Abstract Aims This study assesses the relative effects of hydrology and colonization by vascular plants on belowground C and N mobilization, and emission of CO2 and CH4 in an extracted bog under restoration in Alberta (Canada). Methods A wet (high water table) and dry (low water table) area were identified at the site and plots with cottongrass (Eriophorum vaginatum) or bare peat were established in each area. Plant growth, peat and porewater dissolved C (DOC) and N (TDN), microbial biomass and the emissions of CO2 and CH4 were monitored at the plots throughout the growing season. Results The largest concentrations of DOC were measured in dry and bare sites. Lower E2:E3 ratios suggested a higher aromaticity of the DOC at these sites that were net sources of CO2 and CH4. The concentration of TDN was greater in plots with cottongrass and high water table, supporting a more abundant microbial biomass. Cottongrass dominated plots also had larger gas emissions as compared to bare plots even though they were net C sinks due to their high photosynthetic rates. Conclusion Maintaining a high water table is key to reducing peatland C losses. While vascular plant presence seems to prime the release of N and greenhouse gases, the inputs of C exceeded the losses and recovered the C sink function of the peatland ecosystem in the short term. Carbon inputs are maximized under high water table and plant presence.

Abstract Aims To explore the mechanisms responsible for salt tolerance in Brassicaceae species, a multifactorial approach was used to clarify the functional traits underlying the differential salt tolerance in two Lepidium species, namely the halophyte L. latifolium and its glycophyte relative, L. sativum. Methods Parameters related to photosynthesis, nitrogen assimilation, ion accumulation, water relations and succulence, osmotic adjustment, phenolics metabolism, antioxidative defense, nitric oxide (NO) level and the expression of Na+ antiporter (SOS1 and NHX) were analyzed in plants grown under salt stress in hydroponics. Results In addition to significant differences regarding the majority of salt tolerance indicators, a characteristic early boost, 52 h after exposure to salt, was observed in the concentration of H2O2 and NO in the halophyte, which was almost absent in the glycophyte. Following the application of detrended component analysis, discrimination between the glycophyte and halophyte could only be performed via temporal curves in the antioxdative components and NO, and less effectively, by phenolics metabolism. Conclusion H2O2 and NO signaling and the adaptive modification of phenolics metabolism play crucial roles in determining the halophytic behavior of L. latifolium. These data may result in new insights concerning the studies on halophytism in the Brassicaceae.

Abstract Organisms with annual life cycles are exposed to life stage specific thermal environments across seasons. Seasonal variation in thermal environments can vary across years and among sites. We investigated how organisms with annual life cycles respond to predictable seasonal changes in temperature and unpredictable thermal variation between habitats and years throughout their lives. Field surveys and historical records reveal that the spatially and temporally heterogeneous thermal environments inhabited by the annual mayfly Ephemerella maculata (Ephemerellidae) shift the date for transition to the next, life stage, so that the thermal phenotype of each life stage matches the thermal environment of the specific habitat and year. Laboratory studies of three distinct life stages of this mayfly reveal that life stage transitions are temperature dependent, facilitating timing shifts that are synchronized with the current season’s temperatures. Each life stage exhibited specific thermal sensitivity and performance phenotypes that matched the ambient temperature typically experienced during that life stage. Our study across the whole life cycle reveals mechanisms that allow organisms to achieve lifetime eurythermy in a dynamic seasonal environment, despite having narrower thermal ranges for growth and development in each life stage.

Abstract Avian plumage harbors various pathogens such as feather-degrading bacteria, which have the potential to reduce host fitness. A growing body of evidence suggests that the secretion of the uropygial gland of birds—preen oil—acts as one of the first lines of defence against harmful bacteria. However, previous studies on the antimicrobial impact of preen oil have yielded controversial results. The impact of preen oil on bacterial densities of feathers was experimentally investigated in two passerine species: great tits Parus major and pied flycatchers Ficedula hypoleuca. More specifically, we tested whether the antibacterial effect of the preen oil secreted by the same individual differs from that of the preen oil originating from the gland of other species. In the laboratory, ventral feathers were treated with preen oil from (1) an individual’s own gland, (2) from the gland of another passerine species, or (3) from the gland of a phylogenetically distant bird species. We detected a significant antibacterial effect of preen oil on bacteria that were attached to feathers, though the effect did not depend on whether the oil originated from the individual’s own gland or from the gland of another bird species. However, treatment with preen oil suppressed the density of bacteria more in the pied flycatcher than in the great tit. This is the first study providing experimental evidence that preen oil represents an important antimicrobial mechanism against those plumage bacteria that are attached to feathers.

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.

Soil is a non-renewable environment in which, depending on the prevailing O2 conditions, two opposite processes – methanogenesis and methanotrophy - may take place. The rates of the processes may result in soil acting as a sink or a source of methane (CH4). Due to agricultural practices, heavy metals may accumulate affecting soil microbial processes. We tested the effect of cadmium (Cd) contamination on CH4 emission and uptake in three mineral soils (Eutric Cambisol, Haplic Podzol, Mollic Gleysol). Additionally, in the methanotrophy study, different soil moisture levels (pF 0; 2.2; 3.2) were studied. Based on the European annual and maximum limits, soils were polluted with cadmium in four doses (per dry soil mass): 0.048 mg Cd kg−1 (and its five-fold higher value) and 3.00 mg Cd kg−1 (and its five-fold higher value). The results showed that all tested soils produced and consumed CH4. Methane production rates were not significantly changed by the presence of the cadmium (except annual five-fold Cd dose in Podzol). In methanotrophy study, soil moisture was stronger regulator of CH4 oxidation (p < 0.05) than Cd pollution which effect depended on the soil type, Cd dose and pF level. CH4 was completely consumed in Cambisol (only at pF 0 with the rate significantly different from the rates at pF 2.2 and 3.2) and in Gleysol (at pF 0; pF 2.2; the CH4 oxidation rates were significantly different among all tested moistures with annual Cd dose), but this process was delayed after the application of the higher Cd doses. Among the tested soils, only the Podzol oxidized the added CH4 under all tested moisture levels (with the rate significantly different at pF 2.2 wit annual Cd dose), while Cd addition delayed CH4 uptake as well. In the Podzol, CH4 consumption was inhibited only by the highest Cd dose at low moisture (pF 3.2).

Among the useful tools in characterizing weathering degrees are chemical indices, which combines bulk major elemental oxides into a single metric value and commonly presented along a vertical profile. However, characterizing geomaterials of diverse nature using chemical indices may be problematic. In this study, chemical indices were evaluated to characterize weathering degrees in decomposed volcanic rocks from different depths, locations and formations. This was achieved by conducting comprehensive geochemical tests and statistical analyses. A good index must give appropriate trends, provide meaningful statistics and varies greatly with weathering degrees irrespective of the approach employed. Correlations were made between chemical indices and specific volume, depth, weathering degree as well as geological formation using tentative numerical value. The extent of weathering is best characterized by relating chemical indices with in-situ specific volume rather than depth, which is commonly used. The weathering potential index (WPI), hydration coefficient (Hc), leaching coefficient (Lc) and weathering index of Parker (WIP) are the most appropriate indices that could be used to characterize weathering in decomposed volcanic rocks. The chemical indices that have many mobile elements or cations and water content in their formulations are most useful. The chemical indices that are relating few oxides to each other should be avoided. The influence of formation on using chemical indices to characterize weathering degree is insignificant and the effect of weathering grade is very significant. This approach can be applied to similar geomaterials.

Abstract Invasion by exotic woody species is a major concern in grasslands worldwide. Woody invasions pose a particularly serious threat to forest–grassland mosaics globally, but the factors influencing the success of woody species in these systems, including the role of disturbances such as fire, are not well understood. In this study, we evaluated the role of fire in influencing mortality and regeneration success of three globally widespread woody invasives, Acacia mearnsii (black wattle), Cytisus scoparius (scotch broom) and Ulex europaeus (gorse) in the montane forest–grassland mosaics of the Nilgiri Biosphere Reserve in the Western Ghats biodiversity hotspot, India. Our results indicate that mortality and regeneration responses to fire are species-specific. Fire-induced adult mortality was highest in scotch broom and lowest in gorse, and high, but variable in wattle. Burning greatly increased the abundance of gorse and wattle seedlings, but only marginally increased scotch broom seedling abundance. Fire effects on invasive seedling densities were most pronounced at the edges of invasive patches. Overall, our results indicate that fires are likely to differentially affect invasion patterns of these three species, with fire potentially encouraging invasion by gorse and wattle and discouraging invasion by scotch broom.

Abstract Over 90% of global commercial trade occurs between seaports, which are initial points-of-entry for nonnative, potentially invasive propagules. As such, there is a need to develop means to both rapidly intercept and identify propagules as they arrive. Here, we focus on plant propagules that are assumed to be non-native, in seed form. Because standard morphological techniques alone are laborious and require taxonomic expertise, we sought to address if identification through barcoding of the plastid DNA (rbcL + matK genes) of plant seeds could improve current processes in the early detection and rapid response to prevent entry/establishment of nonnative plant species. This research conducted a preliminary foray to evaluate the utility of widely accepted plant plastid DNA barcodes to identify plant propagules (seeds, hereafter) collected from the air-intake grilles of refrigerated shipping containers of a single agricultural commodity arriving at the Port of Savannah, Georgia, USA. We ask four questions: (1) Can DNA barcoding be used to detect seeds collected from shipping containers at the port? (2) What is the genetic composition of propagules entering the port? (3) How do morphological identifications compare to those based on genetic analysis? (4) Are nonnative invasive plant species present on shipping containers entering the Port of Savannah? This research collected 11,044 seeds from 628 refrigerated shipping containers between 2015 and 2017. Seeds were then morphologically sorted into Seed Types. Barcoding of the matK and rbcL gene regions of the plastid genomes directly isolated from seeds resulted in poor amplification. This is likely due to a host of potential confounding factors. Therefore, we germinated seeds and utilized leaf-tissues for sequencing of these two gene regions. From BLASTn analyses, results returned top hits for a variety of species, with up to 22 possible nonnative plant species and one definite Federal Noxious Weed. This work investigates the interception application of DNA barcoding to improve agro- and bio-security issues posed by nonnative and invasive species. Though this study required the germination of the seeds to obtain leaf-tissue suitable for our DNA barcoding method, we effectively demonstrated seed viability. Our seed identification process was lengthy and understandably not feasible for real-time application. Therefore, we seek to improve our methods for future applications by testing other approaches that may better complement morphological identification. Next reasonable steps include improved extraction protocols, metabarcoding to generate DNA barcode sequences directly from groups of seeds harvested from shipping containers and implementing other next-generation sequencing techniques.

Abstract Seasonal migration is ubiquitous in animals, and yet its underlying cause(s) remain poorly known. Species exhibiting short-distance altitudinal migration and intraspecific variation in migratory behavior (partial or differential migration) are ideal study systems for examining the selective pressures that affect individual migratory decisions. We used an individually marked population of yellow-eyed juncos, breeding along a 1000-m elevational gradient and migrating up and down that gradient, to examine the morphological, behavioral, and reproductive traits associated with migratory behavior. We tested the four most well-known hypotheses proposed to explain partial migration: the thermal tolerance, fasting endurance, dominance, and arrival time hypotheses. Our results indicate that: (1) limits to juncos’ fasting endurance constrain their ability to overwinter at high elevations, in support of the fasting endurance hypothesis, (2) differences in body size mediate fasting ability and are associated with variation in migratory behavior and overwinter apparent survival, (3) migratory behavior interacts with reproductive success, in partial support of the arrival time hypothesis, and (4) additional mechanisms that are not captured by the four well-known hypotheses might better explain individual variation in migratory behavior. Less migratory females achieved greater nesting success the following breeding season. Among males, nesting success influenced migratory tendency the following winter. Successful males may either migrate to a more benign winter climate without paying reproductive costs, or high levels of parental effort might physiologically constrain their ability to overwinter in harsh climates. Significance statement Migration is a costly behavior, so migration must yield fitness benefits, at least for some individuals. Species in which migratory behavior varies among individuals in the same population provide an under-utilized opportunity to understand the costs and benefits that mediate individual migratory decisions. By marking and tracking a population of yellow-eyed juncos, we found that larger individuals were less likely to migrate, and this held true even within a sex class (males). Smaller individuals were not only more likely to migrate but also had lower apparent survival, and these differences were driven by size-related differences in fasting ability. Less migratory females accrued reproductive benefits, but males with the highest reproductive success were not less likely to migrate as predicted by the arrival time hypothesis. Our study demonstrates that migratory decisions balance the potential reproductive benefits and survival risks of overwintering on high-elevation breeding grounds.

Abstract The mother-offspring relationship is paramount in most mammals and infant survival often depends on maternal investment. In species with prolonged periods of development or co-residence, mothers may continue to influence their offspring’s outcomes beyond nutritional independence with benefits biased towards the philopatric sex. Chimpanzees (Pan troglodytes) are long-lived mammals with a protracted period of immaturity during which offspring continue to travel with their mothers. In contrast to most mammals, chimpanzees are also typically male philopatric. Here, we use over 50 years of demographic data from two communities in Gombe National Park, Tanzania, to examine the survival and longevity of both male and female chimpanzees that experienced maternal loss during three different age categories. Males who were orphaned between the ages of 0–4.99 years, 5–9.99 years, and 10–14.99 years all faced significantly lower survival than non-orphans and died earlier than expected. Females faced similarly reduced survival probabilities when orphaned between 0–4.99 and 5–9.99 years of age; however, females who experienced maternal loss between 10 and 14.99 years of age were no more likely to die than non-orphans. Females orphaned in this later age class also lived significantly longer beyond maternal loss than their male counterparts. As observed in other mammals, philopatric male chimpanzees may continue to benefit from their mother’s ecological knowledge, whereas maternal influence on female offspring likely fades as they prepare to emigrate. These results emphasize how maternal influence on offspring outcomes can extend well beyond weaning, particularly for the philopatric sex. Significance statement Mammalian mothers are crucial to their infant’s survival and in species where offspring continue to live with their mothers after weaning, maternal influence may extend beyond dependence on mother’s milk. While in most group-living mammals females remain in their natal group, chimpanzees typically display the opposite pattern with males residing alongside their mothers into adulthood. Using over 50 years of data on wild chimpanzees, we investigated the consequences of maternal loss both before and after weaning. We found that both males and females orphaned up to 10 years of age were less likely to survive than non-orphans; however, only males orphaned between 10 and 15 years also faced lower survival. These results emphasize how chimpanzee mothers continue to matter for offspring beyond infancy and provide novel data on reduced maternal influence on survival for daughters compared to sons.

Abstract Despite widespread occurrence of seasonal sociality among animals, little is still known about the social drivers and population-level social implications of seasonal grouping behaviours, especially in birds. Here, we studied the combined effects of ecological and social factors on seasonal grouping patterns in a sedentary population of Egyptian vultures living on the Eastern Canary Islands. We focussed on the social significance of large-scale gatherings taking place outside the breeding season at a highly preferred feeding station and a nearby temporary roost. Group sizes at this feeding patch followed a strong seasonal pattern characterized by distinct monthly changes in group composition, according to sex, age and territorial status. In between reproductive periods, vulture numbers at the feeding station may reach up 50% of the total population on a single day. GPS-tracking showed that this increase in vulture numbers was in part due to a shift in foraging range towards the centre of Fuerteventura by low-ranked territorial birds breeding in remote areas. During this period, vultures may spend on average 30% of their monthly time in a social gatherings context, depending on social status. We show that seasonal grouping patterns are shaped by the complex interplay between ecological factors (reproductive constraints, resource seasonality, food predictability), age-specific traits and social competitive processes, while social attraction may be an important additional component. We propose that for facultative social foragers living in highly despotic territorial systems, collective foraging may be of particular relevance regarding the development of hierarchical social relations and maintenance of population-level social cohesion. Significance statement We show that seasonal grouping patterns in a sedentary island population of a territorial vulture are shaped by the complex interplay between ecological factors (reproductive constraints, resource seasonality, food predictability), age-specific traits and social competitive processes. We argue that vultures visit large gatherings also for social purposes. Group foraging events may be of special interest to vultures, given opportunities for rank maintenance/improvement, but also for conspecific evaluation and mate-seeking, and play an important role in the social structuring of populations. Vultures may serve as important model species to test the role of scavenging and fission–fusion social dynamics in driving the evolution of avian social cognition, or avian social complexity in general.

Abstract Estimates of last male sperm precedence (P2) are often used to infer mechanisms of sperm competition, a form of post-copulatory sexual selection. However, high levels of mating failure (i.e. copulations resulting in no offspring) in a population can lead to misinterpretations of sperm competition mechanisms. Through simulations, García-González (2004) illustrated how mating failure could cause bimodal distributions of paternity with peaks at P2 = 0 and 1, under a random sperm mixing mechanism. Here, we demonstrate this effect empirically with the seed bug Lygaeus simulans, a species known to exhibit high levels of mating failure (40–60%), using a morphological marker to estimate paternity. Contrary to previous findings in a sister species, we did not find strong evidence for last male sperm precedence. There was a tendency towards last male precedence (P2 = 0.58) but within the expected range for random sperm mixing. Instead, P2 was highly variable, with a bimodal distribution, as predicted by García-González (2004). After taking mating failure into account, the strongest driver of paternity outcome was copulation duration. Furthermore, we found evidence that mating failure could partly be a female-associated trait. Some doubly-mated females were more likely to produce no offspring or produce offspring from two different sires than expected by chance. Therefore, some females are more prone to experience mating failure than others, a result that mirrors an earlier result in male L. simulans. Our results confirm that mating failure needs to be considered when interrogating mechanisms of post-copulatory sexual selection. Significance statement Mating failure arises when animals fail to produce offspring across their lifetime. This may be due to a failure to find a mate or a failure to produce offspring after one or more apparently successful matings. Sperm competition is when ejaculates of rival males compete to fertilize a female’s eggs. Estimates of second male paternity (P2) are often used to infer mechanisms of sperm competition (i.e. which male “wins” and how). However, García-González (2004) suggested that high levels of mating failure can skew paternity (i.e. give spuriously high/low levels of P2) and lead to misinterpretations of these mechanisms. We carried out sperm competition experiments on Lygaeus simulans seed bugs using a morphological marker to estimate paternity. We show empirically that mating failure does skew patterns of paternity, causing a bimodal distribution of P2. Therefore, by disrupting patterns of sperm competition, mating failure influences both the action of post-copulatory sexual selection and also our understanding of the mechanisms of sperm competition.

Abstract Animals raised in captivity go through drastically different life experiences compared with those raised in the wild. The captive environment is usually characterised by highly stable conditions and limited social interactions. Such early developmental environment, alone and interacting with genes, can have long-lasting effects on cognitive performance. By testing pairs of mothers and offspring delicate skinks, Lampropholis delicata, we investigated how being raised in a captive environment shapes spatial learning. Additionally, with this design, we were able to evaluate the additive genetic component and strength of genetic effects in this lizard species. Using a Y-maze task, we compared the spatial learning abilities of wild-caught adult female (mothers) delicate skinks, to their captive-born and raised sexually mature offspring. We found that more mothers completed the task and showed shorter latencies compared with offspring who took longer to complete the maze. The offspring performance did not appear to correlate with their mothers’ performance, indicating little narrow-sense heritability. Furthermore, offspring performance was neither affected nor predicted by their mothers’ performance, indicating a limited overall genetic effect. Our results suggest that early life experiences in a captive environment may have a hindering effect on cognitive performance. Significance statement How important are environmental effects compared with genetics on the development of learning abilities in non-human animals? Studying mother-offspring skink pairs, we show that wild-born mothers outperformed their captive-born offspring in a spatial learning task. We further show that offspring performance in the task was neither explained nor predicted by their mothers’ performance. We suggest that conditions during early-life stages shape spatial learning more than genetics, and stable captive conditions may have a negative effect on the development of spatial learning.

Abstract Among birds exhibiting conspecific brood parasitism (CBP), parasites demonstrate a variety of intriguing tactics for selecting a host nest, including preference for safe nests (i.e., avoiding nests depredated during the previous season). Brood parasites of birds that do not reuse nest sites, however, are limited to nest-site information available to them during the current breeding season. This study explores cues used by brood parasites in a population of red-breasted mergansers nesting in upland vegetation and sandy substrate that prohibits reuse of nest sites in consecutive years. Nest-site and host traits were measured for 33 parasitized and 23 non-parasitized nests. There was no association between CBP and nest-site traits potentially providing cues about nest safety from avian predators (concealment and density of nesting larids), likely due to very low rates of egg predation. Distance to shore for parasitized nests was slightly greater than for unparasitized nests. Parasites did not select nests in relation to host age, mass, date of nest initiation, or stage of nesting (laying or incubation). Artificial nests were used to simulate natural nests without a host and to assess whether host presence serves as a cue for parasites. The proportion of natural nests receiving ≥ 1 foreign egg (60% of 15 nests) was thrice that for artificial nests (21% of 14 nests). Some aspect of host presence may therefore be an important, but not necessary, cue for brood parasites targeting nests that are heavily concealed in uplands. Significance statement Whenever brood parasitism is a well-developed component of reproduction, selection is expected to favor brood parasites that make use of environmental or social information allowing them to discriminate among host nests and maximize reproductive success. We assessed cues used by brood parasites in ground-nesting red-breasted mergansers for which conspecific brood parasitism (CBP) is common, and nests are well concealed in upland vegetation. Observations at parasitized and unparasitized nests revealed that nest-site safety and visibility from habitat edges are not central to laying decisions by parasites in this population. Brood parasites, however, were considerably more likely to lay their eggs in natural nests with a host than in artificial nests without a host, suggesting that some aspect of host presence is important in the nest-site selection process for parasites. The ability of brood parasites to discriminate among nests based on host presence is expected to affect parasite success because individuals can avoid nests in which their eggs are doomed to fail (e.g., abandoned nests).

Abstract Parents are expected to reduce offspring investment when confronted with reliable cues of compromised parentage, yet establishing which cues are reliable is an empirical challenge. Presenting a potential cuckolder to a breeding male is often used in experiments as an indirect cue of paternity loss. However, determining the reliability and hence the utility of this cue is an important but often-overlooked research step. Furthermore, cues of compromised parentage are typically manipulated only during the narrow time window(s) when copulations take place, and so we currently have a poor understanding of whether these cues also convey useful information at other critical timepoints in the reproductive cycle, such as during nest site selection. Here, we present a series of field and laboratory studies using a paternal care giving toadfish, the plainfin midshipman fish (Porichthys notatus) to address these questions. We tested whether the presence of a potential cuckolder near a potential nesting site reduces the odds that males will choose to nest at that site, or reduces the amount of care they provide for offspring. Overall, we found no clear effect of cuckolder presence on the likelihood that a male would occupy nor abandon a nesting site, nor on the amount of paternal care provided. The presentation of a single sneaker male may have been too weak a signal of cuckoldry to elicit a response from guarder males. Alternatively, a single sneaker male may not represent a severe enough threat to paternity to warrant a response. We highlight the importance of considering the diverse range of natural history and ecological factors that underlie paternity cue utility across different model organisms. Significance statement Breeding decisions, such as which nesting sites to occupy or how much to invest into offspring, may be affected by external cues of parentage loss (e.g. cuckoldry) or risk thereof. Here, we tested whether the presence of a cuckolder male in the breeding environment affects male nest site selection and paternal care. Despite being a commonly used putative indirect cue of sperm competition and paternity loss, we found no clear evidence that the presence of a single sneaker male affected these breeding decisions. Our results underscore the importance of first establishing the utility of various cues, which involves considering the ecological context from which the cues arise, before using them to assess the mechanisms underlying animal decision-making.

Growing numbers of large phylogenetic syntheses are being published. Sometimes as part of a hypothesis testing framework, sometimes to present novel methods of phylogenetic inference, and sometimes as a snapshot of the diversity within a database. Commonly used methods to reuse these trees in scripting environments have their limitations. I present a toolkit that transforms data presented in the most commonly used format for such trees into a database schema that facilitates quick topological queries. Specifically, the need for recursive traversal commonly presented by schemata based on adjacency lists is largely obviated. This is accomplished by computing pre‐ and post‐order indexes and node heights on the topology as it is being ingested. The resulting toolkit provides several command line tools to do the transformation and to extract subtrees from the resulting database files. In addition, reusable library code with object–relational mappings for programmatic access is provided. To demonstrate the utility of the general approach I also provide database files for trees published by Open Tree of Life, Greengenes, D‐PLACE, PhyloTree, the NCBI taxonomy and a recent estimate of plant phylogeny. The database files that the toolkit produces are highly portable (either as SQLite or tabular text) and can readily be queried, for example, in the R environment. Programming languages with mature frameworks for object‐relational mapping and phylogenetic tree analysis, such as Python, can use these facilities to make much larger phylogenies conveniently accessible to researcher programmers.

1. The recent availability of high spatial and temporal resolution optical and radar satellite imagery has dramatically increased opportunities for mapping land cover at fine scales. Fusion of optical and radar images has been found useful in tropical areas affected by cloud cover because of their complementarity. However, the multitemporal dimension these data now offer is often neglected because these areas are primarily characterised by relatively low levels of seasonality and because the consideration of multitemporal data requires more processing time. Hence, land cover mapping in these regions is often based on imagery acquired for a single date or on an average of multiple dates.

The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the “sky islands” of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the “sky island” complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.

Inter‐specific root separation is an important example of spatial niche differentiation that drives species coexistence in many ecosystems. Particularly under water‐stressed conditions, it is believed to be an inevitable outcome of species interactions. However, evidence for and against this idea has been found. So far, studies aiming at reconciling the debate mainly focus on abiotic determinants. It remains unclear if and to what extent root separation depends on the type and growth form of interacting plants. We conducted a detailed field study in three adjacently located (with pairwise distances < 500 m) arid patchy communities where a common tussock grass species Achnatherum splendens grew in association with either a tree (Elaeagnus angustifolia), a shrub (Nitraria tangutorum) or a perennial forb species (Sophora alopecuroides). In each community, roots and soils were sampled along the soil layers from five depths (0‐10, 10‐30, 30‐60, 60‐100 and 100‐150 cm) in the patches and in the adjacent bare ground outside the patches. Significant vertical inter‐specific root separation occurred in the species‐association patches of tree‐grass and forb‐grass communities, but not in the shrub‐grass community. As the neighbour changed going from trees to shrubs and to forbs, rooting profiles of the grass Achnatherum became progressively deeper, with progressively less roots allocated in the upmost 10 cm soil layer and more in the subsequent two layers. After controlling for the differences in soil water and nutrient conditions among the three communities, the effects of neighbour type on grass rooting profiles remained robust. Synthesis. We found that the root distributions of plants in the dryland strongly depend on the type of neighbour plants, which can, at least partially, determine the extent of inter‐specific root separation at the community scale. Our work poses new questions about plasticity in root distribution and helps to better understand species interactions and coexistence under stressful conditions.

The oceans’ fisheries contribute to human wellbeing by providing essential nutrients, employment, and income. Changes in fish distribution, due to climate change or stock expansion, jeopardize conservation objectives because fishers catch more than is allocated as quota. Quotas, or catch shares, should, therefore, correspond to the share of the fish stock biomass present within a country's Exclusive Economic Zone, a concept known as Zonal Attachment. Here, we assess the Zonal Attachment of transboundary fish stocks present in northern Europe, in the waters of the United Kingdom, the European Union (without the United Kingdom), and Norway. In 12 of 14 important fish stocks, estimates of Zonal Attachment to the United Kingdom were significantly higher than current quota allocations, explaining the country's substantial discard problem. With environmental change, and stock recovery under improved fisheries conservation, scientific evidence should be used not only to set catch limits, but also to re‐examine catch shares.

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long‐reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi‐C, we generated a high‐continuity chromosome‐scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome‐size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male‐specific duplicate of the anti‐Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex‐specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by−). Our high‐quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex‐determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.

In urban areas, anthropogenic drivers of ecosystem structure and function are thought to predominate over larger‐scale biophysical drivers. Residential yards are influenced by individual homeowner preferences and actions, and these factors are hypothesized to converge yard structure across broad scales. We examined soil total C and total δ13C, organic C and organic δ13C, total N, and δ15N in residential yards and corresponding reference ecosystems in six cities across the United States that span major climates and ecological biomes (Baltimore, Maryland; Boston, Massachusetts; Los Angeles, California; Miami, Florida; Minneapolis‐St. Paul, Minnesota; and Phoenix, Arizona). Across the cities, we found soil C and N concentrations and soil δ15N were less variable in residential yards compared to reference sites supporting the hypothesis that soil C, N, and δ15N converge across these cities. Increases in organic soil C, soil N, and soil δ15N across urban, suburban, and rural residential yards in several cities supported the hypothesis that soils responded similarly to altered resource inputs across cities, contributing to convergence of soil C and N in yards compared to natural systems. Soil C and N dynamics in residential yards showed evidence of increasing C and N inputs to urban soils or dampened decomposition rates over time that are influenced by climate and/or housing age across the cities. In the warmest cities (Los Angeles, Miami, Phoenix), greater organic soil C and higher soil δ13C in yards compared to reference sites reflected the greater proportion of C4 plants in these yards. In the two warm arid cities (Los Angeles, Phoenix), total soil δ13C increased and organic soil δ13C decreased with increasing home age indicating greater inorganic C in the yards around newer homes. In general, soil organic C and δ13C, soil N, and soil δ15N increased with increasing home age suggesting increased soil C and N cycling rates and associated 12C and 14N losses over time control yard soil C and N dynamics. This study provides evidence that conversion of native reference ecosystems to residential areas results in convergence of soil C and N at a continental scale. The mechanisms underlying these effects are complex and vary spatially and temporally.

Climate and land use change modify surface water availability in African savannas. Surface water is a key resource for both wildlife and livestock and its spatial and temporal distribution is important for understanding the composition of large herbivore assemblages in savannas. Yet, the extent to which ungulate species differ in their water requirements remains poorly quantified. Here, we infer the water requirements of 48 African ungulates by combining six different functional traits related to physiological adaptations to reduce water loss, namely minimum dung moisture, relative dung pellet size, relative surface area of the distal colon, urine osmolality, relative medullary thickness and evaporation rate. In addition, we investigated how these differences in water requirements relate to differences in dietary water intake. We observed strong correlations between traits related to water loss through dung, urine and evaporation, suggesting that ungulates minimize water loss through multiple pathways simultaneously, which suggests that each trait can thus be used independently to predict water requirements. Furthermore, we found that browsers and grazers had similar water requirements, but browsers are expected to be less dependent on surface water because they acquire more water through their diet. We conclude that these key functional traits are a useful way to determine differences in water requirements and an important tool for predicting changes in herbivore community assembly resulting from changes in surface water availability.

Urban treatment wetlands purify water and provide various ecological services such as food and habitat. We applied the sustainable structured wetland biotope (SSB) system, which considers site-specific ecological conditions and maximizes water purification efficiency, as a treatment wetland for non-point source pollution with short retention time and high biodiversity. This system is consisted of a forebay area (primary retention basin), a micro-pool area (secondary retention basin), and multi-cell structures of marshes and ponds. A wetland constructed with an SSB system for the treatment of non-point source pollution was completed at a site downstream from Jecheon city, located in the upper river basin of the Han River in the Republic of Korea. In addition to the SSB system, a rainwater detention tank for the inflow of the SSB was constructed. During the initial rainfall event, water through SSB were significantly purified (83–98% in BOD, 96–99% in SS, 41–90% in T-N, and 79–96% in T-P of removal efficiency). The flora in the SSB and its neighboring areas consisted of 125 species of 45 families. Three amphibian species, three reptile species, 17 benthic macroinvertebrate species, and 18 avian species were observed in the wetland. We recorded five mammals, including an endangered Eurasian otter species in Korea, Lutra lutra, present in the wetland. Eight fish species were also observed. The wetland showed high removal efficiency without a specific water-treatment device. In addition, local plant and animal species, including rare species, seemed to successfully settle in the SSB.

Ecological benefits and production of grassland on the Loess Plateau are limited by low soil N and P availability. Extraneous N and P fertilization is an efficient management measure to enhance grassland productivity and accelerate grassland restoration. However, biodiversity decline and species loss induced by N and P addition must be noticed. Two grassland communities dominated by tall clonal grass (TCG) and tall clonal forb (TCF) on Loess Plateau were selected. A two-year split-plot experiment (main-plot: 0, 25, 50, and 100 kgN ha−1 yr−1; subplot: 0, 20, 40 and 80 kg P2O5 ha−1 yr−1) was conducted to evaluate the effect of N and P addition on aboveground net primary production (ANPP), light availability, diversity and functional group composition. N and P addition slightly increased ANPP mainly benefiting from clonal species and had few effects on species composition and diversity due to the deficient precipitation during growing season in 2017. However, N or P addition alone resulted in significant ANPP increase, and adding N and P together had larger effects in 2018. The changes in ANPP and diversity after P alone addition were driven by legumes. The ANPP responses to 50 and 100 kg N ha−1 yr−1 combined with P addition in 2018 were mainly driven by pronounced increases in tall clonal or annual species. This large shift of species composition caused diversity decline only in TCF community. The extent of diversity decline was significantly correlated with the degree of light availability reduction. Diversity decline in TCF was a result of strong and uniform light availability reduction induced by increased tall annual forb. Tall clonal and annual species are the key functional groups that drive changes in productivity and diversity in the two communities. The optimum N and P amount to tradeoff productivity improvement and diversity decline were 50 kg N ha−1 yr−1 and 20 kg P2O5 ha−1 yr−1 combination for TCG and 25 kg N ha−1 yr−1 and 20 kg P2O5 ha−1 yr−1 combination for TCF.

Organic farming has been praised for many profound reasons, but there are some negative effects of organic practices. Research on the interactions between soil insect pests and organic farming practices is still scarce, although such interactions might sometimes lead to severe crop damage. Here, we explore the influences of organic farming inputs and key host crops on the oviposition behaviour of soil insect pests likely to infest crops. We also shed light on the factors driving this behaviour and analyse 4 years of data from an on‐farm investigation. Our study offers clear support that decomposing organic matter and legume crops affect oviposition behaviour and provides evidence that butyric acid and 1‐hexanol are major attractants. The results suggest that poor management or returning decomposing organic matter to the field is risky. The silver lining, however, is that oviposition behaviour can be disrupted by the identified key attractants to benefit crop protection.

Microorganisms release nutrients from minerals. However, this process is not yet well understood despite its importance for soil fertility. The aim of this study was to determine which factors control microbial phosphorus (P) and silicon (Si) release from apatite and weathered rock, and to analyze which microbial-mediated processes cause P and Si solubilization. For this purpose, we conducted a series of incubation experiments with apatite and saprolite (weathered bedrock) and soil extracts of four soils that are located along a climate gradient in the Coastal Cordillera of Chile and differ in soil P fractions and degree of weathering. We developed an approach that allowed us to measure the release of P from apatite and the release of Si from saprolite by microbial consortia in soil solution. The microbial consortia of all soil extracts caused release of P from apatite. The addition of carbon (C) and nitrogen (N) to the soil solution increased the rate of microbial P solubilization from apatite by a factor of about 10 in all soil depth increments. The pH decreased strongly during the incubations. In the depth increments 0.1–0.2 and 0.4–0.6 m, the P solubilization rates were negatively correlated with the pH measured at the end of the incubation (r2 = 0.55 and 0.76, respectively, both p < 0.01). Nine organic acids were detected throughout the experiment. The total concentration of carboxyl groups was positively correlated with the P solubilization rate (r2 = 0.94, p < 0.01). The addition of dissolved inorganic P to the soil extracts did not significantly decrease the P solubilization rates. The rate of microbial Si solubilization from saprolite increased strongly with the surface area of the saprolite. We conclude that microbial solubilization of P from apatite was limited by the availability of easily decomposable C and that microbial solubilization of P from apatite was not affected by P availability, indicating that this process is not or not exclusively controlled by microbial need for P. In conclusion, our results indicate that microbial weathering of bedrock is strongly constrained by the availability of organic C and by the specific surface area of the saprolite.

Conversion of forests to cultivated farms through slash-and-burn or chop-and-char practices often results in rapid loss of soil organic matter (SOM) or conversion of inherent SOM into pyrogenic organic matter (PyOM). However, there is little knowledge about the short-term changes in soil macrofauna that may occur when large amount of biochar are added to the soil. A thirty-day microcosm study was conducted to assess effects of biochar derived from two trees, Croton megalocarpus Hutch. and Zanthoxylum gilletii (De Wild.) P.G.Waterman, on the activity of a geophagous earthworm, Pontoscolex corethrurus. A portion of the biochar was leached with either acetone or 2 M HCl, to remove easily mineralizable organic matter and ash contents, respectively. Each of the biochar types was mixed with soil at a rate equivalent to 5, 10 and 25 Mg ha−1. Casts were collected after 30 days and used as a measure of earthworms’ activity. Casts dry weight was affected more by amount than the type of biochar. The highest cast weight (188.1 g and 176.5 g) was recorded in microcosm that received 5 Mg ha−1 of C. megalocarpus and Z. gilletii biochar, respectively. Notably, the weight decreased with increasing biochar additions. Cast weight decreased by 4% in microcosms that received 10 Mg of C. megalocarpus biochar ha−1 and by 15% in microcosms that received the same biochar type at a rate of 25 Mg ha−1. Similarly, there was a 6% decline in cast weight in microcosms that received 10 Mg of Z. gilletii biochar ha−1 and an 8% decline in microcosms amended with 25 Mg ha−1 of the same biochar type. Easily mineralizable organic matter or nutrients were not responsible for the observed differences in cast production since leaching with acetone or HCl did not change the effects. The C and N in casts and bulk soil were not significantly different, an indication that earthworms did not seek out biochar, but rather indiscriminately utilised the soil rich in biochar.

Including cover crops within agricultural rotations may increase soil organic carbon (SOC). However, contradictory findings generated by on-site experiments make it necessary to perform a comprehensive assessment of interactions between cover crops, environmental and management factors, and changes in SOC. In this study, we collected data from studies that compared agricultural production with and without cover crops, and then analyzed those data using meta-analysis and regression. Our results showed that including cover crops into rotations significantly increased SOC, with an overall mean change of 15.5% (95% confidence interval of 13.8%–17.3%). Whereas medium-textured soils had highest SOC stocks (overall means of 39 Mg ha−1 with and 37 Mg ha−1 without cover crops), fine-textured soils showed the greatest increase in SOC after the inclusion of cover crops (mean change of 39.5%). Coarse-textured (11.4%) and medium-textured soils (10.3%) had comparatively smaller changes in SOC, while soils in temperate climates had greater changes (18.7%) than those in tropical climates (7.2%). Cover crop mixtures resulted in greater increases in SOC compared to mono-species cover crops, and using legumes caused greater SOC increases than grass species. Cover crop biomass positively affected SOC changes while carbon:nitrogen ratio of cover crop biomass was negatively correlated with SOC changes. Cover cropping was associated with significant SOC increases in shallow soils (≤30 cm), but not in subsurface soils (>30 cm). The regression analysis revealed that SOC changes from cover cropping correlated with improvements in soil quality, specifically decreased runoff and erosion and increased mineralizable carbon, mineralizable nitrogen, and soil nitrogen. Soil carbon change was also affected by annual temperature, number of years after start of cover crop usage, latitude, and initial SOC concentrations. Finally, the mean rate of carbon sequestration from cover cropping across all studies was 0.56 Mg ha−1 yr−1. If 15% of current global cropland were to adopt cover crops, this value would translate to 0.16 ± 0.06 Pg of carbon sequestered per year, which is ∼1–2% of current fossil fuels emissions. Altogether, these results indicated that the inclusion of cover crops into agricultural rotations can enhance soil carbon concentrations, improve many soil quality parameters, and serve as a potential sink for atmosphere CO2.

As an important agent of environmental change, atmospheric nitrogen (N) deposition could have profound effects on terrestrial ecosystems. However, previous studies simulating N deposition in forest ecosystems were mostly based on understory manipulations, often neglecting canopy processes (e.g., N retention). Here, we employed a novel field experiment simulating N deposition through the canopy addition of N (CAN), and explored how soil nematode communities change in response to elevated N deposition in comparison with the conventional approach of understory addition of N (UAN), at two levels of N concentration. We found that 52% and 44% of the N added to the forest canopy at two N concentration levels were retained by the forest canopy. The soil nematode community showed contrasting responses to different approaches of N addition. The conventional UAN approach decreased the abundance of most nematode trophic groups and community diversity compared with CAN approach. This detrimental effect was probably due to changes in fine root biomass and/or nematode community composition caused by the high concentration of N directly entering the soils without the canopy N retention process. Our results suggest that the conventional UAN approach might result in an incomplete and potentially misleading understanding of the effects of N deposition on forest ecosystems. The results show that previous studies might have overestimated the negative effects of N deposition on forest ecosystems by overlooking forest canopy processes. In conclusion, forest canopy N-interceptions contribute to maintaining the composition of soil communities and soil biodiversity under elevated N deposition. Our study helps reconcile some of the discrepancies in the existing literature, and demonstrate the urgent need to consider canopy processes in future N deposition studies.

Apex predators can have substantial and complex ecological roles in ecosystems. However, differences in species‐specific traits, population densities, and interspecific interactions are likely to determine the strength of apex predators’ roles. Here we report complementary studies examining how interactions between predator per capita metabolic rate and population density influenced the biomass, population energy use and ecological effects of apex predators on their large mammalian prey. We first investigated how large mammal prey resources and field metabolic rates of terrestrial apex predators, comprising large mammals and the Komodo dragon (Varanus komodoensis), influenced their biomass densities and population energy use requirements. We next evaluated whether Komodo dragons, like apex mammalian predators, exerted top‐down regulation of their large mammal prey. Comparison of results from field studies demonstrates that Komodo dragons attain mean population biomass densities that are 5.75−231.82 times higher than that of apex mammalian predator species and their guilds in Africa, Asia, and North America. The high biomass of Komodo dragons resulted in 1.96−108.12 times greater population energy use than that of apex mammalian predators. Nevertheless, substantial temporal and spatial variation in Komodo dragon population energy use did not regulate the population growth rates of either of two large mammal prey species, rusa deer (Rusa timorensis) and wild pig (Sus scrofa). We suggest that multiple processes weaken the capacity of Komodo dragons to regulate large mammal prey populations. For example, a low per capita metabolic rate requiring an infrequent and inactive hunting strategy (including scavenging), would minimize lethal and non‐lethal impacts on prey populations. We conclude that Komodo dragons differ in their predatory role from, including not being the ecological analogs of, apex mammalian predators.

Peatlands are important carbon (C) stores as a result of acidity, waterlogging conditions and low temperatures slowing decomposition rates. However, climate change is predicted to bring not only changes in abiotic conditions, but also the replacement of peat‐forming vegetation, such as Sphagnum mosses, with vascular plants. In these systems, enchytraeid worms represent the dominant mesofaunal group, and previous climate change manipulations have shown that their abundances and vertical distribution are strongly influenced by temperature and moisture gradients, with important implications for C cycling. Therefore, determining their behavioural responses to changes in both abiotic and biotic factors is crucial to quantify their contribution to decomposition processes.

Increasing the pH of soils by applying limestone alters the sorption of herbicides and their efficiency at controlling weeds. The objectives of this study were to investigate the effects of increasing the pH and adding Ca2+ and Mg2+ on the sorption and desorption of diuron in different soils, and to evaluate the behavior of the herbicide in cationic solutions to determine whether precipitation is involved in the retention process. Sorption and desorption coefficients (Kfs and Kfd) were determined based on the Freundlich isotherms using seven soils, which were incubated or not incubated with agricultural limestone. Liming increased the values of Kfs and Kfd for diuron, even though the organic matter contents of all the soils decreased. The presence of Ca2+ and Mg2+ reduced the concentration of diuron in the aqueous solution. Increasing the pH and Ca2+ and Mg2+ concentrations by applying agricultural limestone increased the sorption and reduced the desorption of diuron in the soils investigated in this study. The behavior of diuron in calcium and magnesium solutions indicates that a precipitation process may be responsible for the increased sorption and reduced desorption of diuron in soils.

Abstract In order to evaluate the differential absorption and toxicity of arsenate (AsV) and arsenite (AsIII), Lemna valdiviana plants were grown in a nutrient solution and subjected to 0.0 (control); 0.5; 1.0; 1.5; 2.0; 3.0; 4.0; 5.0 and 7.5 mg L−1 of AsIII or AsV for three days. Exposure to both chemical forms resulted in As bioaccumulation, although AsIII-grown plants showed higher As content in tissues. In AsV-grown plants, the relative growth rate (RGR) decreased to 50%, at a concentration of 4.0 mg L−1, while for treatments with AsIII, the same decrease was observed at 1.0 mg L−1. The tolerance index decreased with increasing concentrations, with lower values for AsIII. Plants treated with AsIII showed increased superoxide anion levels, whilst higher levels of hydrogen peroxide were present in AsV-treated plants. Moreover, malondialdehyde (MDA) levels were higher for plants subjected to AsIII when compared to AsV at lower concentrations. Concentrations of 1 mg L−1 of AsIII and 4 mg L−1 of AsV showed equivalent MDA levels. Superoxide dismutase and catalase activities were increased at low concentrations and were inhibited at higher concentrations of AsIII and AsV, whereas peroxidase activity was positively modulated by increased AsIII or AsV concentrations. In conclusion, L. valdiviana plants took up and accumulated arsenic as AsIII or AsV, demonstrating the potential for phytoremediation of this metalloid. Furthermore, AsIII-exposed plants showed enhanced toxicity when compared to AsV, at the same applied concentration, although toxicity was more related to internal As concentrations, regardless of the chemical form applied.

Abstract Land-use intensification (LUI) and biological invasions are two of the most important global change pressures driving biodiversity loss. However, their combined impacts on biological communities have been seldom explored, which may result in misleading ecological assessments or mitigation actions. Based on an extensive field survey of 445 paired invaded and control plots of coastal vegetation in SW Spain, we explored the joint effects of LUI (agricultural and urban intensification) and invasion on the taxonomic and functional richness, mean plant height and leaf area of native plants. Our survey covered five invasive species with contrasting functional similarity and competitive ability in relation to the native community. We modeled the response of native communities for the overall and invader-specific datasets, and determined if invader-native functional differences could influence the combined impacts of LUI and invasion. Overall, we found that urban intensification reduced taxonomic richness more strongly at invaded plots (synergistic interactive effects). In contrast, functional richness loss caused by urban intensification was less pronounced at invaded plots (antagonistic interactive effects). Overall models showed also that urban intensification led to reduced mean leaf area, while agriculture was linked to higher mean plant height. When exploring invader-specific models, we observed that the combined effects of agricultural and urban intensification with invasion were heterogeneous. At invaded plots, invader-native functional differences accounted for part of this variability. Our findings demonstrate the importance of considering the interactive effects of global change pressures for a better assessment and management of ecosystems.

Abstract Phenological shifts are occurring in many ecosystems around the world. The capacity of species to adapt to changing phenology will be critical to their success under climate change scenarios. Failure to adjust migratory and reproductive timing to keep pace with the earlier onset of spring has led to negative demographic effects for populations of species across a variety of taxa. For caribou, there have been concerns that earlier spring green-up on calving areas might not be matched by earlier migration and parturition, potentially leading to a trophic mismatch with nutritional consequences for parturient and lactating caribou cows. However, there is limited evidence supporting these concerns. Here, we investigate the response of barren-ground caribou to changing spring phenology using data from telemetry and satellite imagery. From 2004 to 2016, we found that the average start of green-up on the calving area advanced by 7.25 days, while the start of migration advanced by 13.64 days, the end of migration advanced by 6.02 days, and the date of peak calving advanced by 9.42 days. Despite the advancing onset of green-up, we found no evidence for the development of a trophic mismatch because the advancing green-up coincided with earlier migration and calving by caribou. Changing snow cover on the late winter and migratory ranges was the most supported driver of advancing migratory behavior. The ability of caribou to adjust the timing of migratory and reproductive behavior in response to changing environmental conditions demonstrates the potential resilience of the species to some aspects of climate change.

Abstract Plant species vary in their growth response to arbuscular mycorrhizal (AM) fungi, with responses ranging from negative to positive. Differences in response to AM fungi may affect competition between plant species, influencing their ability to coexist. We hypothesized that positively responding species, whose growth is stimulated by AM fungi, will experience stronger intraspecific competition and weaker interspecific competition in soil containing AM fungi, while neutrally or negatively responding species should experience weaker intraspecific and stronger interspecific competition. We grew Plantago lanceolata, which responds positively to AM fungi, and Bromus inermis, which responds negatively to AM fungi, in an additive response surface competition experiment that varied the total density and relative frequency of each species. Plants were grown in sterilized background soil that had been inoculated with whole soil biota, which includes AM fungi, or a microbial wash, that contained other soil microbes but no AM fungi, or in sterilized soil that contained no biota. The positively responding P. lanceolata was more strongly limited by intraspecific than interspecific competition when AM fungi were present. By contrast, the presence of AM fungi decreased the strength of intraspecific competition experienced by the negatively responding B. inermis. Because AM fungi are almost always present in soil, strong intraspecific competition in positively responding species would prevent them from outcompeting species that respond neutrally or negatively to AM fungi. The potential for increased intraspecific competition to offset growth benefits of AM fungi could, therefore, be a stabilizing mechanism that promotes coexistence among plant species.

Abstract Himalayan balsam (Impatiens glandulifera) is a highly invasive annual herb that has become extremely prevalent in riparian zones across the UK. The competitive ability of I. glandulifera, both in terms of resource exploitation and allelopathy (i.e., the release of biochemicals that may be toxic to neighbouring plants), is considered a key determinant of its success. Little is known, however, about the effects of the resident community on the establishment and growth of I. glandulifera. Here, we aim to increase our understanding of the competitive ability of this highly invasive plant by investigating the effects of soil conditioning on the performance of four co-occurring native species (Tanacetum vulgare, Urtica dioica, Chelidonium majus and Arabidopsis thaliana). In addition, we also aim to investigate the effect that the pre-existing species composition have on the performance of I. glandulifera seedlings by establishing artificial communities (monocultures and mixtures of four UK native species, including U. dioica). We found negative effects of soil conditioning by I. glandulifera in all four species, either by reducing above-ground biomass, chlorophyll content or both. Monocultures of U. dioica were the only artificial communities that reduced growth of I. glandulifera, and we did not find any support for the idea that a more diverse community may be more resistant to invasion. Our results confirm the high competitive ability of I. glandulifera and highlight how the identity of the natives in the resident community may be key to limit its success.

Abstract The wild boar (Sus scrofa) is considered an ecosystem engineer. It roots up the ground looking for forage, generating patches of different sizes and without vegetation. Studies of wild boar’s impact on vegetation can be addressed in two contrasting ways: short-term effects (immediately after boar’s disturbance) and long-term effects. Short-term studies in the Monte Desert of Argentina showed that wild boar rooting modifies soil properties, reduces plant cover, and decreases plant richness and diversity. The objective of this study was to analyse the vegetation response in a desert ecosystem after 11 yr of wild boar disturbance establishing a replicated experiment of medium and large-sized animal’s exclusion. In this long-span study, time was the most important variable to predict the cover of different plant life forms and richness in disturbed soils. Herb cover was higher in disturbed soils, with grasses and woody species showing the opposite. Over the long-term, wild boar positively affect alpha diversity and richness, while the species turnover (rate of species replacement) was only influenced by the replacement of herbs. Disturbed soils were mainly dominated by annual species with a relatively high (60%) extent of species turnover. These vegetation changes throughout time are influenced by the occurrence of unexpectedly high rainy episodes, and probably by the system’s own fragility of Monte Desert.

Ecoacoustics has the potential to provide a large amount of information about the abundance of many animal species at a relatively low cost. Acoustic recording units are widely used in field data collection, but the facilities to reliably process the data recorded ‐ recognising calls that are relatively infrequent, and often significantly degraded by noise and distance to the microphone ‐ are not well developed yet.

Tracking devices have become small enough to be widely applied to arthropods to study their movement. However, possible side effects of these devices on arthropod performance and behaviour are rarely considered. We performed a systematic review of 173 papers about research in which tracking devices –Radio Frequency Identification (RFID), harmonic radar, and radio telemetry tags– were attached to terrestrial arthropods. The impact of such tags was quantified in only 12% of the papers, while in 40% the potential impact was completely disregarded. Often‐cited rules of thumb for determining appropriate tag weight had either no empirical basis or were misconstrued. Several properties of a tracking device (e.g. weight, balance, size, drag) can affect different aspects of an arthropod’s life history (e.g. energy, movement, foraging, mating). The impact can differ among species and environments. Taken together, these tag effects can influence the reliability of obtained movement data and conclusions drawn from them. We argue that the impact of tracking devices on arthropods should be quantified for each (1) study species, (2) tag type, and (3) environmental context. As an example, we include a low‐effort impact study of the effect of an RFID tag on a digger wasp. Technological advancements enable studying the movement of arthropods in unprecedented detail. However, we should adopt a more critical attitude towards the use of tracking devices on terrestrial arthropods. The benefits of tracking devices should be balanced against their potential side effects on arthropods and on the reliability of the resulting data.

We present Visual TreeCmp – a package of applications for comparing phylogenetic tree sets.

The resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, both empirical research and conservation measures have been limited by questions regarding the impacts of data set size, data quality thresholds, and the time scale at which barriers to gene flow become detectable. Here, we used restriction site associated DNA sequencing to generate a 2,140 SNP data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an approximately 1000 km2 region of eastern Kentucky, USA. Nonspatial population‐based assignment and clustering methods supported little to no population structure. However, using individual‐based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historically important highway which experienced high traffic volumes from ca. 1920 to 1970 before losing most traffic to a newly constructed alternate route. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, though a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and a range of thresholds for missing data exhibited limited impacts on the spatial patterns we detected. While we were not able to estimate relative effects of land uses or precise time lags, our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of genomic data sets and fine‐scale, spatially informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.

For clonal plants the role of sexual reproduction in the maintenance of populations can vary widely. Some species are dependent on repeated seedling recruitment. For other species, interactions between adults and seedlings within existing populations can affect seedling survival and limit sexual reproduction in existing populations. Genetic studies of seagrass populations increasingly suggest sexual reproduction is important for the resilience and stability of their populations, but as of yet little observational data supports these findings. Because seagrass populations provide important ecosystem services and are threatened with increasing anthropogenic impacts, understanding their reliance on sexual reproduction is evolutionarily and ecologically important.

Much recent research has explored how global warming and increased nitrogen (N) deposition, two important components of global environmental changes, influence the structure and functioning of natural ecosystems. However, how ecosystem dynamics respond to the combination of long‐term warming and N enrichment remains largely unexplored. We investigated the impact of warming and N addition on the temporal stability of plant communities in a decade‐long field experiment, conducted in a desert steppe in northern China, using a split‐plot design with warming as the main‐plot factor and N addition as the split‐plot factor. Long‐term warming and N addition had additive, negative effects on plant community stability. A warming‐induced decrease in species richness was not a significant driver of decreased community stability, which was instead driven by the decreased stability of dominant species under warming. On the other hand, a N‐induced decrease in community stability was ascribed to both decreased stability of dominant and common species and decreased asynchronous population dynamics under N addition. Synthesis. Our results suggest that ongoing anthropogenic environmental changes may have appreciable consequences for the stability of natural grassland functions and services, while also highlighting the different mechanisms associated with the similar effects of climate warming and increased N deposition on grassland community stability.

The European rabbit (Oryctolagus cuniculus) is a notorious economic and environmental pest species in its invasive range. To better understand the population and range dynamics of this species, 41 years of abundance data have been collected from 116 unique sites across a broad range of climatic and environmental conditions in Australia. We analyzed this time series of abundance data to determine whether inter‐annual variation in climatic conditions can be used to map historic, contemporary, and potential future fluctuations in rabbit abundance from regional to continental scales. We constructed a hierarchical Bayesian regression model of relative abundance that corrected for observation error and seasonal biases. The corrected abundances were regressed against environmental and disease variables in order to project high spatiotemporal resolution, continent‐wide rabbit abundances. We show that rabbit abundance in Australia is highly variable in space and time, being driven primarily by inter‐annual variation in temperature and precipitation in concert with the prevalence of a non‐pathogenic virus. Moreover, we show that inter‐annual variation in local spatial abundances can be mapped effectively at a continental scale using highly resolved spatiotemporal predictors, allowing “hotspots” of persistently high rabbit abundance to be identified. Importantly, cross‐validated model performance was fair to excellent within and across distinct climate zones. Long‐term monitoring data for invasive species can be used to map fine‐scale spatiotemporal fluctuations in abundance patterns when accurately accounting for inherent sampling biases. Our analysis provides ecologists and pest managers with a clearer understanding of the determinants of rabbit abundance in Australia, offering an important new approach for predicting spatial abundance patterns of invasive species at the near‐term temporal scales that are directly relevant to resource management.

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.