Logging response alters trajectories of reorganization after loss of a foundation tree species

Forest insect outbreaks cause large changes in ecosystem structure, composition, and function. Humans often respond to insect outbreaks by conducting salvage logging, which can amplify the immediate effects, but it is unclear whether logging will result in lasting differences in forest structure and dynamics when compared with forests affected only by insect outbreaks. We used 15 years of data from an experimental removal of Tsuga canadensis (L.) Carr. (Eastern hemlock), a foundation tree species within eastern North American forests, and contrasted the rate, magnitude, and persistence of response trajectories between girdling (emulating mortality from insect outbreak) and timber harvest treatments. Girdling and logging were equally likely to lead to large changes in forest structure and dynamics, but logging resulted in faster rates of change. Understory light increases and community composition changes were larger and more rapid in the logged plots. Tree seedling and understory vegetation abundance increased more in the girdled plots; this likely occurred because seedlings grew rapidly into the sapling- and tree-size classes after logging and quickly shaded out plants on the forest floor. Downed deadwood pools increased more after logging but standing deadwood pools increased dramatically after girdling. Understory light levels remained elevated for a longer time after girdling. Perhaps because the window of opportunity for understory species to establish was longer in the girdled plots, total species richness increased more in the girdled than logged plots. Despite the potential for greater diversity in the girdled plots, Betula lenta L. (black birch) was the most abundant tree species recruited into the sapling- and tree-size classes in both the girdled and logged plots and is poised to dominate the new forest canopy. The largest difference between the girdling and logging treatments-deadwood structure and quantity-will persist and continue to bolster aboveground carbon storage and structural and habitat diversity in the girdled plots. Human responses to insect outbreaks hasten forest reorganization and remove structural resources that may further alter forest response to ongoing climate stress and future disturbances.

Incorporating plant phenological responses into species distribution models reduces estimates of future species loss and turnover

Anthropogenetic climate change has caused range shifts among many species. Species distribution models (SDMs) are used to predict how species ranges may change in the future. However, most SDMs rarely consider how climate-sensitive traits, such as phenology, which affect individuals' demography and fitness, may influence species' ranges. Using > 120 000 herbarium specimens representing 360 plant species distributed across the eastern United States, we developed a novel 'phenology-informed' SDM that integrates phenological responses to changing climates. We compared the ranges of each species forecast by the phenology-informed SDM with those from conventional SDMs. We further validated the modeling approach using hindcasting. When examining the range changes of all species, our phenology-informed SDMs forecast less species loss and turnover under climate change than conventional SDMs. These results suggest that dynamic phenological responses of species may help them adjust their ecological niches and persist in their habitats as the climate changes. Plant phenology can modulate species' responses to climate change, mitigating its negative effects on species persistence. Further application of our framework will contribute to a generalized understanding of how traits affect species distributions along environmental gradients and facilitate the use of trait-based SDMs across spatial and taxonomic scales.

Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America

Phenology varies widely over space and time because of its sensitivity to climate. However, whether phenological variation is primarily generated by rapid organismal responses (plasticity) or local adaptation remains unresolved. Here we used 1,038,027 herbarium specimens representing 1,605 species from the continental United States to measure flowering-time sensitivity to temperature over time (Stime) and space (Sspace). By comparing these estimates, we inferred how adaptation and plasticity historically influenced phenology along temperature gradients and how their contributions vary among species with different phenology and native climates and among ecoregions differing in species composition. Parameters Sspace and Stime were positively correlated (r = 0.87), of similar magnitude and more frequently consistent with plasticity than adaptation. Apparent plasticity and adaptation generated earlier flowering in spring, limited responsiveness in late summer and delayed flowering in autumn in response to temperature increases. Nonetheless, ecoregions differed in the relative contributions of adaptation and plasticity, from consistently greater importance of plasticity (for example, southeastern United States plains) to their nearly equal importance throughout the season (for example, Western Sierra Madre Piedmont). Our results support the hypothesis that plasticity is the primary driver of flowering-time variation along temperature gradients, with local adaptation having a widespread but comparatively limited role.

Comparing two spatial variables with the probability of agreement

Computing the agreement between 2 continuous sequences is of great interest in statistics when comparing 2 instruments or one instrument with a gold standard. The probability of agreement quantifies the similarity between 2 variables of interest, and it is useful for determining what constitutes a practically important difference. In this article, we introduce a generalization of the PA for the treatment of spatial variables. Our proposal makes the PA dependent on the spatial lag. We establish the conditions for which the PA decays as a function of the distance lag for isotropic stationary and nonstationary spatial processes. Estimation is addressed through a first-order approximation that guarantees the asymptotic normality of the sample version of the PA. The sensitivity of the PA with respect to the covariance parameters is studied for finite sample size. The new method is described and illustrated with real data involving autumnal changes in the green chromatic coordinate (Gcc), an index of "greenness" that captures the phenological stage of tree leaves, is associated with carbon flux from ecosystems, and is estimated from repeated images of forest canopies.

Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk

Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited. Herbaria represent an important, but underutilized source of data for investigating this question. We harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering). Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions. Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.

Science and the legal rights of nature

We review the use of science by lawmakers and courts in implementing or rejecting legal rights for nature in Ecuador, India, the United States, and other jurisdictions where some type of rights of nature have been recognized in the legal system. We then use the "right to evolve" to exemplify how interdisciplinary work can (i) help courts effectively define what this right might entail; (ii) inform how it might be applied in different circumstances; and (iii) provide a template for how scientists and legal scholars can generate the interdisciplinary scholarship necessary to understand and implement the growing body of rights-of-nature laws, and environmental law more generally. We conclude by pointing to what further research is needed to understand and effectively implement the growing body of rights-of-nature laws.

Reproducibility in ecology and evolution: Minimum standards for data and code

We call for journals to commit to requiring open data be archived in a format that will be simple and clear for readers to understand and use. If applied consistently, these requirements will allow contributors to be acknowledged for their work through citation of open data, and facilitate scientific progress.

Phenological displacement is uncommon among sympatric angiosperms

Interactions between species can influence successful reproduction, resulting in reproductive character displacement, where the similarity of reproductive traits - such as flowering time - among close relatives growing together differ from when growing apart. Evidence for the overall prevalence and direction of this phenomenon, and its stability under environmental change, remains untested across large scales. Using the power of crowdsourcing, we gathered phenological information from over 40 000 herbarium specimens, and investigated displacement in flowering time across 110 animal-pollinated species in the eastern USA. Overall, flowering time displacement is not common across large scales. However, displacement is generally greater among species pairs that flower close in time, regardless of direction. Furthermore, with climate change, the flowering times of closely related species are predicted, on average, to shift further apart by the mid-21^st century. We demonstrate that the degree and direction of phenological displacement among co-occurring closely related species pairs varies tremendously. However, future climate change may alter the differences in reproductive timing among many of these species pairs, which may have significant consequences for species interactions and gene flow. Our study provides one promising path towards understanding how the phenological landscape is structured and may respond to future environmental change.

Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot

Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010-2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to describe the composition and structure of the woody plants in this plot, assess their spatial associations within and among the dominant species using univariate and bivariate spatial point-pattern analysis, and examine the interactions between land-use history and ecological processes. The plot includes 108,632 live stems ≥ 1 cm in diameter (2,215 individuals/ha) and 7,595 standing dead stems ≥ 5 cm in diameter. Live tree basal area averaged 42.25 m²/ha, of which 84% was represented by Tsuga canadensis (14.0 m²/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), Acer rubrum (7.2 m²/ ha) and Pinus strobus (eastern white pine; 4.4 m²/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha. Across all species and size classes, the forest contains a preponderance (> 80,000) of small stems (<10-cm diameter) that exhibit a reverse-J size distribution. Significant spatial clustering of abundant overstory species was observed at all spatial scales examined. Spatial distributions of A. rubrum and Q. rubra showed negative intraspecific correlations in diameters up to at least a 150-m spatial lag, likely indicative of crowding effects in dense forest patches following intensive past land use. Bivariate marked point-pattern analysis, showed that T. canadensis and Q. rubra diameters were negatively associated with one another, indicating resource competition for light. Distribution and abundance of the common overstory species are predicted best by soil type, tree neighborhood effects, and two aspects of land-use history: when fields were abandoned in the late 19th century and the succeeding forest types recorded in 1908. In contrast, a history of intensive logging prior to 1950 and a damaging hurricane in 1938 appear to have had little effect on the distribution and abundance of present-day tree species. Our findings suggest that current day composition and structure are still being influenced by anthropogenic disturbances that occurred over a century ago.

Broadening the ecological mindset

Over the past three decades, the Harvard Forest Summer Research Program in Ecology (HF-SRPE) has been at the forefront of expanding the ecological tent for minoritized or otherwise marginalized students. By broadening the definition of ecology to include fields such as data science, software engineering, and remote sensing, we attract a broader range of students, including those who may not prioritize field experiences or who may feel unsafe working in rural or urban field sites. We also work towards a more resilient society in which minoritized or marginalized students can work safely, in part by building teams of students and mentors. Teams collaborate on projects that require a diversity of approaches and create opportunities for students and mentors alike to support one another and share leadership. Finally, HF-SRPE promotes an expanded view of what it means to become an ecologist. We value and support diverse career paths for ecologists to work in all parts of society, to diversify the face of ecology, and to bring different perspectives together to ensure innovations in environmental problem solving for our planet.

Designing (for) Urban Food Webs

Interest is growing in designing resilient and ecologically rich urban environments that provide social and ecological benefits. Regenerative and biocentric designs fostering urban ecological habitats including food webs that provide ecosystem services for people and wildlife increasingly are being sought. However, the intentional design of urban landscapes for food webs remains in an early stage with few precedents and many challenges. In this paper, we explore the potential to design (for) urban food webs through collaborations between designers and ecologists. We start by examining the ecology and management of Jamaica Bay in New York City as a case study of an anthropogenic landscape where ecosystems are degraded and the integrity of extant food webs are intertwined with human agency. A subsequent design competition focusing on ecological design and management of this large-scale landscape for animal habitat and ecosystem services for people illustrates how designers approach this anthropogenic landscape. This case study reveals that both designing urban landscapes for food webs and directly designing and manipulating urban food webs are complicated and challenging to achieve and maintain, but they have the potential to increase ecological health of, and enhance ecosystem services in, urban environments. We identify opportunities to capitalize on species interactions across trophic structures and to introduce managed niches in biologically engineered urban systems. The design competition reveals an opportunity to approach urban landscapes and ecological systems creatively through a proactive design process that includes a carefully crafted collaborative approach to constructing ecologically functioning landscapes that can integrate societal demands. As designers increasingly seek to build, adapt, and manage urban environments effectively, it will be critical to resolve the contradictions and challenges associated with human needs, ecosystem dynamics, and interacting assemblages of species. Ecologists and designers are still discovering and experimenting with designing (for) urban food webs and fostering species interactions within them. We recommend generating prototypes of urban food webs through a learning-by-doing approach in urban development projects. Design and implementation of urban food webs also can lead to research opportunities involving monitoring and experiments that identify and solve challenges of food-web construction while supporting and encouraging ongoing management.

Foraging modes of carnivorous plants

Carnivorous plants are pure sit-and-wait predators: they remain rooted to a single location and depend on the abundance and movement of their prey to obtain nutrients required for growth and reproduction. Yet carnivorous plants exhibit phenotypically plastic responses to prey availability that parallel those of non-carnivorous plants to changes in light levels or soil-nutrient concentrations. The latter have been considered to be foraging behaviors, but the former have not. Here, I review aspects of foraging theory that can be profitably applied to carnivorous plants considered as sit-and-wait predators. A discussion of different strategies by which carnivorous plants attract, capture, kill, and digest prey, and subsequently acquire nutrients from them suggests that optimal foraging theory can be applied to carnivorous plants as easily as it has been applied to animals. Carnivorous plants can vary their production, placement, and types of traps; switch between capturing nutrients from leaf-derived traps and roots; temporarily activate traps in response to external cues; or cease trap production altogether. Future research on foraging strategies by carnivorous plants will yield new insights into the physiology and ecology of what Darwin called “the most wonderful plants in the world”. At the same time, inclusion of carnivorous plants into models of animal foraging behavior could lead to the development of a more general and taxonomically inclusive foraging theory.

Foundation species across a latitudinal gradient in China

Foundation species structure forest communities and ecosystems but are difficult to identify without long-term observations or experiments. We used statistical criteria--outliers from size-frequency distributions and scale-dependent negative effects on alpha diversity and positive effects on beta diversity--to identify candidate foundation woody plant species in 12 large forest-dynamics plots spanning 26 degrees of latitude in China. We used these data (1) to identify candidate foundation species in Chinese forests, (2) to test the hypothesis--based on observations of a midlatitude peak in functional trait diversity and high local species richness but few numerically dominant species in tropical forests--that foundation woody plant species are more frequent in temperate than tropical or boreal forests, and (3) to compare these results with data from the Americas to suggest candidate foundation genera in northern hemisphere forests. Using the most stringent criteria, only two species of Acer, the canopy tree Acer ukurunduense and the shrubby treelet Acer barbinerve, were identified in temperate plots as candidate foundation species. Using more relaxed criteria, we identified four times more candidate foundation species in temperate plots (including species of Acer, Pinus, Juglans, Padus, Tilia, Fraxinus, Prunus, Taxus, Ulmus, and Corlyus) than in (sub)tropical plots (the treelets or shrubs Aporosa yunnanensis, Ficus hispida, Brassaiopsis glomerulata, and Orophea laui). Species diversity of co-occurring woody species was negatively associated with basal area of candidate foundation species more frequently at 5- and 10-m spatial grains (scale) than at a 20-m grain. Conversely, Bray-Curtis dissimilarity was positively associated with basal area of candidate foundation species more frequently at 5-m than at 10- or 20-m grains. Both stringent and relaxed criteria supported the hypothesis that foundation species are more common in mid-latitude temperate forests. Comparisons of candidate foundation species in Chinese and North American forests suggest that Acer be investigated further as a foundation tree genus.

Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem

Incremental increases in a driver variable, such as nutrients or detritus, can trigger abrupt shifts in aquatic ecosystems that may exhibit hysteretic dynamics and a slow return to the initial state. A model system for understanding these dynamics is the microbial assemblage that inhabits the cup-shaped leaves of the pitcher plant Sarracenia purpurea. With enrichment of organic matter, this system flips within three days from an oxygen-rich state to an oxygen-poor state. In a replicated greenhouse experiment, we enriched pitcher-plant leaves at different rates with bovine serum albumin (BSA), a molecular substitute for detritus. Changes in dissolved oxygen (DO) and undigested BSA concentration were monitored during enrichment and recovery phases. With increasing enrichment rates, the dynamics ranged from clockwise hysteresis (low), to environmental tracking (medium), to novel counter-clockwise hysteresis (high). These experiments demonstrate that detrital enrichment rate can modulate a diversity of hysteretic responses within a single aquatic ecosystem, and suggest different management strategies may be needed to mitigate the effects of high vs. low rates of detrital enrichment.

A New Method for Counting Reproductive Structures in Digitized Herbarium Specimens Using Mask R-CNN

Phenology-the timing of life-history events-is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from >3,000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with >87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant responses to ongoing climatic change.

The End-to-End Provenance Project

Data provenance is a machine-readable summary of the collection and computational history of a dataset. Data provenance confers or adds value to a dataset, helps reproduce computational analyses, or validates scientific conclusions. The people of the End-to-End Provenance Project are a community of professionals who have developed software tools to collect and use data provenance.

Lessons and recommendations from three decades as an NSF REU site: A call for systems-based assessment

For more than 30 years, the US National Science Foundation's Research Experiences for Undergraduates (REU) program has supported thousands of undergraduate researchers annually and provides many students with their first research experiences in field ecology or evolution. REUs embed students in scientific communities where they apprentice with experienced researchers, build networks with their peers, and help students understand research cultures and how to work within them. REUs are thought to provide formative experiences for developing researchers that differ from experiences in a college classrooms, laboratories, or field trips. REU assessments have improved through time but they are largely ungrounded in educational theory. Thus, evaluation of long-term impacts of REUs remains limited and best practices for using REUs to enhance student learning are repeatedly re-invented. We describe how one sociocultural learning framework, cultural-historical activity theory (CHAT), could be used to guide data collection to characterize the effects of REU programs on participant's learning in an educationally meaningful context. CHAT embodies a systems approach to assessment that accounts for social and cultural factors that influence learning. We illustrate how CHAT has guided assessment of the Harvard Forest Summer Research Program in Ecology (HF-SRPE), one of the longest-running REU sites in the United States. Characterizing HF-SRPE using CHAT helped formalize thoughts and language for the program evaluation, reflect on potential barriers to success, identify assessment priorities, and revealed important oversights in data collection.

Lessons and recommendations from three decades as an NSF REU site: A call for systems-based assessment

For more than 30 years, the US National Science Foundation's Research Experiences for Undergraduates (REU) program has supported thousands of undergraduate researchers annually and provides many students with their first research experiences in field ecology or evolution. REUs embed students in scientific communities where they apprentice with experienced researchers, build networks with their peers, and help students understand research cultures and how to work within them. REUs are thought to provide formative experiences for developing researchers that differ from experiences in a college classrooms, laboratories, or field trips. REU assessments have improved through time but they are largely ungrounded in educational theory. Thus, evaluation of long-term impacts of REUs remains limited and best practices for using REUs to enhance student learning are repeatedly re-invented. We describe how one sociocultural learning framework, cultural-historical activity theory (CHAT), could be used to guide data collection to characterize the effects of REU programs on participant's learning in an educationally meaningful context. CHAT embodies a systems approach to assessment that accounts for social and cultural factors that influence learning. We illustrate how CHAT has guided assessment of the Harvard Forest Summer Research Program in Ecology (HF-SRPE), one of the longest-running REU sites in the United States. Characterizing HF-SRPE using CHAT helped formalize thoughts and language for the program evaluation, reflect on potential barriers to success, identify assessment priorities, and revealed important oversights in data collection.

Trade-Offs in Cold Resistance at the Northern Range Edge of the Common Woodland Ant Aphaenogaster picea (Formicidae)

Geographic variation in low temperatures at poleward range margins of terrestrial species often mirrors population variation in cold resistance, suggesting that range boundaries may be set by evolutionary constraints on cold physiology. The northeastern woodland ant Aphaenogaster picea occurs up to approximately 45°N in central Maine. We combined presence/absence surveys with classification tree analysis to characterize its northern range limit and assayed two measures of cold resistance operating on different timescales to determine whether and how marginal populations adapt to environmental extremes. The range boundary of A. picea was predicted primarily by temperature, but low winter temperatures did not emerge as the primary correlate of species occurrence. Low summer temperatures and high seasonal variability predicted absence above the boundary, whereas high mean annual temperature (MAT) predicted presence in southern Maine. In contrast, assays of cold resistance across multiple sites were consistent with the hypothesis of local cold adaptation at the range edge: among populations, there was a 4-min reduction in chill coma recovery time across a 2° reduction in MAT. Baseline resistance and capacity for additional plastic cold hardening shifted in opposite directions, with hardening capacity approaching zero at the coldest sites. This trade-off between baseline resistance and cold-hardening capacity suggests that populations at range edges may adapt to colder temperatures through genetic assimilation of plastic responses, potentially constraining further adaptation and range expansion.

Frost controls spring phenology of juvenile Smith fir along elevational gradients on the southeastern Tibetan Plateau

Impacts of climatic means on spring phenology are well documented, whereas the role of climatic variance, such as occurrence of spring frosts, has long been neglected. A large elevational gradient of forests on the southeastern Tibetan Plateau provides an ideal platform to explore correlates of spring phenology and environmental factors. We tested the hypothesis that spring frost was a major factor regulating the timing of bud-leaf phenology by combining 5 years of in situ phenological observations of Abies georgei var. smithii with concurrent air temperature data along two altitudinal gradients. Mean lapse rate for the onset of bud swelling and leaf unfolding was 3.1 ± 0.5 days/100 m and 3.0 ± 0.6 days/100 m, respectively. Random forest analysis and conditional inference trees revealed that the frequency of freezing events was a critical factor in determining the timing of bud swelling, independent of topographic differences, varying accumulation of chilling days, and degree-days. In contrast, the onset of leaf unfolding was primarily controlled by the bud swelling onset. Thus, the timing of bud swelling and leaf unfolding appear to be controlled directly and indirectly, respectively, by spring frost. Using space-for-time substitution, the frequency of spring freezing events decreased by 7.1 days with 1 °C of warming. This study provides evidence for impacts of late spring frosts on spring phenology, which have been underappreciated in research on phenological sensitivity to climate but should be included in phenology models. Fewer spring freezing events with warming have important implications for the upward migration of alpine forests and treelines.

Establish an environmentally sustainable Giant Panda National Park in the Qinling Mountains

The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world and is recognized worldwide as a symbol for conservation. The Qinling subspecies of giant panda (Ailuropoda melanoleuca qinlingensis) is highly endangered; fewer than 350 individuals still inhabit the Qinling Mountains. Last year, China announced the establishment of the first Giant Panda National Park (GPNP) with a goal of restoring and connecting fragmented habitats; the proposal ignored the environmental pollution caused by economic development in panda habitats. The spatial distribution of heavy metals (Cd, Pb, Hg, Cu, Zn, Mn, Cr, Ni and As) was analyzed in giant panda feces, soil, bamboo, and water in four of GPNP's functional areas at different altitudes and latitudes. Heavy metal pollution decreased with anthropogenic influences, from outside the park through the buffer and into the core area. Cu, Mn, Ni and Zn accumulated from natural sources; As, Hg and Cr were associated with fuel combustion; and Pb and Cd were associated with traffic and agriculture sources. The presence of heavy metals at high altitudes and latitudes in the proposed GPNP is due to emissions from Xi'an and other upwind industrial cities. We conclude that reducing emissions and heavy metal input should be included in the design of the GPNP. Policy interventions should consider functional zones planning, wind direction, reducing mining, and the abandonment of existing roads and farmland within the GPNP to reduce other direct human impacts on the Qinling panda.

Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients

Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8-396.0 Mb) and flow cytometry estimates (210.7-690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.

Foundation Species, Non-trophic Interactions, and the Value of Being Common

Foundation species define ecosystems, control the biological diversity of associated species, modulate critical ecosystem processes, and often have important cultural values and resonance. This review summarizes current understanding of the characteristics and traits of foundation species and how to distinguish them from other “important” species in ecological systems (e.g., keystone, dominant, and core species); illustrates how analysis of the structure and function of ecological networks can be improved and enriched by explicit incorporation of foundation species and their non-trophic interactions; discusses the importance of pro-active identification and management of foundation species as a cost-effective and efficient method of sustaining valuable ecosystem processes and services and securing populations of associated rare, threatened, or endangered species; and suggests broader engagement of citizen-scientists and non-specialists in the identification and study of foundation species and their biological and cultural values.

First In Situ Identification of Ultradian and Infradian Rhythms, and Nocturnal Locomotion Activities of Four Colonies of Red Wood Ants ( Formica rufa-Group)

In situ activity patterns of 2 Formica rufa-group species ( F. pratensis; F. polyctena) were continuously studied at 4 different red wood-ant nests for 6 months in each of the years 2010, 2011, 2012, and 2016 and related to weather factors and variations in the Earth's magnetic field. The in situ activity patterns of both species were similarly periodic and exhibited ultradian, and short- and long infradian rhythms under natural LD conditions. Crepuscular and nocturnal activities shorter than or equal to 4 h were observed in both species, especially at the new moon and first quarter after the astronomical twilight in a period of darkness in fall. We hypothesize that local variability in the Earth's magnetic field affects these long-term activity patterns, whereas humidity and temperature were more strongly associated with ultradian rhythms (less than 20 h).

How do climate change experiments alter plot-scale climate?

To understand and forecast biological responses to climate change, scientists frequently use field experiments that alter temperature and precipitation. Climate manipulations can manifest in complex ways, however, challenging interpretations of biological responses. We reviewed publications to compile a database of daily plot-scale climate data from 15 active-warming experiments. We find that the common practices of analysing treatments as mean or categorical changes (e.g. warmed vs. unwarmed) masks important variation in treatment effects over space and time. Our synthesis showed that measured mean warming, in plots with the same target warming within a study, differed by up to 1.6  ∘ C (63% of target), on average, across six studies with blocked designs. Variation was high across sites and designs: for example, plots differed by 1.1  ∘ C (47% of target) on average, for infrared studies with feedback control (n = 3) vs. by 2.2  ∘ C (80% of target) on average for infrared with constant wattage designs (n = 2). Warming treatments produce non-temperature effects as well, such as soil drying. The combination of these direct and indirect effects is complex and can have important biological consequences. With a case study of plant phenology across five experiments in our database, we show how accounting for drier soils with warming tripled the estimated sensitivity of budburst to temperature. We provide recommendations for future analyses, experimental design, and data sharing to improve our mechanistic understanding from climate change experiments, and thus their utility to accurately forecast species' responses.

The Past, Present, and Future of the Hemlock Woolly Adelgid (Adelges tsugae) and Its Ecological Interactions with Eastern Hemlock (Tsuga canadensis) Forests

The nonnative hemlock woolly adelgid is steadily killing eastern hemlock trees in many parts of eastern North America. We summarize impacts of the adelgid on these forest foundation species; review previous models and analyses of adelgid spread dynamics; and examine how previous forecasts of adelgid spread and ecosystem dynamics compare with current conditions. The adelgid has reset successional sequences, homogenized biological diversity at landscape scales, altered hydrological dynamics, and changed forest stands from carbon sinks into carbon sources. A new model better predicts spread of the adelgid in the south and west of the range of hemlock, but still under-predicts its spread in the north and east. Whether these underpredictions result from inadequately modeling accelerating climate change or accounting for people inadvertently moving the adelgid into new locales needs further study. Ecosystem models of adelgid-driven hemlock dynamics have consistently forecast that forest carbon stocks will be little affected by the shift from hemlock to early-successional mixed hardwood stands, but these forecasts have assumed that the intermediate stages will remain carbon sinks. New forecasting models of adelgid-driven hemlock decline should account for observed abrupt changes in carbon flux and ongoing and accelerating human-driven land-use and climatic changes.

Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States

Phenology is a key biological trait that can determine an organism's survival and provides one of the clearest indicators of the effects of recent climatic change. Long time-series observations of plant phenology collected at continental scales could clarify latitudinal and regional patterns of plant responses and illuminate drivers of that variation, but few such datasets exist. Here, we use the web tool CrowdCurio to crowdsource phenological data from over 7000 herbarium specimens representing 30 diverse flowering plant species distributed across the eastern United States. Our results, spanning 120 years and generated from over 2000 crowdsourcers, illustrate numerous aspects of continental-scale plant reproductive phenology. First, they support prior studies that found plant reproductive phenology significantly advances in response to warming, especially for early-flowering species. Second, they reveal that fruiting in populations from warmer, lower latitudes is significantly more phenologically sensitive to temperature than that for populations from colder, higher-latitude regions. Last, we found that variation in phenological sensitivities to climate within species between regions was of similar magnitude to variation between species. Overall, our results suggest that phenological responses to anthropogenic climate change will be heterogeneous within communities and across regions, with large amounts of regional variability driven by local adaptation, phenotypic plasticity and differences in species assemblages. As millions of imaged herbarium specimens become available online, they will play an increasingly critical role in revealing large-scale patterns within assemblages and across continents that ultimately can improve forecasts of the impacts of climatic change on the structure and function of ecosystems.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Environmental toxicants impair liver and kidney function and sperm quality of captive pandas

Captive pandas are exposed to higher concentrations of environmental toxins in their food source and from atmospheric pollution than wild pandas. Moreover, the Qinling panda subspecies had significantly higher concentrations of toxic chemicals in its feces. To determine whether these toxicants also accumulate in panda's blood and impair its health, concentrations of persistent organic pollutants (POPs) and heavy metals were measured in blood samples. Four heavy metals (As, Cd, Cr and Pb), PCDD/Fs and PCBs were detected in blood drawn from captive Qinling pandas. Time spent in captivity was a better predictor of toxicant concentration accumulation than was panda age. More than 50% of the studied pandas were outside the normal levels for 11 health parameters, and five (ALT, LDH, Ca, Cl, TB) of the 11 parameters classified as abnormal were correlated with blood pollutant concentrations. The proportion of live sperm was significantly lower and the aberrance ratio of sperm was significantly greater for captive pandas than for wild ones. A short-term solution to reduce the health impacts of pollution and toxicant exposure of Qinling pandas is to relocate breeding centers to less contaminated areas and to strictly control the quality of their food provided. A longer term solution depends on improving air quality by reducing toxic emissions.

Degassing Rhythms and Fluctuations of Geogenic Gases in A Red Wood-Ant Nest and in Soil in The Neuwied Basin (East Eifel Volcanic Field, Germany)

Geochemical tracers of crustal fluids (CO₂, He, Rn) provide a useful tool for the identification of buried fault structures. We acquired geochemical data during 7-months of continual sampling to identify causal processes underlying correlations between ambient air and degassing patterns of three gases (CO₂, He, Rn) in a nest of red wood ants (Formica polyctena; “RWA”) and the soil at Goloring in the Neuwied Basin, a part of the East Eifel Volcanic Field (EEVF). We explored whether temporal relations and degassing rhythms in soil and nest gas concentrations could be indicators of hidden faults through which the gases migrate to the surface from depth. In nest gas, the coupled system of CO₂-He and He concentrations exceeding atmospheric standards 2-3 fold suggested that RWA nests may be biological indicators of hidden degassing faults and fractures at small scales. Equivalently periodic degassing infradian rhythms in the RWA nest, soil, and three nearby minerals springs suggested NW-SE and NE-SW tectonic linkages. Because volcanic activity in the EEVF is dormant, more detailed information on the EEVF’s tectonic, magmatic, and degassing systems and its active tectonic fault zones are needed. Such data could provide additional insights into earthquake processes that are related to magmatic processes at the lower crust.

Critical temperature and precipitation thresholds for the onset of xylogenesis of Juniperus przewalskii in a semi-arid area of the north-eastern Tibetan Plateau

Background and Aims

The onset of xylogenesis plays an important role in tree growth and carbon sequestration, and it is thus a key variable in modelling the responses of forest ecosystems to climate change. Temperature regulates the resumption of cambial activity, but little is known about the effect of water availability on the onset of xylogenesis in cold but semi-arid regions.

Methods

The onset of xylogenesis during 2009-2014 was monitored by weekly microcoring Juniperus przewalskii trees at upper and lower treelines on the north-eastern Tibetan Plateau. A logistic regression was used to calculate the probability of xylogenic activity at a given temperature and a two-dimensional reverse Gaussian model to fit the differences between the observed and estimated days of xylogenesis onset at given temperatures and precipitation within a certain time window.

Key Results

The thermal thresholds at the beginning of the growing season were highly variable, suggesting that temperature was not the only factor initiating xylem growth under cold and dry climatic conditions. The onset of xylogenesis was well predicted for climatic thresholds characterized by a cumulative precipitation of 17.0 ± 5.6 mm and an average minimum temperature of 1.5 ± 1.4 °C for a period of 12 d.

Conclusions

Xylogenesis in semi-arid regions with dry winters and springs can start when both critical temperature and precipitation thresholds are reached. Such findings contribute to our knowledge of the environmental drivers of growth resumption that previously had been investigated largely in cold regions without water shortages during early growing seasons. Models of the onset of xylogenesis should include water availability to improve predictions of xylem phenology in dry areas. A mismatch between the thresholds of temperature and moisture for the onset of xylogenesis may increase forest vulnerability in semi-arid areas under forecasted warmer and drier conditions.

Widespread sampling biases in herbaria revealed from large-scale digitization

Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via 'founder effects'. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.

Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test

Ecological studies often are subjected to unintentional biases, suggesting that improved research designs for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors, and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants (Formica rufa, RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 m of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE-SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research.

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem

Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea. Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.

If these data could talk

In the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software have enabled the rapid implementation of novel methods to manage and analyze the growing flood of data. However, it has become apparent that many scientific fields exhibit distressingly low rates of reproducibility. Although there are many dimensions to this issue, we believe that there is a lack of formalism used when describing end-to-end published results, from the data source to the analysis to the final published results. Even when authors do their best to make their research and data accessible, this lack of formalism reduces the clarity and efficiency of reporting, which contributes to issues of reproducibility. Data provenance aids both reproducibility through systematic and formal records of the relationships among data sources, processes, datasets, publications and researchers.