolated temperate and mesic island in the desert, resulting in the evolution of these narrow-range endemic flora. Based on the composition of species, this system may represent the northernmost remnant of a continuous belt of mesic vegetation formerly ranging from Africa to Asia, with close links to the flora of East Africa. This has significant implications for future conservation of endemic plants in an arid biodiversity hotspot.

Most terrestrial species on Earth are ectothermic and track temperature at small spatial scales, from sun flecks to cool shaded spots. Current assessments of thermal heterogeneity in complex environments are predominately characterized by ambient temperature. This omission of solar radiation may lead to inaccurate conclusions regarding thermoregulation and distribution of species. We use thermal cameras to gather data on temperature heterogeneity in structurally complex rain forest environments. Using thermographic photographs, we capture the multidimensionality of climate created by vegetation by collecting over 76,000 temperature samples within approximately 1 m2 quadrats. The method was tested against three standard methods that record air temperature to determine possible omissions in capturing thermal heterogeneity in four geographic locations—Colombia, Borneo, Madagascar, and Australia. Across all locations, there was greater thermal heterogeneity in surface temperature than captured from ambient temperature technologies. Spatial variability in surface temperature on 1 d was greater than temporal variability of ambient temperature across the entire month, with extreme deviation from ambient temperatures. Importantly, when compared to the lower bounds for optimal performance for five tropical Anolis species, this technology captured thermal regimes that support the thermoregulatory needs of these species, whereas ambient air temperature methods suggested that these species would be in thermal debt. Sampling surface temperature at high resolutions across space in combination with intensive sampling of ambient temperature and informed spatial modeling should improve our understanding of the distribution of ectothermic species living within thermally heterogeneous environments.

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. Fil: Newbold, Tim. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Hudson, Lawrence N.. Natural History Museum. Department of Life Sciences; Reino Unido Fil: Hill, Samantha L. L.. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Contu, Sara. Natural History Museum. Department of Life Sciences; Reino Unido Fil: Lysenko, Igor. Imperial College London. Department of Life Sciences; Reino Unido Fil: Diaz, Sandra Myrna. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Harrison, Michelle L. K.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Alhusseini, Tamera. Imperial College London. Department of Life Sciences; Reino Unido Fil: Ingram, Daniel J.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Itescu, Yuval. Tel-Aviv University. Faculty of Life Sciences. Deptartment of Zoology; Israel Fil: Kattge, Jens. Max Planck Institute for Biogeochemistry; Alemania. German Centre for Integrative Biodiversity Research; Alemania Fil: Kirkpatrick, Lucinda. Imperial College London. Department of Life Sciences,; Reino Unido Fil: Kleyer, Michael. University of Oldenburg. Institute of Biology and Environmental Sciences. Landscape Ecology Group; Alemania Fil: Pinto Correia, David Laginha. Natural History Museum. Department of Life Sciences; Reino Unido Fil: Martin, Callum D.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Meiri, Shai. Tel-Aviv University. Faculty of Life Sciences. Deptartment of Zoology; Israel Fil: Novosolov, Maria. Tel-Aviv University. Faculty of Life Sciences. Deptartment of Zoology; Israel Fil: Pan, Yuan. Imperial College London. Department of Life Sciences; Reino Unido Fil: Phillips, Helen R. P.. Natural History Museum. Department of Life Sciences; Reino Unido. Imperial College London. Department of Life Sciences; Reino Unido Fil: Purves, Drew W.. Microsoft Research Cambridge. Computational Science Laboratory, ; Reino Unido Fil: Robinson, Alexandra. Imperial College London. Department of Life Sciences; Reino Unido Fil: Simpson, Jake. Imperial College London. Department of Life Sciences; Reino Unido Fil: Tuck, Sean L.. University of Oxford, Department of Plant Sciences; Reino Unido Fil: Weiher, Evan. University of Wisconsin–Eau Claire. Biology Department; Estados Unidos Fil: White, Hannah J.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Ewers, Robert M.. Imperial College London. Department of Life Sciences; Reino Unido Fil: Mace, Georgina M.. University College London. Centre for Biodiversity and Environment Research. Department of Genetics, Evolution and Environment; Reino Unido Fil: Scharlemann, Jörn P. W.. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Purvis, Andy. Natural History Museum. Department of Life Sciences; Reino Unido. Imperial College London. Department of Life Sciences; Reino Unido

Tropical rainforests are subject to extensive degradation by commercial selective logging. Despite pervasive changes to forest structure, selectively logged forests represent vital refugia for global biodiversity. The ability of these forests to buffer temperature-sensitive species from climate warming will be an important determinant of their future conservation value, although this topic remains largely unexplored. Thermal buffering potential is broadly determined by: (i) the difference between the "macroclimate" (climate at a local scale, m to ha) and the "microclimate" (climate at a fine-scale, mm to m, that is distinct from the macroclimate); (ii) thermal stability of microclimates (e.g. variation in daily temperatures); and (iii) the availability of microclimates to organisms. We compared these metrics in undisturbed primary forest and intensively logged forest on Borneo, using thermal images to capture cool microclimates on the surface of the forest floor, and information from dataloggers placed inside deadwood, tree holes and leaf litter. Although major differences in forest structure remained 9-12 years after repeated selective logging, we found that logging activity had very little effect on thermal buffering, in terms of macroclimate and microclimate temperatures, and the overall availability of microclimates. For 1°C warming in the macroclimate, temperature inside deadwood, tree holes and leaf litter warmed slightly more in primary forest than in logged forest, but the effect amounted to0.1°C difference between forest types. We therefore conclude that selectively logged forests are similar to primary forests in their potential for thermal buffering, and subsequent ability to retain temperature-sensitive species under climate change. Selectively logged forests can play a crucial role in the long-term maintenance of global biodiversity.

Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the ‘health’ and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness, and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growing tree species, which could exacerbate the loss of timber value and carbon storage already associated with logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana–tree interaction networks if heavily infested trees (i.e. the most connected ones) were more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of ‘extinction debt’., A.M. was funded by a Basque Government postdoctoral fellowship and an ETH postdoctoral fellowship. Field research support was provided by an ARC Laureate awarded to W.F.L.

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 - www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015. The collation of biodiversity datasets with broad taxonomic and biogeographic extents is necessary to understand historical declines and to project - and hopefully avert - future declines. We describe a newly collated database of more than 1.6 million biodiversity measurements 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. © 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.