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Habitat selection is a dynamic biological process where species respond to spatiotemporal variation in resource availability. The resulting distribution patterns can be detected as presence–absence or heterogeneity in abundance and indicate habitat preferences based on environmental correlations at multiple scales. Variation in habitat selection by ungulates is constrained by trade-offs in top-down and bottom-up trophic processes arising from differences in forage requirements, water dependency, anthropogenic effects, and predation avoidance, and mediated by physiological (feeding guild) and morphological (body size) factors. We conducted distance sampling over 7 years in the Tarangire Ecosystem (TE) of northern Tanzania for six resident ungulate species: Kirk’s dik-dik (Madoqua kirkii), Grant’s gazelle (Nanger granti), Thomson’s gazelle (Eudorcas thomsonii), Masai giraffe (Giraffa camelopardalis tippelskirchi), impala (Aepyceros melampus), and common waterbuck (Kobus ellipsiprymnus), and tested hypotheses related to effects of top-down and bottom-up processes on ungulate presence and abundance. We modeled ecological correlates against two distributional responses to understand which environmental factors constrained these ungulate species at different scales; (i) presence–absence observations modeled in a logistic regression to assess habitat selection at an ecosystem scale; (ii) local abundances from presence-only observations modeled using a negative binomial distribution for finer-scale selection. Browser and grazer species in the TE selected suitable habitat proximal to rivers and avoided the Combretum–Azanza woody plant assemblage. Browsers and grazers also showed strong preference for habitat with more dense cover of preferred forage species, and abundance was influenced by the presence of specific forage species with significant seasonal variation. Mixed feeders were more heterogeneous in habitat suitability implying that broader diets allow avoidance of areas with high human activity. Small-bodied and dehydration-sensitive species selected areas near rivers and seasonal tributaries. Seasonal habitat selection was more pronounced among mixed feeders. Conservation strategies based on spatially and seasonally explicit resource selection studies such as ours can minimize impacts to biodiversity by protecting vital resources to ungulates through all seasons of the year.

The dietary nutrient profile has metabolic significance and possibly contributes to species' foraging behavior. The brown bear (Ursus arctos) was used as a model species for which dietary ingredient and nutrient concentrations as well as nutrient ratios were determined annually, seasonally and per reproductive class. Brown bears had a vertebrate- and ant-dominated diet in spring and early summer and a berry-dominated diet in fall, which translated into protein-rich and carbohydrate-rich diets, respectively. Fiber concentrations appeared constant over time and averaged at 25% of dry matter intake. Dietary ingredient proportions differed between reproductive classes; however, these differences did not translate into a difference in dietary nutrient concentrations, suggesting that bears manage to maintain similar nutrient profiles with selection of different ingredients. In terms of nutrient ratios, the dietary protein to non-protein ratio, considered optimal at around 0.2 (on metabolizable energy basis), averaged around 0.2 in this study in fall and around 0.8 in spring and summer. We introduced the minimal non-fat to fat ratio necessary for efficient maintenance metabolism. This ratio varied across seasons but never fell beneath the theoretically estimated minimum to ensure metabolic efficiency. This population thus managed to ingest diets that never exerted a lack of glucogenic substrate, suggesting that metabolic efficiency may either be a driver of active diet selection or that natural resources available to bears did not constitute a constraint in this respect. Given the considerable proportion of fiber in the diet of brown bears, the relevance of this nutrient and its role in foraging behavior might be underestimated.

Trait‐based ecology holds the promise to explain how plant communities work, for example, how functional diversity may support community productivity. However, so far it has been difficult to combine field‐based approaches assessing traits at the level of plant individuals with limited spatial coverage and approaches using remote sensing (RS) with complete spatial coverage but assessing traits at the level of vegetation pixels rather than individuals. By delineating all individual‐tree crowns within a temperate forest site and then assigning RS‐derived trait measures to these trees, we combine the two approaches, allowing us to use general linear models to estimate the influence of taxonomic or environmental variation on between‐ and within‐species variation across contiguous space.We used airborne imaging spectroscopy and laser scanning to collect individual‐tree RS data from a mixed conifer‐angiosperm forest on a mountain slope extending over 5.5 ha and covering large environmental gradients in elevation as well as light and soil conditions. We derived three biochemical (leaf chlorophyll, carotenoids, and water content) and three architectural traits (plant area index, foliage‐height diversity, and canopy height), which had previously been used to characterize plant function, from the RS data. We then quantified the contributions of taxonomic and environmental variation and their interaction to trait variation and partitioned the remaining within‐species trait variation into smaller‐scale spatial and residual variation. We also investigated the correlation between functional trait and phylogenetic distances at the between‐species level. The forest consisted of 13 tree species of which eight occurred in sufficient abundance for quantitative analysis.On average, taxonomic variation between species accounted for more than 15% of trait variation in biochemical traits but only around 5% (still highly significant) in architectural traits. Biochemical trait distances among species also showed a stronger correlation with phylogenetic distances than did architectural trait distances. Light and soil conditions together with elevation explained slightly more variation than taxonomy across all traits, but in particular increased plant area index (light) and reduced canopy height (elevation). Except for foliage‐height diversity, all traits were affected by significant interactions between taxonomic and environmental variation, the different responses of the eight species to the within‐site environmental gradients potentially contributing to the coexistence of the eight abundant species.We conclude that with high‐resolution RS data it is possible to delineate individual‐tree crowns within a forest and thus assess functional traits derived from RS data at individual level. With this precondition fulfilled, it is then possible to apply tools commonly used in field‐based trait ecology to partition trait variation among individuals into taxonomic and potentially even genetic variation, environmental variation, and interactions between the two. The method proposed here presents a promising way of assessing individual‐based trait information with complete spatial coverage and thus allowing analysis of functional diversity at different scales. This information can help to better understand processes shaping community structure, productivity, and stability of forests., Trait‐based ecology holds the promise to explain how functional diversity may support community productivity. However, so far it has been difficult to combine field‐based and remote sensing (RS) approaches. By delineating all individual‐tree crowns within a temperate forest site and then assigning RS‐derived trait measures to these trees, we combine the two approaches, allowing us to estimate the influence of taxonomic or environmental variation on between‐ and within‐species variation across contiguous space.

In organisms with dormant stages, life‐history responses to past pollution can be studied retrospectively. Here, we study such responses in a rotifer (Brachionus calyciflorus) from the once heavily copper‐polluted Lake Orta (Italy). We extracted resting eggs from sediments, established clonal lineages from hatchlings, and exposed newborns of these lineages to one of three copper concentrations that each mimicked a specific period in the lake's pollution history. For each rotifer, we daily collected life‐table data. We then estimated treatment‐specific vital rates and used a stage‐structured population model to project population growth rate λ. We also estimated elasticities of λ to vital rates and contributions of vital rates to observed Δλ between copper treatments. As expected, λ decreased with increasing copper concentration. This decrease resulted mostly from a decline in juvenile survival rate (SJ) and partly from a decline in the survival rate of asexually reproducing females (SA). Maturation rate, and with one exception fecundity, also declined but did not contribute consistently to Δλ. λ was most elastic to SJ and SA, indicating that survival rates were under stronger selection than maturation rate and fecundity. Together, our results indicate that variation in juvenile survival is a key component in the rotifers’ copper response. The consistent decrease in SJ with increasing copper stress and the sensitivity of λ to that decrease also suggest that juvenile survival is a useful indicator of population performance under environmental pollution.

Populations are typically defined as spatially contiguous sets of individuals, but large populations of social species can be composed of discrete social communities that often overlap in space. Masai giraffes (Giraffa camelopardalis tippelskirchi) of Tanzania live in distinct social subpopulations that overlap spatially, enabling us to simultaneously explore environmental and social factors correlated with demographic variation in a metapopulation of >1,400 adult females and calves. We considered statistically distinct communities in the social network as subpopulations and tested for variation among the 10 subpopulations in adult female survival, calf survival, and reproductive rate (calf‐to‐adult female ratio). We then related variation in demographic rates among subpopulations to differences in vegetation, soil type, proximity to 2 types of human settlements, local giraffe population density, and social metrics of relationship strength and exclusivity among adult females. We did not find any among‐subpopulation effects on adult female survival, suggesting adult female survival is buffered against environmental heterogeneity among subpopulations. Variation in calf demographic rates among subpopulations were correlated with vegetation, soils, anthropogenic factors, and giraffe population density but not with adult female relationship metrics, despite substantial spatial overlap. Subpopulations with more dense bushlands in their ranges had lower calf survival probabilities, and those closer to human settlements had higher reproductive rates, possibly because of spatial gradients in natural predation. Reproductive rates were higher in subpopulations with more volcanic soils, and calf survival probabilities were greater in subpopulations with higher local adult female densities, possibly related to higher‐quality habitat associated with fertile soils or lower predation risk, or to greater competitive ability. The variation in fitness among subpopulations suggests that giraffes do not move unhindered among resource patches to equalize reproductive success, as expected according to an ideal free distribution. The differences in calf survival and reproductive rates could rather indicate intercommunity differences in competitive ability, perception, learning, or experience. Our approach of comparing demography among spatially overlapping yet distinct socially defined subpopulations provides a biologically meaningful way to quantify environmental and social factors influencing fine‐scale demographic variation for social species. published

The merging of community ecology and phylogenetic biology allows us to link broader evolutionary processes to local ecological processes, thereby increasing our understanding of community assembly. A recurrent way to test how species assemblages respond to different abiotic conditions and evaluate the role of evolutionary constraints in community assembly is through using environmental gradients as natural treatments. Here, we combine phylogenetic and trait-based methods to evaluate how the phylogenetic diversity and composition of bird assemblages and their community-weighted traits vary along an elevational gradient in the Swiss Alps. For this purpose, we used four life-history traits considered to be key indicators of individual species response to environmental changes: clutch size, number of breeding attempts, dispersal capacity and lifespan. Controlling for phylogeny, we determined whether environmental filters (elevation, habitat type) act on these traits independently of the level of relatedness among species. We found that phylogenetic dispersion decreases with elevation, but the signature of phylogenetic clustering was weak. Phylogenetic fuzzy weighting showed that the distribution of bird species across plots was related to the two environmental gradients; nonetheless, such influence was not determined by the phylogenetic relationships in either case. That is, there are no specific clades associated with particular elevation or habitat types. We also found that high elevation communities around the treeline were composed of species with lower reproductive rates, reduced lifespan, and lower dispersal capacity, which would make them less resilient to environmental change. Although traits showed moderate phylogenetic signal, only the lifespan was phylogenetically structured. In the remaining cases, the trait-environment association was not mediated by the phylogenetic relationships among taxa. Our study indicates that evolutionary constraints do not represent a significant driver of community assembly in Alpine bird communities and support the notion that phylogeny may often not be a good proxy for traits subject to environmental filtering.

Habitat suitability models (HSM) based on remotely sensed data are useful tools in conservation work. However, they typically use species occurrence data rather than robust demographic variables, and their predictive power is rarely evaluated. These shortcomings can result in misleading guidance for conservation. Here, we develop and evaluate a HSM based on correlates of long‐term breeding success of an open nest building boreal forest bird, the Siberian jay. In our study site in northern Sweden, nest failure of this permanent resident species is driven mainly by visually hunting corvids that are associated with human settlements. Parents rely on understory nesting cover as protection against these predators. Accordingly, our HSM includes a light detection and ranging (LiDAR) based metric of understory density around the nest and the distance of the nest to the closest human settlement to predict breeding success. It reveals that a high understory density 15–80 m around nests is associated with increased breeding success in territories close to settlements (, A LiDAR informed habitat suitability model for breeding success based on biotic interactions and verified with large scale occurrence data, showed that corvids around human settlements suppress breeding success in a Taiga specialist, the Siberian jay. However, dense understory around the nest alleviated the nest predation pressure by corvids while an open understory led to highest breeding success, in the absence of corvids. This study suggests that redistributing forest thinning efforts according to the distance of the forest stand from human settlements may provide a cost‐neutral opportunity to restore high‐quality breeding habitat for Siberian jays.

Food web models explain and predict the trophic interactions in a food web, and they can infer missing interactions among the organisms. The allometric diet breadth model (ADBM) is a food web model based on the foraging theory. In the ADBM, the foraging parameters are allometrically scaled to body sizes of predators and prey. In Petchey et al. (

Ecological niche theory predicts the coexistence of closely related species is promoted by resource partitioning in space and time. Australian snubfin (

Duckweeds (Lemnaceae) are increasingly studied for their potential for phytoremediation of heavy-metal polluted water bodies. A prerequisite for metal removal, however, is the tolerance of the organism to the pollutant, e.g., the metal zinc (Zn). Duckweeds have been shown to differ in their tolerances to Zn, however, despite them most commonly co-occurring with other species, there is a lack of research concerning the effect of species interactions on Zn tolerance. Here we tested whether the presence of a second species influenced the growth rate of the three duckweed species Lemna minor, Lemna gibba, and Lemna turionifera. We used four different Zn concentrations in a replicated microcosm experiment under sterile conditions, either growing the species in isolation or in a 2-species mixture. The response to Zn differed between species, but all three species showed a high tolerance to Zn, with low levels of Zn even increasing the growth rates. The growth rates of the individual species were influenced by the identity of the competing species, but this was independent of the Zn concentration. Our results suggest that species interactions should be considered in future research with duckweeds and that several duckweed species have high tolerance to metal pollution, making them candidates for phytoremediation efforts.

Parasites can impact the behavior of animals and alter the interplay with ecological factors in their environment. Studying the effects that parasites have on animals thus requires accurate estimates of infections in individuals. However, quantifying parasites can be challenging due to several factors. Laboratory techniques, physiological fluctuations, methodological constraints, and environmental influences can introduce measurement errors, in particular when screening individuals in the wild. These issues are pervasive in ecological studies where it is common to sample study subjects only once. Such factors should be carefully considered when choosing a sampling strategy, yet presently there is little guidance covering the major sources of error. In this study, we estimate the reliability and sensitivity of different sampling practices at detecting two internal parasites—Serratospiculoides amaculata and Isospora sp.—in a model organism, the great tit Parus major. We combine field and captive sampling to assess whether individual parasite infection status and load can be estimated from single field samples, using different laboratory techniques—McMaster and mini-FLOTAC. We test whether they vary in their performance, and quantify how sample processing affects parasite detection rates. We found that single field samples had elevated rates of false negatives. By contrast, samples collected from captivity over 24 h were highly reliable (few false negatives) and accurate (repeatable in the intensity of infection). In terms of methods, we found that the McMaster technique provided more repeatable estimates than the mini-FLOTAC for S. amaculata eggs, and both techniques were largely equally suitable for Isospora oocysts. Our study shows that field samples are likely to be unreliable in accurately detecting the presence of parasites and, in particular, for estimating parasite loads in songbirds. We highlight important considerations for those designing host–parasite studies in captive or wild systems giving guidance that can help select suitable methods, minimize biases, and acknowledge possible limitations. published

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Wildlife trade is a multi-billion-dollar sector that impacts a wide range of species, and thus is of significant research and conservation interest. Wildlife trade has also become a prominent topic in the public-facing media, where coverage has intensified following the outbreak of the global COVID-19 pandemic due to the potential connection between wildlife trade and the origin of the SARS Cov2 virus. Given the importance of the media in shaping public understanding and discourse of complex topics such as wildlife trade, this could impact the implementation of and public support for policy decisions. In this study, we followed a standardised protocol to extract wildlife trade-related discussion from 285 professional opinion pieces (NGO reports or articles in conservation-themed forums) and 107 scientific articles published in two time periods: "pre-COVID" (June 1-December 31, 2019) and "during-COVID" (January 1-May 31, 2020). We compared opinion pieces and scientific articles across the two time periods and to each other to investigate potential differences in the presentation of wildlife trade and associated speakers. We found a shift in the way that wildlife trade was discussed in professional opinion pieces between the periods, in that the discussion became less specific in terms of defining the legality and purpose of trade, and the animal groups involved in the "during-COVID" period. The generalised framing of wildlife trade in our dataset also coincided with an increased discussion of highly generalised management strategies, such as blanket bans on wildlife trade. We also found that publications included more quotes from researchers in the "during-COVID" period. In both professional opinion pieces and scientific articles, we found that quotations or research were often from speakers whose affiliation region was different to the geographic range of the trade they were speaking about. This highlights the importance of incorporating local knowledge and considering the diversity of speakers and interviewees in both research and the public-facing media about the wildlife trade.

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad-scale geographic origin assignment using nuclear markers to support law enforcement.

Monitoring biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution and species richness models. Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared three different approaches in order to better understand assessments of aquatic macroinvertebrate diversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species richness model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species richness model, that is, a generalized linear model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the kicknet and eDNA approaches, particularly at a local scale. We found the EPT-specific primer set fwhF2/EPTDr2n, detected a greater number of targeted EPT species compared to the more general primer set mlCOIintF/HCO2198. Moreover, we found that the species richness measured by eDNA from either primer set was poorly correlated to the richness measured by kicknet sampling (Pearson correlation = 0.27) and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the species richness model (Pearson correlation = 0.30 and 0.44, respectively). The weak relationships between the traditional kicknet sampling and eDNA with this model indicates inherent limitations in upscaling species richness estimates, and possibly a limited ability of the model to meet real world expectations. It is also possible that the number of replicates was not sufficient to detect ambiguous correlations. Future challenges include improving the accuracy and sensitivity of each approach individually, yet also acknowledging their respective limitations, in order to best meet stakeholder demands and address the biodiversity crisis we are facing., Metabarcoding and Metagenomics, 6, ISSN:2534-9708

Management of rangelands requires knowledge of forage species that are preferred or avoided by wildlife and livestock. A recent expansion of woody vegetation into previously open grasslands in African savanna ecosystems negatively impacts many mammalian grazers. Nevertheless, the ecological role of bush encroacher plant species as food may present a benefit for browsing species. We quantified diet selection by Masai giraffes (Giraffa camelopardalis tippelskirchi) through foraging observations and vegetation sampling in the Tarangire Ecosystem of Tanzania, which includes large areas of a native shrub that livestock managers have classified as an encroacher species (Dichrostachys cinerea). We compared woody plant species used by giraffes for foraging with availability at two different spatial scales during the wet and dry seasons. Giraffes selected some woody plants such as Vachellia species while significantly avoiding others, both at the local and landscape scales. Giraffes preferred foraging on D. cinerea at both spatial scales and in both the wet and dry seasons. Management that has focused on benefiting grazing livestock by removal of encroaching species (e.g., D. cinerea) may have unintended consequences for wildlife, especially for browsing species like giraffes that feed extensively on the expanding bush species.

Human-caused mortality of wildlife is a pervasive threat to biodiversity. Assessing the population-level impact of fisheries bycatch and other human-caused mortality of wildlife has typically relied upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional methods. Building on the widely applied potential biological removal (PBR) equation, we devised a new population modeling approach for estimating sustainable limits to human-caused mortality and applied it in a case study of bottlenose dolphins affected by capture in an Australian demersal otter trawl fishery. Our approach, termed sustainable anthropogenic mortality in stochastic environments (SAMSE), incorporates environmental and demographic stochasticity, including the dependency of offspring on their mothers. The SAMSE limit is the maximum number of individuals that can be removed without causing negative stochastic population growth. We calculated a PBR of 16.2 dolphins per year based on the best abundance estimate available. In contrast, the SAMSE model indicated that only 2.3-8.0 dolphins could be removed annually without causing a population decline in a stochastic environment. These results suggest that reported bycatch rates are unsustainable in the long term, unless reproductive rates are consistently higher than average. The difference between the deterministic PBR calculation and the SAMSE limits showed that deterministic approaches may underestimate the true impact of human-caused mortality of wildlife. This highlights the importance of integrating stochasticity when evaluating the impact of bycatch or other human-caused mortality on wildlife, such as hunting, lethal control measures, and wind turbine collisions. Although population viability analysis (PVA) has been used to evaluate the impact of human-caused mortality, SAMSE represents a novel PVA framework that incorporates stochasticity for estimating acceptable levels of human-caused mortality. It offers a broadly applicable, stochastic addition to the demographic toolbox to evaluate the impact of human-caused mortality on wildlife.La mortalidad de la fauna causada por humanos es una amenaza continua para la biodiversidad. El análisis del impacto a nivel poblacional de la captura pesquera incidental y otras causas humanas de la mortalidad de la fauna comúnmente ha dependido de métodos determinísticos. Sin embargo, las declinaciones poblacionales con frecuencia se aceleran por los factores estocásticos que no son considerados en dichos métodos convencionales. A partir de la ecuación de extirpación biológica potencial (EBP) de extensa aplicación diseñamos una nueva estrategia de modelación poblacional para estimar los límites sustentables de la mortalidad causada por humanos y la aplicamos en un estudio de caso de los delfines nariz de botella afectados por la captura en una pesquería australiana de arrastre demersal. Nuestra estrategia, denominada mortalidad antropogénica sustentable en ambientes estocásticos (MASAM) incorpora la estocasticidad ambiental y demográfica, incluyendo la dependencia que tienen las crías por sus madres. El límite MASAM es el número máximo de individuos que pueden extirparse sin causar un crecimiento poblacional estocástico negativo. Calculamos un EBP de 16.3 delfines por año con base en la mejor estimación de abundancia disponible. Como contraste, el modelo MASAM indicó que sólo podían extirparse entre 2.3 y 8.0 delfines anualmente sin ocasionar una declinación poblacional en un ambiente estocástico. Estos resultados sugieren que las tasas reportadas de captura incidental no son sustentables a largo plazo, a menos que las tasas reproductivas sean sistemáticamente más altas que el promedio. La diferencia entre el cálculo determinístico del EBP y los límites de MASAM mostró que los enfoques determinísticos pueden subestimar el verdadero impacto de la mortalidad de la fauna causada por humanos. Lo anterior resalta la importancia de integrar la estocasticidad al evaluar el impacto de la captura incidental y otras causas humanas de la mortalidad como la caza, las medidas letales de control y las colisiones con turbinas de viento. Aunque el análisis de viabilidad poblacional (AVP) se ha utilizado para evaluar el impacto de la mortalidad causada por humanos, MASAM representa un marco novedoso de AVP que incorpora la estocasticidad para estimar los niveles aceptables de mortalidad causada por humanos. Este enfoque ofrece una adición estocástica de aplicación generalizada para las herramientas demográficas usadas para evaluar el impacto de la mortalidad causada por humanos sobre la fauna.在不断变化的情景下估计野生动物死亡率的持续性限度的随机模型 人类造成的野生动物死亡是对生物多样性的普遍威胁。目前, 通常依赖于确定性方法来评估渔业副渔获物和其它人为造成的野生动物死亡在种群水平上的影响。然而, 随机因素往往会加速种群数量的下降, 但这种常规方法没有将其纳入考虑。我们在已得到广泛应用的生物可移除潜在量(Potential Biological Removal, PBR)方程的基础上, 设计了一种新的种群建模方法来估计人为造成的死亡的可持续限度, 并将其应用于澳大利亚底层拖网渔业中受影响的瓶鼻海豚的案例研究。我们的方法可以称为“随机环境中的可持续人为影响死亡率(SAMSE)”, 包含了环境和种群的随机性, 还包括了后代对母亲的依赖性。SAMSE的极限是指在不引起负面的种群随机增长的情况下可以移除的最大个体数。我们根据现有最佳的丰度估计, 计算出海豚的生物可移除潜在量为每年16.2头。相比之下, SAMSE模型则显示, 在随机环境中, 为了不引起种群下降, 每年只能移除2.3至8.0头海豚。这些结果表明, 除非繁殖率持续高于平均水平, 否则长期来看报告的副渔获率是不可持续的。确定性的PBR计算和SAMSE限制之间的差异表明, 确定性方法可能低估了人为造成野生动物死亡的真实影响。这突出了整合随机性在评估副渔获或其它人为造成的死亡(如狩猎、灭杀控制措施和风力涡轮机碰撞)对野生动物的影响中的重要性。尽管种群生存力分析(PVA)已被用于评估人为造成死亡的影响, 但SAMSE代表了一个包含随机性的PVA新框架, 可以用于估计人为造成死亡的可接受水平。它为种群统计学工具补充了一种广泛适用的随机性方法, 以评估人类造成的死亡对野生动物的影响。【翻译:胡怡思;审校:聂永刚】.

The high mountain ranges of Western Europe had a profound effect on the biotic recolonization of Europe from glacial refugia. The Alps present a particularly interesting case because they form an absolute barrier to dispersal for most taxa, obstructing recolonization from multiple refugia in northern Italy. Here, we investigate the effect of the European Alps on the phylogeographic history of the European common frog Rana temporaria. Based on partial cytochrome b and COXI sequences from Switzerland, we find two mitochondrial lineages roughly north and south of the Alpine ridge, with contact zones between them in eastern and western Switzerland. The northern haplogroup falls within the previously identified Western European haplogroup, while the southern haplogroup is unique to Switzerland. We find that the lineages diverged ~110 kya, at approximately the onset of the last glacial glaciation; this indicates that they are from different glacial refugia. Phylogenetic analyses suggest that the northern and southern haplogroups colonized Switzerland via trans‐ and circum‐Alpine routes from at least two separate refugia in northern Italy. Our results illustrate how a complex recolonization history of the central European Alps can arise from the semi‐permeable barrier created by high mountains., The European Alps presented a barrier to the post‐glacial recolonization of Europe for many taxa. However, a few cold‐tolerant species were able to colonize Switzerland across the Alps via multiple colonization routes from refugia in Northern Italy. We show that the complex colonization history of Rana temporaria across the Alps has resulted in unusually high genetic diversity within Switzerland.

Diel activity patterns of animal species reflect constraints imposed by morphological, physiological, and behavioral trade‐offs, but these trade‐offs are rarely quantified for multispecies assemblages. Based on a systematic year‐long camera‐trap study in the species‐rich mammal assemblage of Lake Manyara National Park (Tanzania), we estimated activity levels (hours active per day) and circadian rhythms of 17 herbivore and 11 faunivore species to determine the effects of body mass and trophic level on activity levels and cathemerality (the degree to which species are active throughout the day and night). Using generalized least squares and phylogenetic generalized least squares analyses, we found no support for the hypothesis that trophic level is positively associated with activity levels. We found no support for activity levels to scale positively with body mass in herbivores or to differ between ruminants and nonruminants; in faunivores, we also did not detect relationships between body mass and activity levels. Cathemerality was positively associated with activity levels but did not scale significantly with body mass. Overall, our findings caution against trophic level or body mass‐associated generalized conclusions with regard to diel activity patterns., Based on camera‐trap data, we estimated diel activity levels and activity patterns of 28 mammal species in Lake Manyara National Park. Using generalized least squares and phylogenetic generalized least squares analyses, we found no support for the hypothesis (1) that trophic level is positively associated with activity levels, (2) that activity levels scale with body mass, and (3) that activity levels differ between ruminants and nonruminants; but cathemerality was positively associated with activity levels.

In paleontology and biology, measures that correlate with specific traits are often used as proxies for these traits without a clear concept of how their discriminatory power is assessed. This note warns about this practice.

Globalization has facilitated the emergence and spread of novel pathogens, representing a major conservation challenge. The amphibian disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis, epitomizes this unprecedented threat, being responsible for declines and extinctions of amphibians worldwide. Chytridiomycosis has had both immediate catastrophic impacts during initial epidemics, as well as more variable, ongoing effects as the pathogen transitions to endemicity in its new distribution. Where B. dendrobatidis is now endemic, effective management actions are needed to prevent further extinctions of species. Yet, after nearly 20 years of research, management solutions remain rare or largely untested. Here, we highlight the potential for mitigation strategies focused on the environmental part of the host-pathogen-environment triangle to facilitate coexistence with the pathogen. We provide an extensive literature review to demonstrate that environmental conditions and demographic processes can strongly mediate the impact of B. dendrobatidis, and the capacity of amphibian populations to withstand disease-associated mortality. In particular, novel management approaches to achieve coexistence could focus on manipulating environmental conditions to decrease suitability for B. dendrobatidis and/or increase demographic resilience to disease-associated mortality. Such strategies include translocation to, or creation of, environmental refuges, and habitat manipulation to increase recruitment and offset elevated adult mortality. We argue that responding to chytridiomycosis requires a conceptual readjustment of our baselines to recognize that endemic B. dendrobatidis infection is the ‘new normal’ in surviving populations of many susceptible amphibian species. We conclude with recommendations for research and management actions that can help achieve coexistence of amphibian species susceptible to B. dendrobatidis.

Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.

The study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.

For ruminants and arboreal herbivores (sloths and colobine monkeys), an influence of digestive physiology on resting postures has been postulated that is linked to the interplay of digestive anatomy and the gravity vector. To further explore this putative relationship, we observed 253 individual terrestrial mammalian herbivores at zoological gardens, noting 29,478 resting events in 36 species during the day and 7,383 resting events of 18 species at night, providing a catalogue of mammalian resting postures. We confirm the constraint of ruminants to sternal recumbency and expand this observation to camelids, which rely on a similar sorting mechanism in their forestomach for rumination, but which use lateral recumbency to a slight but distinctively larger proportion. Generally, larger herbivores rest more in a standing position, and use lateral recumbency more when lying. The use of lateral recumbency in large hindgut fermenters (perissodactyls, elephants) and nonruminant foregut fermenters (macropods, hippos) corresponds to the concept that there is no interplay between gravity and digestive physiology in these species. By contrast, peccaries, hyraxes, and hystricomorph rodents never used lateral recumbency. While this may be related to body size, body shape, or other species-specific characteristics, it also suggests that the interplay of gravity and digestive processes, in particular with the colonic separation mechanism in hystricomorph rodents, should be further investigated.

Mangrove forests, vital for the conservation of biodiversity, protection of coastlines, and carbon capture, are decreasing globally at a rate higher than most other tropical forests. They are threatened by sea level rise, drought and storm surge, especially on low-lying islands where forests are directly exposed to the elements and have limited land area. We investigated changes in the spatial extent of mangroves on Aldabra Atoll, Seychelles – a protected area without direct human pressures, over 21 years using Landsat images. Over the 21-year study period, mean mangrove extent was 1283 ha with an overall net increase of 60 ha (0.23% year-1). The majority of extent changes were small (

Knowledge on the diversity and distribution of subterranean organisms is still scattered, even in faunistically relatively well-researched countries such as Switzerland. This is mostly due to the restricted access to these subterranean habitats. Better knowledge on these organisms is needed, because they contribute substantially to overall biodiversity of a region, often contain unique elements of biodiversity, and can potentially be indicative of the ecological status of subterranean ecosystems that are providing important ecosystem services such as drinking water. Past research on subterranean organisms has often used highly specialised sampling techniques and expert knowledge. Here, we show that inclusion of non-professionals can be an alternative and highly promising sampling strategy. We retrieved citizen science-based samples from municipal groundwater wells across Switzerland, mainly from the Swiss Plateau. Opportunistic samples from 313 sites revealed a previously undocumented groundwater fauna including organisms from different major invertebrate groups, with a dominance of crustaceans. Here, we studied amphipods of the genus Niphargus. Among all 363 individuals sampled, we found in total eight nominal species. Two of them, namely N. fontanus and N. kieferi, are reported for Switzerland for the first time. We also found four further phylogenetic lineages that are potentially new species to science. One of them is here formally described as Niphargus arolaensissp. nov. The description is based on molecular and morphometric data. Our study proves the suitability of citizen science to document subterranean diversity, supports groundwater conservation efforts with data, and raises awareness for the relevance and biodiversity of groundwater amphipods among stakeholders.

The knowledge of soil indicators during forest restoration is essential for understanding the recovery of ecosystem functions such as biomass production and water regulation. Despite this importance, in most restoration programs over the world, the soil remains under‐investigated. Here, we conducted a systematic literature review in order to determine: (1) the extent to which soil indicators are monitored during forest restoration in Colombia; (2) the type of soil indicators (e.g. physical, chemical, or biological) that are used for the monitoring; and (3) the regions where soil indicators are measured. We found 34 studies that report soil indicators. The most frequently studied restoration sites were 0–5 years old (36%). The majority (71%) of the studies only measured the soil characteristics at the topsoil. Soil sodium (Na) and phosphorus (P) concentrations were the most common chemical soil indicators reported by the studies. Soil biological indicators were the least frequently reported indicators. The studies rarely reported soil indicators that affect water movement directly. Of the retrieved studies, most included information about old‐growth forests (63%) or degraded sites (56%) for comparisons with forests undergoing restoration. Based on these results we provide recommendations for monitoring soil characteristics to assess the effectiveness of forest restoration projects in Colombia, and other tropical countries.

Patterns of selection in South American camelids (Lamini) and their unique demographic history establish the llama and alpaca as remarkable cases of domestication among large herd animals. Skull shape is implicated in many changes reported between wild and domestic taxa. We apply 3D geometric morphometric methods to describe skull shape, form, and size, differences among the four species of Lamini. In so doing, we test if domesticated Lamini exhibit changes similar to those in other domesticated groups: not only in the skull, but also in brain and body size. In contrast to other domesticated artiodactyls, very little change has occurred in domestic alpacas and llamas compared to their wild counterparts. Nevertheless, their differences are statistically significant and include a flatter cranium, inclined palate and increased airorhynchy in the domestics. Selection pressures that contrast with those on other herd animals, as well as recent population bottlenecks, likely have influenced the morphological patterns we note in Lamini. High-resolution 3D morphospace allows skull size, shape, and form (shape + size), to discriminate all four species, with form providing the greatest separation. These results help differentiate morphologically the Lamini, which in nature are distinguished mainly by body size, and provide an additional tool to archaeologists for distinction of wild and domestic remains. Most of our shape analyses suggest a marginally closer relationship between the alpaca and vicuña, to the exclusion of the guanaco, supporting the genetic relationships for this group. The expected brain size change between wild and domestic populations is lower than previously thought, with a 15.4% reduction in llama, and 6.8% reduction in alpaca. This is the lowest reduction in brain size thus far reported among domesticated Artiodactyla.

Close to two thousand environmental human rights defenders have been killed in 57 countries since 2002, with about four losing their lives every week in 2019. Many of these defenders represent Indigenous Peoples and local communities protecting ecosystems from large‐scale environmentally destructive projects. As the positive contributions of Indigenous and local communities to biodiversity conservation become better recognized, so should the losses and risks that they face. Despite major efforts at documenting abuses and protecting defenders, many blind spots and gaps remain. Here, we call for the conservation community to put the protection of defenders at the heart of its strategy to slow down and reverse the current onslaught on the environment. The conservation community can respond in a number of ways including reaching out to its constituencies, working together with the human rights community, and mobilizing its networks, field offices, and presence in remote areas to denounce abuses and counter isolation. In doing so the conservation community can advance the collective agenda bringing together conservation and environment‐related human rights through the Post‐2020 Global Biodiversity Framework.

The increasing scale and interconnection of many environmental challenges–from climate change to land use–has resulted in the need to collaborate across borders and boundaries of all types. Traditional centralized, top-down and sectoral approaches to governance of single-issue areas or species within social-ecological systems often have limited potential to alleviate issues that go beyond their jurisdiction. As a result, collaborative governance approaches have come to the forefront. A great deal of past research has examined the conditions under which collaborative efforts are likely to achieve desired outcomes. However, few studies have analyzed how the means to achieve successful collaborative outcomes differ based on context when examined across multiple studies. In this research, we begin to chart a means for doing this. Building onto a Context-Mechanism-Outcome (CMO) Framework, we provide a coding manual to analyse how contextual variables mediate the effects of mechanism variables on outcomes of the collaborative governance of social-ecological systems. Through the examination of four cases, we provide a proof-of-concept assessment and show the utility of the CMO framework and coding manual to draw comparisons across cases for understanding how collaborative outcomes are contingent on the social-ecological context in which they occur.

The island of Mauritius in the Mascarenes has already suffered high levels of extinction, and habitat destruction and invasive alien species have pushed many of the remaining endemic species to the brink of extinction. Round Island, a small island northeast of Mauritius, is home to remnant populations of several reptile species that were once distributed across Mauritius. One of the most threatened of these is Gunther’s gecko Phelsuma guentheri, where despite extensive management efforts, population size remains small and below expectation. We identify determinants of nest-site suitability across Round Island, and examine whether suitable nest sites are a limiting factor for the abundance of P. guentheri. Over one breeding season, we recorded and monitored a high number (269) of nest sites harbouring a total of 1475 eggs. We used the number of eggs at each nest, and the hatching success as proxies for nest-site suitability. To study the reproductive behaviour of P. guentheri, we installed trail cameras at three nest sites. We did not find the expected high frequency of use of hardwood trees as nest sites, as found on Ile aux Aigrettes to the southeast of Mauritius, probably because hardwood trees are still relatively sparse and small on Round Island. Instead, the endemic palm Latania loddigesii was the most used nest sites, harbouring 78.8% of all nests with 56.3% of all eggs. Hatching success was high for palm nest sites (90.6%), rock surfaces (91.8%), and on the endemic screw pine Pandanus vandermeeschii (96%), rates that are similar to that reported from hardwood trees on Ile aux Aigrettes (~90%). Communal nesting occurred on all substrates, with up to five individuals using the same nest site. Egg-laying took place at dusk or at night, lasting around 30 min, whereas hatching occurred mostly during the day, lasting 2–107 min. Females laid eggs every 34 days on average, and produced up to four clutches of 1–2 eggs each within the season. We conclude that P. guentheri does not suffer from nest site limitation on Round Island, and that reproductive success is high in terms of both numbers of eggs laid and hatching success, likely due to ongoing habitat restoration. Further research is needed to investigate the factors inhibiting abundance and distribution of P. guentheri on Round Island.

Funder: MAVA Foundation, Funder: Universität Zürich, In many social vertebrates, variation in group persistence exerts an important effect on individual fitness and population demography. However, few studies have been able to investigate the failure of groups or the causes of the variation in their longevity. We use data from a long-term study of cooperatively breeding meerkats, Suricata suricatta, to investigate the different causes of group failure and the factors that drive these processes. Many newly formed groups failed within a year of formation, and smaller groups were more likely to fail. Groups that bred successfully and increased their size could persist for several years, even decades. Long-lived groups principally failed in association with the development of clinical tuberculosis, Mycobacterium suricattae, a disease that can spread throughout the group and be fatal for group members. Clinical tuberculosis was more likely to occur in groups that had smaller group sizes and that had experienced immigration.

Feeding of wild Asian elephants at the Udawalawe National Park perimeter electric fence by the general public is longstanding. We monitored the elephants and feeding activities, and conducted questionnaire surveys of stakeholders. Over 50 individual adult male elephants engaged in the activity. The exclusive male presence was consistent with a high-risk high-gain male strategy. The elephants were mostly offered fruits and vegetables. Over a thousand people a day watched and fed the elephants. Most people bought food for elephants from roadside stalls and vendors had significantly more sales if elephants were present. The feeding of elephants brought significant economic benefit to communities bordering the park. We found the impacts of feeding on the elephants and environment to be largely neutral. Impacts on people and conservation were mainly positive. Actions taken by authorities to stop the feeding have targeted the elephants and resulted in the decrease of feeding but not its elimination. Managing the activity instead would help increase economic benefits and ensure safe interaction between people and elephants. Such management, by directly benefitting local communities, could make them partners in the conservation process and form the basis of an effective outreach program.

The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non‐mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island‐averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large‐scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome at the individual level., This study uses the Galápagos mockingbird species complex to test the relationship between gut microbiome composition and host genetic structure at the population level based on both MHC and microsatellite genotypes. We found no relationship between microbiome composition and genetic distance based on either MHC or microsatellite markers. This suggests that, at this geographic scale, host population genetics exerts little influence on the gut microbiome.

Theory predicts that organism–environment feedbacks play a central role in how ecological communities respond to environmental change. Strong feedback causes greater nonlinearity between environmental change and ecosystem state, increases the likelihood of hysteresis in response to environmental change, and augments the possibility of alternative stable regimes. To illustrate these predictions and their dependence on a temporal scale, we simulated a minimal ecosystem model. To test the predictions, we manipulated the feedback strength between the metabolism and the dissolved oxygen concentration in an aquatic heterotrophic tri‐trophic community in microecosystems. The manipulation consisted of five levels, ranging from low to high feedback strength by altering the oxygen diffusivity: free gas exchange between the microcosm atmosphere and the external air (metabolism not strongly affecting environmental oxygen), with the regular addition of 200, 100, or 50 ml of air and no gas exchange. To test for nonlinearity and hysteresis in response to environmental change, all microecosystems experienced a gradual temperature increase from 15 to 25°C and then back to 15°C. We regularly measured the dissolved oxygen concentration, total biomass, and species abundance. Nonlinearity and hysteresis were higher in treatments with stronger organism–environment feedbacks. There was no evidence that stronger feedback increased the number of observed ecosystem states. These empirical results are in broad agreement with the theory that stronger feedback increases nonlinearity and hysteresis. They therefore represent one of the first direct empirical tests of the importance of feedback strength. However, we discuss several limitations of the study, which weaken confidence in this interpretation. Research demonstrating the causal effects of feedback strength on ecosystem responses to environmental change should be placed at the core of efforts to plan for sustainable ecosystems., The organism–environment feedbacks play a central role in how ecological community response to environmental change. We simulated the “minimal ecosystem model” and incorporated different rates of environmental change to establish new predictions on the observation of nonlinearity and hysteresis. We confirmed those predictions using an experiment that manipulated the metabolism‐dissolved oxygen concentration feedback strength in response to a gradual change of temperature.

Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology and ecology. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a general framework for estimating rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate ( d ) as a function of the abiotic environment ( a ), the biotic environment ( b ) and clade-specific phenotypes or traits ( c ); thus d ~ a , b , c . We refer to the four components ( a − d ) and their interactions collectively as the ‘Evolutionary Arena’. We outline analytical approaches to this conceptual model that open up new avenues for research, and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples based on existing literature: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating fragmentation due to climatic oscillation; oceanic island radiations in the context of archipelago isolation and island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys . The results of the conifer case study are consistent with the long-standing scenario that large niches, lack of competition, and high-rates of niche evolution differentially promote diversification, but these results go further by quantifying the statistical interactions between variables representing these three drivers. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework results in highlighting gaps in current knowledge, and thus help to identify future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

The success of habitat enhancements is typically assessed by subsequent monitoring of the focal taxonomic group. However, enhancement actions are likely to affect other, non-targeted species. On a south-facing slope in the Swiss Jura mountains, a mixed-forest stand was thinned out by irregular removal cuttings to improve the habitat conditions for reptiles. We used this enhancement action as a case study to monitor changes in the macrofungal community that came along with it. During 3 years before and after forest thinning, the site was visited between six and twelve times per year. Thereby, all apparent fungal species were recorded along a ringlike transect, split into 32 transect sections. We used site-occupancy models to estimate fungal species richness and abundance. These models allow to separately estimate occurrence probability and detection probability of species, and to account for differences in detection probability, depending on habitat and season. After the forest thinning, the occurrence probabilities of ectomycorrhizal and saprobic fungi were significantly higher than before. As a result, we estimated a mean increase in overall species richness by 4.4% (median 4.3%, CI 2.1–6.8%) and an increase in abundance by 20.0% (median 19.9%, CI 14.8–25.7%). The two major habitat changes associated with forest thinning, the decrease in living wood and the increase in dead wood on most transect sections, could not explain the whole extent of the estimated increase in species richness and abundance. We believe that forest thinning may have fostered fungal species richness by creating a larger density and diversity of suitable microhabitats. With some caution, we conclude that the small-scale habitat enhancement for reptiles at the Bolberg, creating islands of open forest, did not negatively affect species richness and abundance of macrofungi, a non-targeted species group.

Conservation policy relies on input from science, yet scientists are often frustrated by the ‘gap’ between their recommendations and policy decisions. In this paper we examine one such ‘gap’: how a long-standing conflict of values functioned to ‘infect’ the synthesis and application of riparian science for salmon habitat restoration projects. We do this by analysis of a policy debate over the required minimum width of riparian buffers in voluntary conservation programs on agricultural lands in the Puget Sound region of Washington State. Based on an analysis of expert interviews and document analysis, we first outline the key features of the values debate. We then show the ways values ‘infected’ the debate over the science of riparian restoration. We identify a set of four ‘stumbling blocks’ in the science to policy gap that together led to both an intractable debate and an oversimplification of the science: conflation of science and policy, application of science out of context, limited consideration of alternatives, and obscuring debate via technical and bureaucratic language. We conclude with a set of ‘waypoints’ that can help ecologists, conservation managers and policy makers to better navigate the journey from science to policy.

Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well‐known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R‐package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three‐dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R‐packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general., Recently, research on spatial dynamics in ecology and evolution has bloomed. However, spatial structures used in theoretical and empirical ecological studies are often not representative of realistic landscapes. This is particularly true for river networks, which are of paramount interest to ecologists owing to their wide (but currently severely declining) biodiversity. Indeed, most of ecological work has been neglecting the scaling character of real river networks, despite well‐established knowledge in the fields of geomorphology and hydrology. Here, we present a method to create optimal channel networks (OCNs, i.e., river network analogues reproducing all topographic and scaling features of natural rivers), and the respective R‐package allowing their generation and analysis. We review the theoretical background underlying the OCN concept, present the main package functionalities, discuss possible applications in the realm of ecology and evolution, and detail how the package can be integrated with other popular R‐packages in spatial ecology.

Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes., Ecology and Evolution, 8 (16), ISSN:2045-7758

‘Genetic resources’ is a key concept of the Convention on Biological Diversity (CBD) and the Nagoya Protocol (NP). However, the term was coined to describe value in biodiversity and create an incentive for its protection and is thus of practical relevance for biological conservation beyond the legal context. The scope of this concept is also of interest to researchers, who may be unsure for which types of analysis they are legally and ethically expected to enter access and benefit sharing (ABS) negotiations. This article presents a biologically informed analysis, which leads to an understanding of ‘genetic resources’ that considers various associations and implications of this notion, such as its relation to biodiversity and the role that intellectual property rights (IPR) play in the discourse. The aim is to provide a coherent, consistent and comprehensive understanding of the concept that can integrate and explain these aspects and consider both classical and novel ways of using genetic resources. Based on the biological function of genetic resources and an analysis of how they are currently used and valued, this article argues that genetic resources are a particular type of natural resource that is informational rather than tangible. This interpretation clearly identifies utilising digital genomic sequences as a form of using genetic resources. However, the article also discusses regulatory exceptions for certain utilisations of genetic resources and it mentions the possibility of treating digital sequences as such an exception.

We studied the temperature relations of wild and zoo Aldabra giant tortoises (Aldabrachelys gigantea) focusing on (1) the relationship between environmental temperature and tortoise activity patterns (n = 8 wild individuals) and (2) on tortoise body temperature fluctuations, including how their core and external body temperatures vary in relation to different environmental temperature ranges (seasons; n = 4 wild and n = 5 zoo individuals). In addition, we surveyed the literature to review the effect of body mass on core body temperature range in relation to environmental temperature in the Testudinidae. Diurnal activity of tortoises was bimodally distributed and influenced by environmental temperature and season. The mean air temperature at which activity is maximized was 27.9°C, with a range of 25.8–31.7°C. Furthermore, air temperature explained changes in the core body temperature better than did mass, and only during the coldest trial, did tortoises with higher mass show more stable temperatures. Our results, together with the overall Testudinidae overview, suggest that, once variation in environmental temperature has been taken into account, there is little effect of mass on the temperature stability of tortoises. Moreover, the presence of thermal inertia in an individual tortoise depends on the environmental temperatures, and we found no evidence for inertial homeothermy. Finally, patterns of core and external body temperatures in comparison with environmental temperatures suggest that Aldabra giant tortoises act as mixed conformer–regulators. Our study provides a baseline to manage the thermal environment of wild and rewilded populations of an important island ecosystem engineer species in an era of climate change.

The Tropics are global centers of biodiversity. Ecological and land use gradients play a major role in the origin and maintenance of this diversity, yet a comprehensive synthesis of the corresponding large body of literature is still missing. We searched all ISI-listed journals for tropical gradient studies. From the resulting 1023 studies, we extracted study-specific information, and analyzed it using descriptive analytical tools and GLMs. Our results reveal that dry tropical areas are vastly understudied compared to their humid counterparts. The same holds true for large parts of Africa, but also the Philippines and the South Asian region. However, we also found that (applied) research output of developing tropical countries is nowadays on par with the output of developed countries. Vegetation and elevation were the most studied response variable and gradient, respectively. By contrast, inconspicous organisms such as oribatid mites and edaphic gradients were largely missing in the literature. Regarding biodiversity, tropical gradient studies dealt extensively with species richness and ecosystem diversity, but much less with genetic diversity. We encourage a wider use of modern statistical learning tools such as non-linear (spatio-temporal) regression and classification techniques, and simulations. Finally, we would embrace an even further development of synergies between applied and basic research and between researchers based in developed and in tropical countries.

The stress-gradient hypothesis predicts a higher frequency of facilitative interactions as resource limitation increases. Under severe resource limitation, it has been suggested that facilitation may revert to competition, and identifying the presence as well as determining the magnitude of this shift is important for predicting the effect of climate change on biodiversity and plant community dynamics. In this study, we perform a meta-analysis to compare temporal differences of species diversity and productivity under a nurse plant (Retama sphaerocarpa) with varying annual rainfall quantity to test the effect of water limitation on facilitation. Furthermore, we assess spatial differences in the herbaceous community under nurse plants in situ during a year with below-average rainfall. We found evidence that severe rainfall deficit reduced species diversity and plant productivity under nurse plants relative to open areas. Our results indicate that the switch from facilitation to competition in response to rainfall quantity is nonlinear. The magnitude of this switch depended on the aspect around the nurse plant. Hotter south aspects under nurse plants resulted in negative effects on beneficiary species, while the north aspect still showed facilitation. Combined, these results emphasize the importance of spatial heterogeneity under nurse plants for mediating species loss under reduced precipitation, as predicted by future climate change scenarios. However, the decreased water availability expected under climate change will likely reduce overall facilitation and limit the role of nurse plants as refugia, amplifying biodiversity loss., Consejo Superior de Investigaciones Científicas by MINECO, Grant/Award Number: CGL2014-59010-R; Schweizerischer National fonds zur Förderung der Wissenschaftlichen Forschung, Grant/Award Number: P2ZHP3_161986, P300PA_167758, PBBEP3_128361 and PZ00P3_148261; Spanish Government, Grant/Award Number: RYC-2012-12277; MINECO

Here we build on the manifesto ‘World Scientists’ Warning to Humanity, issued by the Alliance of World Scientists. As a group of conservation biologists deeply concerned about the decline of insect populations, we here review what we know about the drivers of insect extinctions, their consequences, and how extinctions can negatively impact humanity. We are causing insect extinctions by driving habitat loss, degradation, and fragmentation, use of polluting and harmful substances, the spread of invasive species, global climate change, direct overexploitation, and co-extinction of species dependent on other species. With insect extinctions, we lose much more than species. We lose abundance and biomass of insects, diversity across space and time with consequent homogenization, large parts of the tree of life, unique ecological functions and traits, and fundamental parts of extensive networks of biotic interactions. Such losses lead to the decline of key ecosystem services on which humanity depends. From pollination and decomposition, to being resources for new medicines, habitat quality indication and many others, insects provide essential and irreplaceable services. We appeal for urgent action to close key knowledge gaps and curb insect extinctions. An investment in research programs that generate local, regional and global strategies that counter this trend is essential. Solutions are available and implementable, but urgent action is needed now to match our intentions.