The results of multi-disciplinary research carried out on the deposits of the Moerbeke “Driehoek” site, located along the northern bank of the extensive Moervaart palaeolake (NW Belgium), are presented. The multi-proxy study, including sedimentological (organic matter, calcium carbonate and grain-size) and botanical (pollen, macrofossils, NPP) analyses, provided evidence of repeated aeolian deflation during the Allerød. Our results demonstrate, in combination with evidence from other soil archives within the Moervaart area, that the Allerød period in NW Europe was sedimentologically much less stable than hitherto assumed, especially during the GI-1c2 event and middle Allerød. Some of the Allerød deflation events were caused by centennial abrupt climatic oscillations, such as the short but pronounced cold GI-1c2 event, while others were likely the result of intense forest fires or a combination of both. These observations call for a revision of the existing Lateglacial litho- and chronostratigraphic schemes for the sand-belt of northern Europe.

Abstract Nearly half of freshwater wetlands have been lost due to human disturbance. In response, wetlands are being restored to retain their ecosystem services. A potentially adverse consequence of wetland function is the production of methylmercury (MeHg). We measured concentrations of mercury (Hg) species and ancillary parameters in groundwaters and surface waters from four natural and 16 restored wetlands in northern New York State, USA to investigate differences in concentrations of Hg species among wetlands. We found no obvious differences in concentrations of total mercury (THg) and methylmercury in pond waters between natural and restored wetlands. High values of %methylmercury were evident in both ground (38.8 ± 27.6%) and surface waters (43.4 ± 25.6%) suggesting these wetland complexes are highly efficient in converting ionic Hg to methylmercury, regardless if restored or natural. High methylation efficiency may be due to observed drying and rewetting cycles. Hg in pond waters is likely derived from direct atmospheric deposition or by mobilization from near-wetland shallow sediments, in addition to groundwater inflows. Water flow of groundwaters from the associated watershed into pond waters resulted in increases in concentrations of THg and methylmercury. Dissolved organic matter likely plays an important role in the supply of Hg to pond waters. Relationships between methylmercury and %methylmercury with sulfate and nitrate in groundwaters may suggest some chemical limitation on Hg methylation at higher concentrations of these anions. Because of the similarity in Hg dynamics for natural and restored wetlands, the most effective strategy to mitigate methylmercury production would be to decrease atmospheric Hg deposition.

Many freshwater ecosystems are becoming saltier and/or warmer, but our understanding of how these factors interact and affect the physiology and life history outcomes of most aquatic species remain unknown. We hypothesize that temperature modulates ion transport rates. Since ion transport is energetically expensive, increases in salinity and/or temperature may influence ion flux rates and ultimately, organismal performance. Radiotracer (22Na+, 35SO4-2, and 45Ca2+) experiments with lab-reared mayflies (N. triangulifer) and other field-collected insects showed that increasing temperature generally increased ion transport rates. For example, increasing temperature from 15 °C to 25 °C, increased 22Na+ uptake rates by two-fold (p < 0.0001) and 35SO4-2 uptake rates by four-fold (p < 0.0001) in the caddisfly, Hydropsyche sparna. Smaller changes in 22Na+ and 35SO4-2 uptake rates were observed in the mayflies, Isonychia sayi and Maccaffertium sp., suggesting species-specific differences in the thermal sensitivity of ion transport. Finally, we demonstrated that the toxicity of SO4 was influenced by temperature profoundly in a 96 -h bioassay. Under the saltiest conditions (1500 mg/L SO4), mayfly survival was 78% at 15 °C, but only 44% at 25 °C (p < 0.0036). Conceivably, the energetic cost of osmoregulation in warmer, saltier environments may cause significant major ion toxicity in certain freshwater insects.

In the original version of this article, equations 4 and 9 unfortunately contained errors

Abstract The preference–performance hypothesis (PPH) states that herbivorous female insects prefer to oviposit on those host plants that are best for their offspring. Yet, past attempts to show the adaptiveness of host selection decisions by herbivores often failed. Here, we tested the PPH by including often neglected oviposition-induced plant responses, and how they may affect both egg survival and larval weight. We used seven Brassicaceae species of which most are common hosts of two cabbage white butterfly species, the solitary Pieris rapae and gregarious P. brassicae. Brassicaceous species can respond to Pieris eggs with leaf necrosis, which can lower egg survival. Moreover, plant-mediated responses to eggs can affect larval performance. We show a positive correlation between P. brassicae preference and performance only when including the egg phase: 7-day-old caterpillars gained higher weight on those plant species which had received most eggs. Pieris eggs frequently induced necrosis in the tested plant species. Survival of clustered P. brassicae eggs was unaffected by the necrosis in most tested species and no relationship between P. brassicae egg survival and oviposition preference was found. Pieris rapae preferred to oviposit on plant species most frequently expressing necrosis although egg survival was lower on those plants. In contrast to the lower egg survival on plants expressing necrosis, larval biomass on these plants was higher than on plants without a necrosis. We conclude that egg survival is not a crucial factor for oviposition choices but rather egg-mediated responses affecting larval performance explained the preference–performance relationship of the two butterfly species.

Mutualists can vary in the quantity and quality of service which they provide to their partners. Variation in seed disperser quality depends on seed-processing traits, dispersal distance, and deposition location, all of which ultimately affect plant fitness. Here, we compared these aspects of seed dispersal quality between a native and an invasive ant species, and examined how they affect competition and plant performance. Using experimental mesocosm communities, we examined how these two ant species affect the spatial pattern of recruitment and establishment for four myrmecochorous plant species, including one invasive species. We measured the locations of dispersed seedlings relative to ant nests, adult plants, and other dispersed seedlings, as well as measured the effects of location on plant performance. The invasive ant, Myrmica rubra, secondarily dispersed seeds farther from its nests, creating a less clumped pattern of seedling recruitment compared to the native ant, Aphaenogaster rudis. Plant species responded differently to dispersal. Invasive seedlings recruited farther from adult plants than native seedlings, and had higher survival the farther they were from conspecifics. In contrast, native plants had higher survival and grew taller when dispersed farther from invasive plants. We show that seed-dispersing ant partners differ in mutualist quality creating differences in dispersal distance and deposition location that affects a plant's competitive environment. Our results reveal the potential for long-term consequences on plant community structure with changing ant partner identity. We emphasize the need to examine dispersal quality in addition to quantity to uncover the importance of partner identity in structuring communities.

Abstract Invasive species represent a threat to aquatic ecosystems globally; however, impacts can be heterogenous across systems. Documented impacts of invasive zebra mussels (Dreissena polymorpha) and spiny water fleas (Bythotrephes cederströmii; hereafter Bythotrephes) on native fishes are variable and context dependent across locations and time periods. Here, we use a hierarchical Bayesian analysis of a 35-year dataset on two fish species from 9 lakes to demonstrate that early life growth of ecologically important fishes are influenced by these aquatic invasive species. Walleye (Sander vitreus) in their first year of life grew more slowly in the presence of either invader after correcting for temperature (measured by degree days), and were on average 12 or 14% smaller at the end of their first summer following invasion by Bythotrephes or zebra mussels, respectively. Yellow perch (Perca flavescens) growth was less affected by invasion. Yellow perch on average grew more slowly in their first year of life following invasion by zebra mussels, although this effect was not statistically distinguishable from zero. Early life growth of both walleye and yellow perch was less tightly coupled to degree days in invaded systems, as demonstrated by increased variance surrounding the degree day-length relationship. Smaller first-year size is related to walleye survival and recruitment to later life stages and has important implications for lake food webs and fisheries management. Future research quantifying effects of zebra mussels and Bythotrephes on other population-level processes and across a wider gradient of lake types is needed to understand the mechanisms driving observed changes in walleye growth.

Abstract Herbivore and plant invasions can modify the structure and functioning of ecosystems through positive interactions that facilitate their mutual establishment. An important consequence of the feeding behaviour of rabbits is that they can play a key role in seed dispersal by endozoochory. We examined the diet and potential for dispersing Rosa rubiginosa and R. canina (Rosa spp.) of European rabbits introduced in a semiarid protected area of Argentina. We found entire seeds in 100% of the samples of Rosa spp. analysed (n = 11, 187 pellets). Our results indicate that the passage of Rosa spp. seeds through the digestive tract of rabbits (64%) did not diminish their viability in comparison to the seeds taken directly from fruits (66%) (χ2 = 0.09, p > 0.05). This study has identified new positive interactions between an invasive mammal and two invasive plants, a finding that suggests that these invader complexes could have a reciprocal effect on one another, which would potentially aid their invasive process in a semiarid protected area of Argentina.

Abstract The trade in marine ornamental fishes includes over 1800 species and is regarded as an introduction source for non-native fishes. Given this large pool of potential invaders, a targeted approach that evaluates risk for groups of fishes with demonstrated invasion history is both practical and feasible. In this way, proactive risk management frameworks can be used to identify risky species prior to introduction. Though the establishment of introduced marine ornamental species is uncommon, the invasion of Pterois volitans and P. miles in the western Atlantic Ocean has demonstrated the risks associated with the marine ornamental industry. These species, along with several other lionfishes, are regularly imported into the United States. We used the Aquatic Species Invasiveness Screening Kit to evaluate the risk of invasion for 14 species of traded lionfishes in the genera Pterois, Dendrochirus, and Parapterois for southeastern United States coastal waters of the Gulf of Mexico and Atlantic Ocean. The lionfish invasion is widely considered to be one of the worst marine invasions to date. Despite this, risk associated with the trade of lionfishes was estimated to be low, with notable exceptions. We identify Pterois russelii, Pterois lunulata, and Dendrochirus brachypterus as species with potentially elevated invasion risk. State and federal management agencies within the western Atlantic, Gulf of Mexico, and Caribbean should consider a detailed evaluation of these species to inform management action. This study is the one of the largest risk screening application of marine fishes to date and demonstrates the utility of prioritizing risk assessment of taxa found in pathways with related or otherwise similar species with previous invasion history.

Abstract Scent-marking is a way for individuals to indirectly communicate; however, the information is not exclusive to a single species and can be informative to a whole community. Prey or competitively inferior species can use scent-marks from predators/dominant species to avoid interactions. Cheetahs are a subordinate member of the large carnivore guild in Africa, yet olfactory communication in this guild has yet to be explored. We explore whether intraguild or intraspecific communication is occurring at cheetah scent-marking sites as well as whether dominant predator avoidance by cheetah occurs in response to predator presence or predator scent-marking. We recorded cheetah behaviour with video recording camera traps at cheetah scent-marking sites where a ‘landscape of fear’ was provided through natural predator presence or manipulated cues of predator presence. We found that cheetah took longer to return to scent-marking sites when a lion or a leopard was the previous species to visit the site. Moreover, cheetah increased the amount of time that they spent sniffing at scent-marking sites when another predator, as opposed to a cheetah, was the previous visitor. Finally, we noted that females never visited a scent-marking site after a predator was present nor when a predators’ scent-mark was present. Our results demonstrate that cheetahs use scent-marking sites for intraspecific communication, but also obtain intraguild information at these sites. Dominant predators can inhibit or at least delay important intraspecific communication around estrous events that occurs between cheetah at scent-marking sites, a novel form of interference competition. Significance statement Competition occurs between species, and dominant species deprive subordinate species from key resources. Individuals are able to avoid the cost of direct interactions with competitors by using cues (both direct and indirect) such as scents to assess such risks. Using video recording cameras at cheetah scent-marking sites, we provide novel insight into how dominant predator species shape cheetah behaviour through the use of avoidance by cheetah to the presence of dominant predators. Scent-marking sites are important to cheetah communication around reproduction opportunities and territory maintenance; however, dominant predator species’ cues blocked female reproductive signalling at the sites and delay male visitation. This serves as a novel form of interference competition for cheetah, but we suggest that cheetahs maintain communication through the use of multiple sites.

Leaf‐wood separation in terrestrial LiDAR data is a prerequisite for non‐destructively estimating biophysical forest properties such as standing wood volumes and leaf area distributions. Current methods have not been extensively applied and tested on tropical trees. Moreover, their impacts on the accuracy of subsequent wood volume retrieval were rarely explored. We present LeWoS, a new fully automatic tool to automate the separation of leaf and wood components, based only on geometric information at both the plot and individual tree scales. This data‐driven method utilizes recursive point cloud segmentation and regularization procedures. Only one parameter is required, which makes our method easily and universally applicable to data from any LiDAR technology and forest type. We conducted a twofold evaluation of the LeWoS method on an extensive dataset of 61 tropical trees. We first assessed the point‐wise classification accuracy, yielding a score of 0.91 ± 0.03 in average. Second, we evaluated the impact of the proposed method on 3D tree models by cross‐comparing estimates in wood volume and branch length with those based on manually separated wood points. This comparison showed similar results, with relative biases of less than 9% and 21% on volume and length respectively. LeWoS allows an automated processing chain for non‐destructive tree volume and biomass estimation when coupled with 3D modelling methods. The average processing time on a laptop was 90s for 1 million points. We provide LeWoS as an open‐source tool with an end‐user interface, together with a large dataset of labelled 3D point clouds from contrasting forest structures. This study closes the gap for stand volume modelling in tropical forests where leaf and wood separation remain a crucial challenge.

Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio‐temporal context of the study, providing predictive insights into community assembly processes from non‐manipulative observational data of species communities. The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user‐friendly r implementation. We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio‐temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single‐species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence–absence data. The package, along with the extended vignettes, makes JSDM fitting and post‐processing easily accessible to ecologists familiar with r.

The disparity in species’ traits arises through variation in the tempo and mode of evolution over time and between lineages. Understanding these patterns is a core goal in evolutionary biology. Here we present the comprehensively updated r package MOTMOT: Models Of Trait Macroevolution On Trees that contains methods to fit and test models of continuous trait evolution on phylogenies of extant and extinct species. MOTMOT provides functions to investigate a range of evolutionary hypotheses, including flexible approaches to investigate heterogeneous rates and modes of evolution, models of trait change under interspecific competition and patterns of trait change across significant evolutionary transitions such as mass extinctions. We introduce and test novel algorithms of heterogeneous tempo and mode of evolution that allow for phylogeny‐wide shifts in evolution at specific times on a tree. We use these new MOTMOT functions to highlight an exceptionally high rate of mammalian body mass evolution for 10 million years following the Cretaceous–Palaeogene mass extinction. These methods provide biologists and palaeontologists with the tools to analyse continuous trait data on phylogenies, including large trees of up to thousands of species.

The ancestral sequence reconstruction (ASR) is a molecular evolution technique that provides applications to a variety of fields such as biotechnology and biomedicine. To infer ancestral sequences with realistic biological properties, the accuracy of ASR methods is crucial. We previously developed an ASR framework for proteins, called ProtASR, which is based on our site‐specific stability‐constrained substitution (SCS) model with selection on protein folding stability against both unfolding and misfolding. This model improved the empirical substitution models traditionally applied in ASR without increasing the computational complexity. However, it adopted a global exchangeability matrix, an approximation that we overcome here by considering site‐specific exchangeability matrices based on the Halpern–Bruno approach. Here we present ProtASR2, a new version of our ASR framework that implements novel SCS models of protein evolution, namely mean‐field (MF) and wild‐type (WT). ProtASR2 under MF and WT SCS models outperforms empirical models and previous SCS models in terms of goodness of fit and site‐specific distributions of amino acids. Importantly, the framework infers ancestral sequences with more realistic predicted folding stability with respect to simulated sequences, while empirical, CAT and other SCS models tend to overestimate the folding stability. We applied ProtASR2 to explore the evolution of two protein families present in diverse Prokaryota and found fluctuations of protein stability over time in both families. ProtASR2 is available from https://github.com/miguelarenas/protasr and the new SCS models are also available from https://github.com/ugobas/protevol. Use of ProtASR2 will allow more realistic inferences of ancestral proteins in terms of folding stability with respect to those based on traditional empirical and CAT substitution models of protein evolution.

We examined the relative importance of competitor abundance and environmental variables in determining the species distributions of 175 bird species across North America. Unlike previous studies, which tend to model distributions in terms of presence and absence, we take advantage of a geographically extensive dataset of community time series to model the temporal occupancy of species at sites throughout their expected range.

We may be able to buffer biodiversity against the effects of ongoing climate change by prioritizing the protection of habitat with diverse physical features (high geodiversity) associated with ecological and evolutionary mechanisms that maintain high biodiversity. Nonetheless, the relationships between biodiversity and habitat vary with spatial and biological context. In this study, we compare how well habitat geodiversity (spatial variation in abiotic processes and features) and climate explain biodiversity patterns of birds and trees. We also evaluate the consistency of biodiversity–geodiversity relationships across ecoregions.

Large‐scale patterns in flower and fruit traits provide crucial insights into selection processes and the evolutionary history of plant lineages. To isolate and identify the role of selective pressures, including different plant–animal interactions and the factors driving trait evolution, we investigated the convergence and divergence between flower and fruit traits in shared environments.

Knowledge of broad‐scale biogeographical patterns of animal migration is important for understanding ecological drivers of migratory behaviours. Here, we present a flyway‐scale assessment of the spatial structure and seasonal dynamics of the Afro‐Palaearctic bird migration system and explore how phenology of the environment guides long‐distance migration.

In 2010 world governments agreed to eliminate, phase out or reform incentives that harm biodiversity by 2020. Yet few governments have even identified such incentives, never mind taking action on them. While some subsidies are well studied, such as in fisheries and fossil fuel production, there is an urgent need for the conservation community to study the potential effects a broader array of subsidies have on biodiversity. In addition, we need a better understanding of who benefits from these subsidies. We term this pursuit ‘subsidy accountability’, which is crucial but challenging work crossing disciplines and government ministries. It requires ecologists, forensic accountants, and policy wonks, calculating and forecasting the positive and negative effects of subsidies and their elimination on biodiversity and vulnerable human populations. The Intergovernmental Panel for Biodiversity and Ecosystem Services recently concluded that action on biodiversity loss requires transformative economic change; true action on subsidies is one step towards such change.

The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome‐level reference genome for T. obscurus was constructed using long‐read Pacific Biosciences (PacBio) Sequel sequencing and a Hi‐C‐based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single‐molecule real‐time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome‐scale scaffolds using a Hi‐C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one‐to‐one orthologous relationship was observed between the two species, supporting the chromosome‐level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu‐specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms.

Plant–animal interactions are fundamentally important in ecosystems, but have often been ignored by studies of climate-change impacts on biodiversity. Here, we present a trait-based framework for predicting the responses of interacting plants and animals to climate change. We distinguish three pathways along which climate change can impact interacting species in ecological communities: (i) spatial and temporal mismatches in the occurrence and abundance of species, (ii) the formation of novel interactions and secondary extinctions, and (iii) alterations of the dispersal ability of plants. These pathways are mediated by three kinds of functional traits: response traits, matching traits, and dispersal traits. We propose that incorporating these traits into predictive models will improve assessments of the responses of interacting species to climate change.

Mangroves sequester large quantities of carbon (C) that become significant sources of greenhouse gases when disturbed through land‐use change. Thus, they are of great value to incorporate into climate change adaptation and mitigation strategies. In response, a global network of mangrove plots was established to provide policy‐relevant ecological data relating to interactions of mangrove C stocks with climatic, tidal, plant community, and geomorphic factors. Mangroves from 190 sites were sampled across five continents encompassing large biological, physical and climatic gradients using consistent methodologies for the quantification of total ecosystem C stocks (TECS). Carbon stock data were collected along with vegetation, physical and climatic data to explore potential predictive relationships. There was a 28‐fold range in TECS (79 ‐ 2,208 Mg C ha‐1) with a mean of 856 ± 32 Mg C ha‐1. Belowground C comprised an average 85% of the TECS. Mean soil depth was 216 cm, ranging from 22 to> 300 cm, with 68 sites (35%) exceeding a depth of 300 cm. TECS were weakly correlated with metrics of forest structure, suggesting that aboveground forest structure alone cannot accurately predict TECS. Similarly, precipitation was not a strong predictor of TECS. Reasonable estimates of TECS were derived via multiple regression analysis using precipitation, soil depth, tree mass and latitude (R2 = 0.54) as variables. Soil carbon to a one meter depth averaged 44 % of the TECS. Limiting analyses of soil C stocks to the top 1 m of soils results in large underestimates of TECS as well as in the greenhouse gas emissions that would arise from their conversion to other land uses. The current IPCC Tier 1 default TECS value for mangroves is 511 Mg C ha‐1, which is only 60% of our calculated global mean. This study improves current assessments of mangrove C stocks providing a foundation necessary for C valuation related to climate change mitigation. We estimate mangroves globally store about 11.7 Pg C: an aboveground carbon stock of 1.6 Pg C and a belowground carbon stock of 10.2 Pg C). The differences in the estimates of total ecosystem carbon stocks based upon on climate, salinity, forest structure, geomorphology or geopolitical boundaries is not as much of an influence as the choice of soil depth included in the estimate. Choosing to limit soils to a 1‐m depth resulted in estimates of < 5 Pg whereas those that included the soil profile> 1‐m depth resulted in global carbon stock estimates that exceeded 11.2 Pg C.

Improved soil quality is required to sustainably achieve food security. Although the recycling of organic materials to fields is considered a key practice for improving soil quality, the effects of this procedure on productivity shows inconsistent results from strongly positive to negative. A long‐term field experiment was conducted over six crop seasons to test the hypothesis that large improvements in grain yield and soil quality of organic recycling could be achieved under high‐yielding management practices. The performance parameters of crop and soil were examined after applying two different organic amendment treatments: the continual application of manure in each season (chemical fertilizer [CF] + manure), and one application of a large volume of peat and vermiculite (PV; CF + PV); controls received CF only. All three treatments were applied at an optimal N rate with high‐yield management procedures. Treatments with organic soil amendments increased grain yields by 2.5–2.9 Mg ha−1 yr−1 compared with CF alone. These high‐yield plots had higher levels of soil organic carbon (65.3–111.0% higher), less bulk density (7.2–13.8% lower), and a larger proportion of macroaggregates in the topsoil. Compared with CF + manure treatment, the CF + PV produced similarly improved yields and soil properties, but the soil microbial biomass carbon and microbial community structure (including richness and diversity) differed between treatments. The recycling of organic materials was found to reduce farm profitability due to increases in material costs and labour. Our study provides an opportunity to increase both productivity and soil quality under integrated management, and the data will help adequately inform policies and strategic plans for food security and land use.

Ecological restorations of abandoned farmland have been performed in degraded ecosystems with the goal of increasing ecosystem sustainability. The environmental benefits of ecological restoration can at least be partially neutralized by enhanced nitrogen (N) loss and potential nitrous oxide (N2O) emissions via denitrification. However, few studies have focussed on comparative analysis of the contributions of ecological restoration strategies to soil denitrifying microbes, particularly in arid and semiarid degraded ecosystems, where N is often the limiting nutrient. In this study, artificial afforestation (artificial forest sites) and natural revegetation (grassland sites) of abandoned farmland have an enhanced effect on reducing potential denitrification rates (PDR) compared with farmland sites and orchard sites, leading to lower N losses and potential N2O emissions. Combined analyses indicated that the greatest differences in microbial abundance, species richness, and diversity were observed among different ecological restoration strategies. The abundance, richness, and diversities of denitrifying microbes (nirS, nirK, and nosZ genes) were decreased by natural revegetation and artificial afforestation, leading to attenuated denitrifying activity responsible for the reduced PDR. Notably, the abundance and diversity of denitrifying microbes were dominant variables that explained the changes in PDR (up to 0.96). Overall, our results contribute to a better understanding of the feedback of denitrifying microorganisms to ecological restoration strategies and how these microorganisms collaboratively contribute to N loss and potential N2O emissions in arid and semiarid degraded ecosystems.

Urban park managers are tasked with maintaining ecological function and quality of parks while also meeting visitor preferences. The purpose of this study was to better understand how managers currently manage vegetation in parks in Portland, Oregon. Twenty‐one urban park manager interviews were completed regarding 15 parks, which included natural‐passive use, recreational‐active use, and multi‐use park types. Responses were coded for themes and patterns of meaning. Mixed methods were used to evaluate the urban park manager interview data in the context of visitor interview and plant community composition data collected at the same parks. Non‐metric multidimensional scaling ordinations were used to identify urban park manager and visitor perspectives correlated with different park types and their vegetation. Across park types, managers discussed maintenance as a favorite aspect of plant management, while ecosystem management was often described by managers of natural‐passive use parks. Some managers indicated that they would make no changes to plant management, but the majority provided detailed recommendations such as enhancing maintenance, increasing staffing, adding plants, updating infrastructure, and improving plant species selection. There are opportunities to better meet the preferences of both managers and visitors by continuing to maintain large trees and trail/path vegetation for accessibility, removing invasive/harmful plants, and improving plant selection to include those which are heartier, more colorful, produce flowers, and are disease‐resistant, climate‐adapted, and provide habitat for a variety of species. While urban park managers discussed how they incorporated visitor preferences and accessibility in plant management, they also described limitations such as funding, staff resources, and undesirable visitor behaviors. Increased communication and collaboration among governmental agencies, non‐profit organizations, and community members, as well as continued investment in park management and interdisciplinary mixed methods research have the potential to enhance the many ecological and social benefits of urban parks.

The feeding ecology of soil animals is seldom investigated in the winter when the soil is covered with a layer of snow. Collembola (springtails) are winter-active arthropods that appear on the snow surface, especially on sunny days, and remain active in microhabitats under the snow. Since winter-active Collembola must be consuming food, we assessed the food resources for these Collembola with stable isotope and bacterial 16S rRNA gene amplicon sequencing methods. We collected two Desoria species from the snow surface and Tomocerus cf. jilinensis from subnivean microhabitats. The stable isotope signatures of winter-active Collembola species differed significantly from the soil litter layer. The isotopic signature of Desoria sp.1 was similar to the snow. Furthermore, the putative food resource (bacteria) ingested by Desoria sp.3 and Tomocerus cf. jilinensis had a similar isotopic signature as snow, but not litter. All three Collembola species ingested a large proportion of Cyanobacteria. Moreover, a large proportion of bacteria associated with Collembola were putative symbionts. Bacterial communities and their associated metabolic functions were more similar in the two congeneric Desoria species than with Tomocerus cf. jilinensis. Our findings suggest that winter-active Collembola mainly feed on resources present in the snow layer. Stable isotope and amplicon sequencing methods are promising techniques to evaluate the diets of soil animals that remain active in snow-covered soils.

Clay-sized soil minerals are known to protect organic carbon (OC) from mineralisation by formation of organo-mineral associations limiting its availability to microorganisms. The impact of soil fauna on these processes is poorly known. The aim of this study was to investigate the effect of earthworms on organic matter (OM) decomposition and association with minerals during a laboratory experiment. We used a model system consisting of fresh OM incubated with and without epigeic earthworms (Eisenia andrei and foetida) in presence of different types and amounts of phyllosilicates (kaolinite, montmorillonite) and an iron oxide (goethite) and combinations of these minerals. Our experimental setup included a high OM:mineral ratio to represent the soil-litter interphase. We monitored OC mineralization during 196 days. Additionally, we investigated physicochemical parameters and chemical OM characteristics of decomposition products by determination of water-soluble OC (WSOC) and acquisition of solid-state 13C NMR spectra. We also analysed microscale organisation of the organo-mineral associations produced with and without earthworms by transmission electron microscopy (TEM). Earthworms enhanced OC mineralisation in all treatments. They also led to greater reductions of OC emissions in the presence of minerals as compared to the mineral-free control, depending on the type and amount of minerals added. The presence of earthworms affected microbial biomass, the concentration of WSOC and increased the contribution of aromatic compounds to OM decomposition products. Microscale analyses by TEM showed that earthworms favoured association of minerals with partly degraded OM along with completely degraded material, while in absence of earthworms only completely degraded OM was associated with minerals. We conclude that earthworms impact OM decomposition through (1) their effect on microbial biomass and the physicochemical parameters of microbial habitat and (2) the formation of OM associations by changing the OM types associated to minerals and possibly by creating closer association of partly degraded OM and iron oxides. The stability of these associations remains to be investigated.

Plant germination ecology involves continuous interactions between changing environmental conditions and the sensitivity of seed populations to respond to those conditions at a given time. Ecologically meaningful parameters characterizing germination capacity (or dormancy) are needed to advance our understanding of the evolution of germination strategies within plant communities. The germination traits commonly examined (e.g., maximum germination percentage under optimal conditions) may not adequately reflect the critical ecological differences in germination behavior across species, communities, and seasons. In particular, most seeds exhibit primary dormancy at dispersal that is alleviated by exposure to dry after‐ripening or to hydrated chilling to enable germination in a subsequent favorable season. Population‐based threshold (PBT) models of seed germination enable quantification of patterns of germination timing using parameters based on mechanistic assumptions about the underlying germination physiology. We applied the hydrothermal time (HTT) model, a type of PBT model that integrates environmental temperature and water availability, to study germination physiology in a guild of coexisting desert annual species whose seeds were after‐ripened by dry storage under different conditions. We show that HTT assumptions are valid for describing germination physiology in these species, including loss of dormancy during after‐ripening. Key HTT parameters, the hydrothermal time constant (θHT) and base water potential distribution among seeds (Ψb(g)), were effective in describing changes in dormancy states and in clustering species exhibiting similar germination syndromes. θHT is an inherent species‐specific trait relating to timing of germination that correlates well with long‐term field germination fraction, while Ψb(g) shifts with depth of dormancy in response to after‐ripening and seasonal environmental variation. Predictions based on variation among coexisting species in θHT and Ψb(g) in laboratory germination tests matched well with 25‐yr observations of germination dates and fractions for the same species in natural field conditions. Seed dormancy and germination strategies, which are significant contributors to long‐term species demographics under natural conditions, can be represented by readily measurable functional traits underlying variation in germination phenologies.

Mycorrhizal fungi have considerable effects on soil carbon (C) storage, as they control the decomposition of soil organic matter (SOM), by modifying the amount of soil nitrogen (N) available for free‐living microbes. Through their access to organic N, ectomycorrhizal (ECM) fungi compete with free‐living soil microbes; this competition is thought to slow down SOM decomposition. However, arbuscular mycorrhizal (AM) fungi cannot decompose SOM, and therefore must wait for N to first be processed by free‐living microbes. It is unclear what form of N the ECM fungi and free‐living microbes compete for, or which microbial groups compete for N with ECM fungi. To investigate this, we focused on the N transformation steps (i.e., the degradation of high‐molecular‐weight organic matter, mineralization, and nitrification) and the microbes driving each step. Simple comparisons between AM forests and ECM forests are not sufficient to assert that mycorrhizal types would determine the N transformation steps in soil, because soil physiochemistry, which strongly affects N transformation steps, differs between the forests. We used an aridity gradient with large differences in soil moisture, pH, and SOM quantity and quality, to distinguish the mycorrhizal and physicochemical effects on N transformation. Soil samples (0–10 cm depth) were collected from AM‐symbiotic black locust forests under three aridity levels, and from ECM‐symbiotic oak forests under two aridity levels. Soil physicochemical properties, extractable N dynamics and abundance, composition, and function of soil microbial communities were measured. In ECM forests, the ammonia‐oxidizing prokaryotic abundance was low, whereas that of ECM fungi was high, resulting in lower nitrate N content than in AM forests. Since ECM forests did not have lower saprotrophic fungal abundance and prokaryotic decompositional activity than the AM forests, the hypothesis that ECM fungi could reduce SOM decay and ammonification by free‐living microbes, might not hold in ECM forests. However, the limitation of ECM fungi on nitrate N production would result in a feedback that will accelerate plant dependence on these fungi, thereby raising soil C storage through an increase in the ECM biomass and plant C investment in soils.

Following natural disturbances, additional anthropogenic disturbance may alter community recovery by affecting the occurrences of species, functional groups, and evolutionary lineages. However, our understanding of whether rare, common, or dominant species, functional groups, or evolutionary lineages are most strongly affected by an additional disturbance, particularly across multiple taxa, is limited. Here, we used a generalized diversity concept based on Hill numbers to quantify the community differences of vascular plants, bryophytes, lichens, wood‐inhabiting fungi, saproxylic beetles, and birds in a storm‐disturbed, experimentally salvage logged forest. Communities of all investigated species groups showed dissimilarities between logged and unlogged plots. Most species groups showed no significant changes in dissimilarities between logged and unlogged plots over the first seven years of succession, indicating a lack of community recovery. In general, the dissimilarities of communities were mainly driven by rare species. Convergence of dissimilarities occurred more often than divergence during the early stages of succession for rare species, indicating a major role in driving decreasing taxonomic dissimilarities between logged and unlogged plots over time. Trends in species dissimilarities only partially match the trends in dissimilarities of functional groups and evolutionary lineages, with little significant changes in successional trajectories. Nevertheless, common and dominant species contributed to a convergence of dissimilarities over time in the case of the functional dissimilarities of wood‐inhabiting fungi. Our study shows that salvage logging following disturbances can alter successional trajectories in early stages of forest succession following natural disturbances. However, community changes over time may differ remarkably in different taxonomic groups and are best detected based on taxonomic, rather than functional or phylogenetic dissimilarities.

Natural ecosystems provide humans with different types of ecosystem services, often linked to biodiversity. The dilution effect (DE) predicts a negative relationship between biodiversity and risk of infectious diseases of humans, other animals, and plants. We hypothesized that a stronger DE would be observed in studies conducted at smaller spatial scales, where biotic drivers may predominate, compared to studies at larger spatial scales where abiotic drivers may more strongly affect disease patterns. In addition, we hypothesized a stronger DE in studies from temperate regions at mid latitudes than in those from subtropical and tropical regions, due to more diffuse species interactions at low latitudes. To explore these hypotheses, we conducted a meta‐analysis of observational studies of diversity–disease relationships for animals across spatial scales and geographic regions. Negative diversity–disease relationships were significant at small (combined site and local), intermediate (combined landscape and regional), and large (combined continental and global) scales and the effect did not differ depending on size of the study areas. For the geographic region analysis, a strongly negative diversity–disease relationship was found in the temperate region while no effect was found in the subtropical and tropical regions. However, no overall effect of absolute latitude on the strength of the dilution effect was detected. Our results suggest that a negative diversity–disease relationship occurs across scales and latitudes and is especially strong in the temperate region. These findings may help guide future management efforts in lowering disease risk.

Many plant and fungal species use volatile organic compounds (VOCs) as chemical signals to convey information about the location or quality of their fruits or fruiting bodies to animal dispersers. Identifying the environmental factors and biotic interactions that shape fruit selection by animals is key to understanding the evolutionary processes that underpin chemical signaling. Using four Elaphomyces truffle species, we explored the role of fruiting depth, VOC emissions, and protein content in selection by five rodent species. We used stable isotope analysis of nitrogen (δ15N) in truffles to estimate fruiting depth, proton‐transfer‐reaction mass spectrometry to determine volatile emission composition, and nitrogen concentrations to calculate digestible protein of truffles. We coupled field surveys of truffle availability with truffle spore loads in rodent scat to determine selection by rodents. Despite presumably easier access to the shallow fruiting species, E. americanus (0.5‐cm depth) and E. verruculosus (2.5‐cm depth), most rodents selected for truffles fruiting deeper in the soil, E. macrosporus (4.1‐cm depth) and E. bartlettii (5.0‐cm depth). The deeper fruiting species had distinct VOC profiles and produced significantly higher quantities of odiferous compounds. Myodes gapperi (southern red‐backed vole), a fungal specialist, also selected for truffles with high levels of digestible protein, E. verruculosus and E. macrosporus. Our results highlight the importance of chemical signals in truffle selection by rodents and suggest that VOCs are under strong selective pressures relative to protein rewards. Strong chemical signals likely allow detection of truffles deep within the soil and reduce foraging effort by rodents. For rodents that depend on fungi as a major food source, protein content may also be important in selecting truffles.

Tropical forests hold 30% of Earth’s terrestrial carbon and at least 60% of its terrestrial biodiversity, but forest loss and degradation are jeopardizing these ecosystems. Although the regrowth of secondary forests has the potential to offset some of the losses of carbon and biodiversity, it remains unclear if secondary regeneration will be affected by climate changes such as higher temperatures and more frequent extreme droughts. We used a data set of 10 repeated forest inventories spanning two decades (1999–2017) to investigate carbon and tree species recovery and how climate and landscape context influence carbon dynamics in an older secondary forest located in one of the oldest post‐Columbian agricultural frontiers in the Brazilian Amazon. Carbon accumulation averaged 1.08 Mg·ha−1·yr−1, and species richness was effectively constant over the studied period. Moreover, we provide evidence that secondary forests are vulnerable to drought stress: Carbon balance and growth rates were lower in drier periods. This contrasts with drought responses in primary forests, where changes in carbon dynamics are driven by increased stem mortality. These results highlight an important climate change–vegetation feedback, whereby the increasing dry‐season lengths being observed across parts of Amazonia may reduce the effectiveness of secondary forests in sequestering carbon and mitigating climate change. In addition, the current rate of forest regrowth in this region was low compared with previous pan‐tropical and Amazonian assessments—our secondary forests reached just 41.1% of the average carbon and 56% of the tree diversity in the nearest primary forests—suggesting that these areas are unlikely to return to their original levels on politically meaningful time scales.

Sex ratios are commonly skewed and variable in wild populations, but few studies track temporal trends in this demographic parameter. We examined variation in the operational sex ratio at two protected and declining breeding colonies of Magellanic Penguins (Spheniscus magellanicus) in Chubut, Argentina. Penguins from the two colonies, separated by 105 km, migrate north in the non‐breeding season and have overlapping distributions at sea. Conditions during the non‐breeding season can impact long‐term trends in operational sex ratio (i.e., through sex‐specific survival) and interannual variation in operational sex ratio (i.e., through sex‐specific breeding decisions). We found an increasingly male‐biased operational sex ratio at the two disparate colonies of Magellanic Penguins, which may contribute to continued population decline. We also found that the two colonies showed synchronous interannual variation in operational sex ratio, driven by variation in the number of females present each year. This pattern may be linked to sex‐specific overwintering effects that cause females to skip breeding, i.e., to remain at sea rather than returning to the colony to breed, more often than males. Contrary to our predictions, colony‐wide reproductive success was not lower in years with a more male‐biased operational sex ratio. We did find that males showed more evidence of fighting and were less likely to pair when the operational sex ratio was more male biased. Our results highlight an indirect mechanism through which variation in the operational sex ratio can influence populations, through a higher incidence of fighting among the less abundant sex. Because biased sex ratios can reduce the size of the breeding population and influence rates of conflict, tracking operational sex ratio is critical for conservation.

In the last few decades, riverine sediment flux to the coastal zones has been decreasing globally. The sediment flux from rivers to seas is usually estimated based on the lowermost gauging stations free of tides in the rivers, for example the Yangtze River. Knowledge of decadal sediment budget and the morphological evolution in the tidal reach is still limited. Here, using historical bathymetry of the tidal reach of the Yangtze, the changes in the sediment budget and local morphology in this reach for three periods between 1970 and 2008 were investigated. In terms of input sediment flux, Period I 1970–1992 is a relatively steady period, Period II 1992–2003 is a decline period with a significant decrease in the sediment flux, and Period III 2003–2008 is a decline period after the closure of the Three Gorges Dam (TGD). The reach was nearly in equilibrium during Period I. Net erosion occurred in the reach during both the pre- and post-TGD decline periods 1992–2003 and 2003–2008, with annual erosion of approximately 65 and 37 Mt/yr, respectively. The contribution of the annual erosion in the reach to the annual sediment flux at the downstream end of the reach increased from around 16.9% during 1992–2003 to 19.1% during 2003–2008. These changes in the sediment budget are closely related to the decrease in the input sediment flux, coarsening of the sediment grain size after the closure of the TGD, and changes in the riverine water flux and tidal conditions. Characterized by a length scale of 4–32 km, local deposition/erosion patterns were quite complex, which relates to the complexity of the local geometry, bathymetry and flow condition. The horizontal location of the thalweg of the reach had limited changes during 1992–2008, likely owing to the fixed riverbank due to human intervention.

Cylindrospermopsin (CYN) is a cyanotoxicant which occurrence is increasing due to climate change. Cylindrospermopsin is able to exert damage in the organism at several levels, among them, in the nervous system. Moreover, it is important to take into account that it is not usually present isolated in nature, but in combination with some other pollutants, being the case of the pesticide chlorpyrifos (CPF). Thus, the aim of the present work was to assess the effects of the interaction of CYN in combination with CPF in the human neuroblastoma cell line SH-SY5Y by evaluating cytotoxicity and mechanistic endpoints. The mixtures 0.25 + 21, 0.5 + 42, 1 + 84 μg/mL of CYN + CPF based on cytotoxicity results, were evaluated, and the isobologram method detected an antagonistic effect after 24 and 48 h of exposure. Moreover, although no alterations of reactive oxygen species were detected, a significant decrease of glutathione levels was observed after exposure to both, CPF alone and the combination, at all the concentrations and times of exposure assayed. In addition, CYN + CPF caused a marked decrease in the acetylcholinesterase activity, providing similar values to CPF alone. However, these effects were less severe than expected. All these findings, together with the morphological study results, point out that it is important to take into account the interaction of CYN with other pollutants. Further research is required to contribute to the risk assessment of CYN and other contaminants considering more realistic exposure scenarios.

The potential for the phytoremediation of halophytes has been widely recognized. However, the effects of salt on Cd accumulation characteristics in different halophytic species, which may also be related to their salt tolerance, are still unclear. This study investigated the effects of salinity on Cd accumulation and distribution in two distinct halophytes, Suaeda glauca (euhalophyte) and Limonium aureum (recretohalophyte). Seedlings of the two species were treated with 0, 3, and 6 mg kg−1 soil Cd in combination with or without 0.3% NaCl in a pot experiment. The amount of Cd within the rhizosphere and plant tissues, plant biomass, and the subcellular distribution and chemical forms of Cd were examined. Results showed that the addition of NaCl significantly increased Cd bioavailability at high Cd levels due to the rhizosphere acidification effect. Meanwhile, salinity differently impacted plant biomass allocation, and enhanced Cd uptake and translocation in both studied halophytes. Excess Cd was excreted from the leaf surface, possibly by salt glands of L. aureum, with the salinity facilitating this process. Majority of the Cd was found within the cell walls and vacuolar compartments of two species. However, S. glauca plants had higher proportions of inactive Cd (extracted by 2% HAc and 0.6 M HCl) and lower proportions of active Cd (extracted by 80% ethanol and water), as opposed to L. aureum, which would better inform S. glauca's higher Cd accumulation. Based on these results, S. glauca seems more applicable for phytomanagement of Cd-contaminated saline soils due to its higher capacity for Cd enrichment and tolerance amplified by NaCl.

Monitoring variations in vegetation net primary productivity (NPP) contributes greatly to the evaluation of terrestrial ecosystem structure and function. Current research has focused on the trend changes of vegetation productivity but has largely ignored spatial correlation. This study selected MOD17A3 NPP data in Inner Mongolia to explore the spatiotemporal variations of NPP using spatial autocorrelation indices (Global Moran’s I, Getis-Ord General G, Getis-Ord Gi*, and Anselin Local Moran’s I). This is helpful to examine whether NPP in Inner Mongolia has exhibited significant spatial cluster based on temporal variations and spatial patterns. NPP in Inner Mongolia has shown significant spatial cluster in high-value areas from 2000 to 2014 and demonstrated a polarized distribution. Although the east part of the study area generally showed a high NPP pattern, the northeast turned to low NPP pattern in 2001, 2004, 2007, and 2010 and the southeast turned to low NPP pattern in 2009 and 2013. The former variations were primarily affected by precipitation, while the latter variations were affected by both hydrothermal conditions and human activities. These results are useful to analyze spatial correlations and local abnormalities of NPP and provide references for integrated ecosystem management in Inner Mongolia.

Land use change and agricultural intensification in developing countries affect terrestrial carbon (C) stocks, CO2 efflux, microbial communities and overall soil health. This study assesses the effects of four land use types typical for northern Ethiopia (forests, exclosures, grazing lands and intensively cultivated croplands) on various soil health indicators. We quantified and compared microbial biomass carbon (MBC), water extractable organic carbon (WOC), metabolic quotient (qCO2), substrate use efficiency (SUE) and dynamics of 14C-labelled glucose added to soil. Irrespective of the land use, MBC but not SUE decreased 2- to 8-fold with increasing depth, demonstrating the C limitation of subsoil microbial communities under all land use forms. Sandy soils, however, which permit seepage and leaching of WOC into lower layers and promote subsoil microbial communities, adapted to frequent input of easily accessible C substrates. Significantly higher qCO2 were recorded in subsoils compared to topsoils, especially in croplands with low MBC. In croplands, high glucose-14C incorporation (≈20%) into their low microbial biomass indicates a high SUE and reflects a better nutrient supply of these microbial communities. Mineralization of up to 95% of 14C-labeled glucose in topsoils of forest and grazing lands was higher than in croplands, and exclosures never reached the level of natural ecosystems. This demonstrates that 6–10 years of exclosure establishment does not result in soil microbial communities and soil C dynamics resembling those of natural forests. Our study demonstrates that land use can negatively affect the ecological performance of microbial communities and that these impacts are more severe in sandy than in clayey soils. Mitigation strategies such as minimum tillage or residue retention in intensively cultivated croplands can increase microbial abundance and activity and help ensure environmental sustainability and mitigation of climate change. Nonetheless, such measures need to be carefully accompanied by monitoring indicators of soil health to confirm the sustainability of the chosen mitigation strategies.

Based on the first-hand data of field investigation, existing literature, books and plant specimens database resources, the complete and available spatial database of wild Akebia trifoliate in China was established firstly. After analyzing the geographical distribution of Akebia trifoliate and its ecological factors, such as climate, soil and topographic characteristics, based on the existing literature, we selected 16 climatic indicators and used statistical analysis to study key climatic variables affecting its growth from a macro perspective. The results show that: (1) According to the characteristic roots and contribution rate obtained by principal component method, three principal factors are determined. Their corresponding value of three principal factors were 6.0538 and 37.84%, 4.7487 and 29.68%, 3.3822 and 21.14% respectively. All the characteristic roots indicate that the three principal factors are playing a dominant role in climate variables of influencing the distribution of Akebia trifoliate. (2) The first principal factor is called “heat factor”, the most important role determining geographical distribution of Akebia trifoliate, including the variables with larger factor load such as active accumulated temperature (≥10℃), warm index, biological temperature and annual average temperature. It shows that Akebia trifoliate tends to grow in areas with higher heat conditions. The second principal factor is called “humidity factor”, the second role for Akebia trifoliate, including the variables with larger factor load such as evapotranspiration rate, humidity index, annual precipitation, growing season precipitation and relative humidity. So it shows that Akebia trifoliate tends to be in areas with sufficient precipitation and high humidity. The third principal factor is called “illumination factor”, including the variables with larger load such as annual sunshine hours, growing season sunshine hours and extreme low temperature. So Akebia trifoliate likes the areas with relatively short sunshine hours. (3) Heat factor and humidity factor are the main limiting factors for its growth. The significant climatic variables offer a basis for the selection of ecological factors and the determination of weight in the suitability analysis of Akebia trifoliate. These results could provide a theoretical basis for the artificial cultivation of Akebia trifoliate. The ideas and methods for wild Akebia trifoliate in this paper could give a reference for the study of other valuable wild plants.

As forest fragmentation continues in many parts of the tropics, the conservation value of forest remnants remains controversial. Our study aimed to assess the structure and tree species diversity of mixed dipterocarp forest remnants from the Planted Forest Zone (PFZ) located in the Bintulu Division, Sarawak, compared with a forest considered relatively undisturbed (i.e. that has experienced no recent logging activities). We also compared three plot methods (50 × 50 m, 20 × 50 m and 10 × 50 m plots) in order to evaluate which could be used for time- and cost-effective inventories of structure and tree species diversity in fragmented forests. No significant differences were found between the fragmented forests and the relatively undisturbed forest for stem density, species richness and diversity indices (Shannon and Simpson). Dissimilarities in species, genus and family composition were observed between fragmented and relatively undisturbed forest, as well as between forest remnants themselves. These dissimilarities were likely to be related to intrinsic variation in these highly diverse tropical forests. However, an unusually high abundance of pioneer species (i.e. Macaranga) was found in plots from forest remnants. The forest remnants also had significantly lower basal areas due to a lack of trees in large diameter classes, which is likely a result of impacts from past logging activities. Otherwise, our results highlight the current high conservation value of the forest remnants—although the studied communities are likely to experience time-delayed shifts in species composition and/or extinctions in the future, with the effect of fragmentation on biodiversity being currently underestimated. Finally, for further studies of fragmented forests we recommend the use of 10 × 50 m plots which are faster and easier to implement in the field while providing estimates of structure and tree species diversity that are consistent with those from larger plots.

Canada’s oil sands industry continues to expand and the volume of diluted bitumen (dilbit) transported across North America is increasing, adding to spill risk and environmental contamination. Dilbit exposure is known to cause adverse effects in fish, but linking molecular and cellular changes with ecologically-relevant individual performance metrics is needed to better understand the potential consequences of a dilbit spill into the aquatic environment. Therefore, this study examined the effects of dilbit exposure on subcellular responses in cardiac and skeletal muscle in relation to swimming performance in a migratory fish species at risk of exposure, Atlantic salmon. Smolts were exposed subchronically to environmentally relevant concentrations of the water-soluble fraction of dilbit (WSFd) for 24 d, and then a subset of exposed fish underwent a depuration period of 7 or 14 d, for a total of 3 experimental time points. At each time point, repeat swimming performance was assessed using sequential critical swimming speed tests (Ucrit) separated by a 24 h rest period, and then several tissues were collected to determine biotransformation enzyme activation, energetic responses, and gene expression changes. Ucrit was unaffected in fish exposed to 67.9 μg/L total initial polycyclic aromatic compounds (PAC), but fish showed a decreased reliance on lipid metabolism for adenosine triphosphate (ATP) in the heart that was maintained through 7 d depuration. In contrast, Ucrit increased in fish exposed to 9.65 μg/L PAC, corresponding to an increased reliance on anaerobic metabolic pathways in cardiac and red skeletal muscle, with partial recovery after 7 d depuration. As expected, at both concentrations WSFd hepatic cyp 1A-mediated biotransformation reactions increased, as measured by EROD activity, which remained elevated for 7 d but not after 14 d depuration. Transcript abundance of cyp1a was also increased in muscle tissue and recovered by 14 d depuration. The expression of other stress-related genes increased in white muscle of dilbit-exposed fish, but were largely unchanged in cardiac and red muscle. The transcriptional profile of cardiac tissue was compared to that of sockeye salmon similarly exposed to WSFd in a previous experiment, and is provided in supplemental text. Combined, these results demonstrate that dilbit exposure alters gene expression and enzyme activities related to xenobiotic exposure, cellular stress, and muscle energetics in juvenile Atlantic salmon without impairing swimming performance, and that most of these changes are recoverable within 14 d depuration.

Abstract Garlic mustard is an invasive Eurasian biennial that has spread throughout the eastern United States and southern Canada. Populations of this plant vary in their susceptibility to Erysiphe cruciferarum, a causal agent of powdery mildew disease in Brassicaceous plants. We examined whether there were biogeographic patterns in the distribution of resistance in invasive North American and native European populations of this plant. We grew plants from 78 invasive and 20 native populations and screened them for powdery mildew resistance in the greenhouse. We found that populations were mostly monomorphic for either resistance or susceptibility but that some polymorphic populations were found from both continents. The proportion of populations showing resistance versus susceptibility was similar in both Europe and North America. Within continents, the spatial distribution of resistant and susceptible populations did not deviate significantly from random. We also examined whether the possession of the resistance trait alter intraspecific competitive dynamics. In two trials, we competed plants from resistant and susceptible populations in a target-neighbor design in the presence and absence of powdery mildew inoculum and examined the growth of the target plant. Target plants from resistant populations were overall larger than target plants from susceptible populations. Target plants were overall larger when grown in competition with susceptible neighbors. Further, resistant target plants showed a greater degree of release from competition when grown with a susceptible neighbor versus a resistant neighbor than the degree of release shown by susceptible target plants. This suggests a benefit of possessing the resistance trait with little apparent costs which should promote selection for this trait within plant populations.

Abstract Invasive species are a major driver of global biodiversity loss. However, we often lack a mechanistic understanding why some non-native species become invasive. Missing coevolutionary history between invasive predators and native prey can lead to a lack of predator avoidance by native prey and consequently higher consumption rates by invasive predators. We compared predation rates of four native European lady beetle species and the invasive lady beetle species Harmonia axyridis Pallas (Coleoptera: Coccinellidae), using the native pea aphid Acyrthosiphon pisum Harris (Hemiptera: Aphididae) for prey. Here, we also quantified initial dropping of A. pisum from host plants. In an additional plant-choice experiment, we tested for aphid avoidance of plants bearing lady beetle cues. Differences in predation were determined by predator body size. Initial dropping of aphids did not differ between the invasive lady beetle species H. axyridis and the remaining native lady beetle species. However, A. pisum showed no avoidance behavior towards H. axyridis cues, but to cues of the most voracious native species. Thus, relatively large body size and missing chemical cue avoidance by aphids can benefit the invasive H. axyridis.

Abstract Predicting changes in the abundance and distribution of introduced species over time is difficult, but clues regarding the underlying causes of these changes may come from long-term surveys. Resurveys conducted over large spatial scales, for example, can be used to discriminate between site-specific causes of decline and those that act at the population level. Here we used regional resurvey data to address changes in Argentine ant site occupancy in urban, agricultural, and natural environments in coastal southern California. We resurveyed 145 locations originally sampled 12–14 years ago and observed a slight decrease in Argentine ant site occupation, from 85 to 79% across all sites. At the majority of sites where apparent absences were recorded, however, the Argentine ant had merely retreated outside of the proscribed sampling area (a 25-m radius circle) and was still present within 80 m, on average, of the original sampling point. This finding thus suggests that the apparent absences observed most likely reflect contractions of the area occupied by polydomous supercolonies, possibly in response to local-scale changes in environmental conditions, as opposed to processes acting at larger spatial scales. We also conducted back-to-back annual resurveys (in 2018 and 2019) of all urban sampling points (n = 95) to quantify annual turnover in site occupancy. These resurveys revealed 2.4% site turnover with 97% (92/95) sites being classified as either presences (n = 85) or absences (n = 7) in both years. Our results support the findings of resurveys conducted in northern California, where Argentine ant distributions have slowly expanded over decadal time scales. Historical resurveys can provide insights into why populations of introduced species change over time and should incorporate an appreciation of how invader traits affect detectability.

Network analysis of infectious disease in wildlife can reveal traits or individuals critical to pathogen transmission and help inform disease management strategies. However, estimates of contact between animals are notoriously difficult to acquire. Researchers commonly use telemetry technologies to identify animal associations; but such data may have different sampling intervals and often captures a small subset of the population. The objectives of this study were to outline best practices for telemetry sampling in network studies of infectious disease by determining (1) the consequences of telemetry sampling on our ability to estimate network structure, (2) whether contact networks can be approximated using purely spatial contact definitions, and (3) how wildlife spatial configurations may influence telemetry sampling requirements.

1. Animal social networks are often used to describe dynamic social systems, where individual behaviour generates network‐level structures that subsequently influence individual‐level behaviour. This interdependence between individual behaviour and group structuring is of central concern for questions concerning the evolution and development of social systems and collective animal behaviour more generally.

Aggression is a quantitative trait deeply entwined with individual fitness. Mapping the genomic architecture underlying such traits is complicated by complex inheritance patterns, social structure, pedigree information and gene pleiotropy. Here, we leveraged the pedigree of a reintroduced population of grey wolves (Canis lupus) in Yellowstone National Park, Wyoming, USA, to examine the heritability of and the genetic variation associated with aggression. Since their reintroduction, many ecological and behavioural aspects have been documented, providing unmatched records of aggressive behaviour across multiple generations of a wild population of wolves. Using a linear mixed model, a robust genetic relationship matrix, 12,288 single nucleotide polymorphisms (SNPs) and 111 wolves, we estimated the SNP‐based heritability of aggression to be 37% and an additional 14% of the phenotypic variation explained by shared environmental exposures. We identified 598 SNP genotypes from 425 grey wolves to resolve a consensus pedigree that was included in a heritability analysis of 141 individuals with SNP genotype, metadata and aggression data. The pedigree‐based heritability estimate for aggression is 14%, and an additional 16% of the phenotypic variation was explained by shared environmental exposures. We find strong effects of breeding status and relative pack size on aggression. Through an integrative approach, these results provide a framework for understanding the genetic architecture of a complex trait that influences individual fitness, with linkages to reproduction, in a social carnivore. Along with a few other studies, we show here the incredible utility of a pedigreed natural population for dissecting a complex, fitness‐related behavioural trait.

Many diapausing insects undergo a nutrient storage period prior to their entry into diapause. Bumble bee queens diapause as adults in the winter preceding their spring nest initiation period. Before diapause, they sequester glycogen and lipids, which they metabolize during the overwintering period. We used RNA sequencing to examine how age and nectar diet (specifically, the concentration of sucrose in nectar) impact gene expression in the pre‐overwintering bumble bee queen fat body, the “liver‐like” organ in insects with broad functions related to nutrient storage and metabolism. We found that diet on its own, and in combination with age, impact the expression of genes involved in detoxification. Age was also a strong driver of gene expression, especially at earlier ages (up to 3 days). In addition to these molecular correlates of diet and age, we also found a putative molecular signature of diapause entry or preparation in adult queens in the oldest age group (12 days) fed the most sucrose‐rich diet, based on comparisons between our dataset and another transcriptome dataset from bumble bee queens. This transcriptomic pattern suggests that preparation for (or entry into) diapause might be in part mediated by nutritional state in bumble bee queens. Collectively, these findings show that there are molecular processes in the fat body that are responsive to sucrose levels in the diet and/or associated with age‐related maturational changes. Better understanding of these processes may shed light on important aspects of bumble bee biology, such as queen responses to nutritional and other forms of stress, and the factors that regulate their entrance into diapause.

Hybridization and introgression can have complex consequences for both species evolution and conservation. Here, we investigated the origin and characteristics of a putative hybrid zone between two South American poison dart frog species, O. anchicayensis and the critically endangered O. lehmanni, which are heavily sought after on the illegal pet market. Using a combination of phenotypic (49 traits) and genomic (ddRADseq) data, we found that the putative hybrids are morphologically distinct from their parental species and confirmed genomic signatures of admixture in these populations. Several lines of evidence (hybrid indices, interspecific hybrid heterozygosity, genomic clines, comparisons with simulated hybrids and demographic modelling) support the conclusion that these populations are not comprised of early‐generation hybrids and thus, they likely did not arise as a result of illegal translocations associated with wildlife trafficking. Instead, they likely represent an independent lineage which has persisted through isolation and has only relatively recently re‐established gene flow with both parental species. Furthermore, we detected signals of differential introgression from parental species into these hybrid populations which suggest relaxed stabilizing selection on these aposematic color morphs, potentially via context‐dependent female choice. These populations thus provide a fascinating window into the role of hybridization, isolation and female choice in the diversification of South American poison dart frogs. In addition, our results underline the importance of landscape conservation measures to protect, not only known localities of nominal species, but also the phenotypic and genomic variation harbored by admixed lineages which represent crucial repositories for the impressive diversity in this system.

Davidia involucrata Baill, also known as the dove‐tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report a chromosome‐scale genome of this species using single‐molecule real‐time long reads and chromosome conformation capture (Hi‐C) techniques. This species has a larger genome size of 1,169 Mb and contains relatively more genes (42,554) than the closely related species Camptotheca acuminata (397 Mb and 31,825 genes). Both species shared one recent whole genome duplication before their divergence. The expansion of the repetitive elements after their divergence contributed greatly to the increase in the genome size of the dove‐tree. The photosynthesis‐related genes were almost absent or showed reduced expression in the bracts of the dove‐tree, while the defense‐ and chemical‐related genes increased greatly, highlighting the important roles of the bracts in protecting flowers and attracting pollinators. The effective population size of the dove‐tree continuously decreased during the Quatenary climate changes. Such climate sensitivity should be fully considered in conserving this relict endangered species in the context of continuous climate warming in the future.