pinecone/core-2020-05-10-deduplication huggingface dataset:
The mismatch between current statistical practice and doctoral training in ecology

Ecologists are studying increasingly complex and important issues such as climate change and ecosystem services. These topics often involve large data sets and the application of complicated quantitative models. We evaluated changes in statistics used by ecologists by searching nearly 20,000 published articles in ecology from 1990 to 2013. We found that there has been a rise in sophisticated and computationally intensive statistical techniques such as mixed effects models and Bayesian statistics and a decline in reliance on approaches such as ANOVA or t tests. Similarly, ecologists have shifted away from software such as SAS and SPSS to the open source program R. We also searched the published curricula and syllabi of 154 doctoral programs in the United States and found that despite obvious changes in the statistical practices of ecologists, more than one-third of doctoral programs showed no record of required or optional statistics classes. Approximately one-quarter of programs did require a statistics course, but most of those did not cover contemporary statistical philosophy or advanced techniques. Only one-third of doctoral programs surveyed even listed an optional course that teaches some aspect of contemporary statistics. We call for graduate programs to lead the charge in improving training of future ecologists with skills needed to address and understand the ecological challenges facing humanity.ECU Open Access Publishing Support Fun
The interaction of land-use legacies and hurricane disturbance in subtropical wet forest: twenty-one years of change

Disturbance shapes plant communities over a wide variety of spatial and temporal scales. How natural and anthropogenic disturbance interact to shape ecological communities is highly variable and begs a greater understanding. We used five censuses spanning the years 1990–2011 from the 16-ha Luquillo Forest Dynamics Plot (LFDP) in northeast Puerto Rico to investigate the interplay of human land-use legacies dating to the early 20th century and two recent hurricanes (Hugo, 1989 and Georges, 1998). The LFDP is a landscape mosaic comprised of an area of mature subtropical wet forest and three areas of secondary forest with differing past land-use intensities. We examined the degree to which hurricane disturbance–effect and subsequent community recovery varied across past land-use classes. We expected areas with greater intensity of human land use to be more affected by hurricane disturbance therefore exhibiting greater initial damage and longer successional recovery times. Structurally, areas of secondary forest contained smaller trees than old-growth areas; hurricanes caused widespread recruitment of shrubs and saplings that thinned with time since the first hurricane. Species richness of the plot declined over time, mostly due to the loss of rare species, but also due to the loss of some heliophilic, pioneer species that became abundant after the first hurricane. Species composition differed strongly between areas of secondary and mature forest, and these differences were largely constant over time, except for an increase in compositional differences following the second hurricane. An indicator species analysis attributed this pattern to the longer persistence of pioneer species in areas of greater past land-use intensity, likely due to the more open canopy in secondary forest. When secondary forest areas of differing past land-use intensity were considered separately, few species of low community rank were found as indicators. When these areas were combined, more and higher-ranked species emerged as indicators, creating ecologically meaningful indicator species combinations that better captured the broad-scale plant community response to past land use. Our findings support the idea that effects of past land use can persist for decades to centuries following land-use abandonment, illustrating the importance of land-use legacies in shaping regenerating tropical secondary forests
Predation or scavenging? Prey body condition influencesdecision-making in a facultative predator, the wolverine

The interaction between predators and their prey is a key factor driving population dynamics and shaping wildlife communities. Most predators will scavenge in addition to killing their own prey, which alters predation effects and implies that one cannot treat these as independent processes. However, the relative importance of predation vs. scavenging and the mechanisms driving variation of such are relatively unstudied in ecological research on predator–prey relationships. Foraging decisions in facultative predators are likely to respond to environmental conditions (e.g., seasonality) and inter-or intraspecific interactions (e.g., prey availability, presence of top predators, scavenging competition). Using data on 41 GPS-collared wolverines (Gulo gulo) during 2401 monitoring days, in four study sites in Scandinavia, we studied variation in diet and feeding strategies (predation vs. scavenging), along a gradient of environmental productivity, seasonality, density, and body mass of their main prey, semidomestic reindeer (Rangifer tarandus). The most important factor affecting the relative extent of predation and scavenging was mean prey body mass. Predation was more pronounced in summer, when vulnerable reindeer calves are abundant, and individual kill rates were negatively related to local reindeer body mass. This relationship was absent in winter. The probability of scavenging was higher in winter and increased with decreasing local reindeer body mass, likely as a response to increased carrion supply. Wolverine feeding strategy was further influenced by predictable anthropogenic food resources (e.g., slaughter remains from hunted ungulates) and the presence of a top predator, Eurasian lynx (Lynx lynx), which provided a continuous carrion supply promoting scavenging. Our results suggest that wolverine feeding strategies are flexible and strongly influenced by seasonally dependent responses to prey body condition in combination with carrion supply. This study demonstrates that large-scale environmental variation can result in contrasting predator feeding strategies, strongly affecting trophic interactions and potentially shaping the dynamics of ecological communities
Patch-burn grazing increases habitat heterogeneity and biodiversity of small mammals in managed rangelands

Citation: Ricketts, A. M., & Sandercock, B. K. (2016). Patch-burn grazing increases habitat heterogeneity and biodiversity of small mammals in managed rangelands. Ecosphere, 7(8). doi:10.1002/ecs2.1431Habitat heterogeneity is a key driver of biodiversity in many ecosystems. Wildlife inhabiting the native prairies of North America evolved in a heterogeneous mosaic of habitat conditions created by fire and grazing by native ungulates. Current rangeland management practices in the tallgrass prairie ecosystem evenly distribute fire and grazing across management units and promote homogeneous habitat conditions. Patch-burn grazing is a rangeland management strategy that seeks to restore heterogeneity to rangelands via fire-grazing interactions. Our 3.5-year study tested the effects of patch-burn grazing on habitat heterogeneity and small mammal community dynamics in the Flint Hills ecoregion of eastern Kansas. To study the ecological effects of patch-burn grazing, we sampled habitat conditions and the small mammal community. We assessed habitat conditions once each growing season in a negative control that was annually burned and grazed, a positive control that was burned every four years and ungrazed, and within each of three units of a patch-burn grazing experiment (PBG) managed with rotational fire. Habitat conditions were significantly different among treatments, and a principal components analysis showed that the patch-burn grazing treatment had higher canopy cover of forbs and habitat heterogeneity than our two control units. To sample the small mammal community, we conducted monthly live trapping of small mammals on two randomly located trap grids in each of our two controls and three units of our PBG treatment. Small mammal diversity was significantly higher in the patch-burn grazing treatment and in the positive control, vs. the negative control. Moreover, a canonical correspondence analysis showed that a fire-grazing interaction was the major driver structuring small mammal communities. Patch-burn grazing is an effective strategy for restoring heterogeneity to vegetative structure and composition, and can increase biodiversity of small mammals in managed rangelands in the tallgrass prairie ecosystem. © 2016 Ricketts and Sandercock
Emerging opportunities and challenges in phenology: a review

Plant phenology research has gained increasing attention because of the sensitivity of phenology to climate change and its consequences for ecosystem function. Recent technological development has made it possible to gather invaluable data at a variety of spatial and ecological scales. Despite our ability to observe phenological change at multiple scales, the mechanistic basis of phenology is still not well understood. Integration of multiple disciplines, including ecology, evolutionary biology, climate science, and remote sensing, with long-term monitoring data across multiple spatial scales are needed to advance understanding of phenology. We review the mechanisms and major drivers of plant phenology, including temperature, photoperiod, and winter chilling, as well as other factors such as competition, resource limitation, and genetics. Shifts in plant phenology have significant consequences on ecosystem productivity, carbon cycling, competition, food webs, and other ecosystem functions and services. We summarize recent advances in observation techniques across multiple spatial scales, including digital repeat photography, other complementary optical measurements, and solar induced fluorescence, to assess our capability to address the importance of these scale-dependent drivers. Then we review phenology models as an important component of earth system modeling. We find that the lack of species-level knowledge and observation data lead to difficulties in the development of vegetation phenology models at ecosystem or community scales. Finally, we recommend further research to advance understanding of the mechanisms governing phenology and the standardization of phenology observation methods across networks. With the opportunity for “big data” collection for plant phenology, we envision a breakthrough in process-based phenology modeling
Characteristics of lesser prairie-chicken (Tympanuchus pallidicinctus) long-distance movements across their distribution

Citation: Earl, J. E., Fuhlendorf, S. D., Haukos, D., Tanner, A. M., Elmore, D., & Carleton, S. A. (2016). Characteristics of lesser prairie-chicken (Tympanuchus pallidicinctus) long-distance movements across their distribution. Ecosphere, 7(8). doi:10.1002/(ISSN)2150-8925Long-distance movements are important adaptive behaviors that contribute to population, community, and ecosystem connectivity. However, researchers have a poor understanding of the characteristics of long-distance movements for most species. Here, we examined long-distance movements for the lesser prairie-chicken (Tympanuchus pallidicinctus), a species of conservation concern. We addressed the following questions: (1) At what distances could populations be connected? (2) What are the characteristics and probability of dispersal movements? (3) Do lesser prairie-chickens display exploratory and round-trip movements? (4) Do the characteristics of long-distance movements vary by site? Movements were examined from populations using satellite GPS transmitters across the entire distribution of the species in New Mexico, Oklahoma, Kansas, and Colorado. Dispersal movements were recorded up to 71 km net displacement, much farther than hitherto recorded. These distances suggest that there may be greater potential connectivity among populations than previously thought. Dispersal movements were displayed primarily by females and had a northerly directional bias. Dispersal probabilities ranged from 0.08 to 0.43 movements per year for both sexes combined, although these movements averaged only 16 km net displacement. Lesser prairie-chickens displayed both exploratory foray loops and round-trip movements. Half of round-trip movements appeared seasonal, suggesting a partial migration in some populations. None of the long-distance movements varied by study site. Data presented here will be important in parameterizing models assessing population viability and informing conservation planning, although further work is needed to identify landscape features that may reduce connectivity among populations. © 2016 Earl et al
Presence of substitute diets alters plant resistance to specialist and generalist herbivores: a meta-analysis

How herbivores respond to resource heterogeneity is important for predicting plant resistance to herbivores. Experimental studies thus far have revealed that herbivore responses differ depending on whether herbivores are offered single or multiple plant types, but the reports have rarely been combined. Here, we conducted a meta-analysis of 47 publications on choice and no-choice experiments to reveal how the presence/absence of multiple plants (i.e., choice/no-choice conditions) alters the extent of behavioral avoidance by herbivores. The herbivore diet breadth and response traits (feeding, growth, or oviposition) explained a significantly large amount of heterogeneity in the herbivore response under choice and no-choice conditions. In contrast, a small amount of heterogeneity was explained by the herbivore types (vertebrates, exophagous, or endophagous invertebrates), plant resistance traits (chemical or nonchemical), plant life form, and relatedness of plant pairs (intraspecific or interspecific) as well as interactions between the herbivore and plant characteristics. Compared with the no-choice conditions, specialist herbivores further avoided suboptimal plants under choice conditions. Generalist herbivores more evenly utilized optimal and suboptimal plants under choice conditions. The avoidance of suboptimal plants under choice conditions was the most prominent in oviposition response. Thus, our meta-analysis found that herbivore characteristics rather than plant traits were more responsible for driving behavioral avoidance by herbivores to a particular plant. The contrasting response between specialist and generalist herbivores to plant heterogeneity may be more ubiquitous than previously thought
Noninvasive unmanned aerial vehicle provides estimates of the energetic cost of reproduction in humpback whales

An animal\u27s body condition will affect its survival and reproductive success, which influences population dynamics. Despite its importance, relatively little is known about the body condition of large whales and its relationship to reproduction. We assessed the body condition of humpback whales (Megaptera novaeangliae) at a breeding/resting ground from aerial photographs recorded using an unmanned aerial vehicle (UAV). Photogrammetry methods were used to measure the surface area of individual whales, which was used as an index for body condition. Repeated measurements of the same individuals were not possible; hence, this study represents a cross-sectional sample of the population. Intraseasonal changes in the body condition of four reproductive classes (calves, immature, mature, and lactating) were investigated to infer the relative energetic cost that each class faces during the breeding season. To better understand the costs of reproduction, we investigated the relationship between female body condition (FBC) and the linear growth and body condition of their dependent calves (CBC). We documented a linear decline in the body condition of mature whales (0.027 m2/d; n = 20) and lactating females (0.032 m2/d; n = 31) throughout the breeding season, while there was no change in body condition of immature whales (n = 51) and calves (n = 32). The significant decline in mature and lactating female\u27s body condition implies substantial energetic costs for these reproductive classes. In support of this, we found a positive linear relationship between FBC and CBC. This suggests that females in poorer body condition may not have sufficient energy stores to invest as much energy into their offspring as better conditioned females without jeopardizing their own body condition and survival probability. Measurement precision was investigated from repeated measurements of the same animals both from the same and different photographs, and by looking at residual errors in relation to the positioning of the whales in the photographs. The resulting errors were included in a sensitivity analysis to demonstrate that model parameters were robust to measurement errors. Our findings provide strong support for the use of UAVs as a noninvasive tool to measure the body condition of whales and other mammals
Age distributions of Greenlandic dwarf shrubs support concept of negligible actuarial senescence

Many plants and sessile animals may not show actuarial senescence, the increase in mortality with age predicted to be ubiquitous by classic evolutionary theories of aging. Age-structured demographic information is, however, limited for most organisms. We assessed the age distributions of nine dwarf shrub species from 863 taproot samples collected in coastal east Greenland. Penalized composite link models (pclm) were used to fill gaps in the observed age ranges, caused by low species-specific sample sizes in relation to life span. Resulting distributions indicate that mortality patterns are independent of age. Actuarial senescence is thus negligible in these dwarf shrub populations. We suggest that smoothing techniques such as pclm enable consideration of noisy age data for determining age distributions. These distributions may, in turn, reveal age effects on demographic rates. Moreover, age determination from the root collars of small plants constitutes a powerful technique to further investigate age dependency of the demography of many plant species, including eudicot herbs. Using these methods for long-lived plants where long-term monitoring is unrealistic, we show that age is unlikely to be an important variable for making population projections and determining extinction risks
Predator hunting mode and host plant quality shape attack-abatement patterns of predation risk in an insect herbivore

Group formation reduces individual predation risk when the proportion of prey taken per predator encounter declines faster than the increase in group encounter rate (a ack-abatement). Despite a ack-abatement being an important component of group formation ecology, several key aspects have not been empirically studied, that is, interactions with the hunting mode of the predator and how these relationships are modi ed by local habitat quality. In 79 cage trials, we examined individual egg predation risk in di erent-sized egg clutches from the blue willow beetle Phratora vulgatissima for two predators with di erent hunting modes (consumption of full group [Orthotylus marginalis] vs. part group [Anthocoris nemorum]). Because these predators also take nutrients from plant sap, we could examine how the quality of alternative food sources (high- vs. low-quality host plant sap) in uenced a ack-abatement pa erns in the presence of di erent hunting strategies. For the O. marginalis predator, individual egg predation risk was largely independent of group size. For A. nemorum, egg predation risk clearly declined with increasing group size. However, approximately one-third of the grouping bene t was lost to an increase in group detectability. There were clear di erences in a ack-abatement pa erns between plants with high- vs. low-quality sap. When O. marginalis was the predator, there was no clear change in a ack-abatement in relation to host plant quality. However, for A. nemorum there was a clear reduction in overall predation risk and a stronger a ack-abatement pa ern with increasing group size when plant sap quality increased. This implies that the relative bene ts of prey grouping behavior for any species might show diurnal or seasonal changes as other aspects of resource/habitat quality change for the focal predator. Modulation of a ack-abatement by bo om-up e ects such as plant-based food resources is yet to be incorporated into general theory, despite the ubiquity of omnivorous predators and with omnivory being important for shaping food webs, ecosystem functions, and in biological control. Thus, ongoing re nement of a ack- abatement theory by focusing on bo om-up vs. top-down processes could have signi cant impacts on many important contemporary elds of study
A new paradigm of quantifying ecosystem stress through chemical signatures

Stress-induced emissions of biogenic volatile organic compounds (VOCs) from terrestrial eco- systems may be one of the dominant sources of VOC emissions worldwide. Understanding the ecosystem stress response could reveal how ecosystems will respond and adapt to climate change and, in turn, quan- tify changes in the atmospheric burden of VOC oxidants and secondary organic aerosols. Here, we argue, based on preliminary evidence from several opportunistic measurement sources, that chemical signatures of stress can be identified and quantified at the ecosystem scale. We also outline future endeavors that we see as next steps toward uncovering quantitative signatures of stress, including new advances in both VOC data collection and analysis of “big data.
Static and dynamic controls on fire activity at moderate spatial and temporal scales in the Alaskan boreal forest

Wildfire, a dominant disturbance in boreal forests, is highly variable in occurrence and behavior at multiple spatiotemporal scales. New data sets provide more detailed spatial and temporal observations of active fires and the post‐burn environment in Alaska. In this study, we employ some of these new data to analyze variations in fire activity by developing three explanatory models to examine the occurrence of (1) seasonal periods of elevated fire activity using the number of MODIS active fire detections data set (MCD14DL) within an 11‐day moving window, (2) unburned patches within a burned area using the Monitoring Trends in Burn Severity fire severity product, and (3) short‐to‐moderate interval (<60 yr) fires using areas of burned area overlap in the Alaska Large Fire Database. Explanatory variables for these three models included dynamic variables that can change over the course of the fire season, such as weather and burn date, as well as static variables that remain constant over a fire season, such as topography, drainage, vegetation cover, and fire history. We found that seasonal periods of high fire activity are associated with both seasonal timing and aggregated weather conditions, as well as the landscape composition of areas that are burning. Important static inputs to the model of seasonal fire activity indicate that when fire weather conditions are suitable, areas that typically resist fire (e.g., deciduous stands) may become more vulnerable to burning and therefore less effective as fire breaks. The occurrence of short‐to‐moderate interval fires appears to be primarily driven by weather conditions, as these were the only relevant explanatory variables in the model. The unique importance of weather in explaining short‐to‐moderate interval fires implies that fire return intervals (FRIs) will be sensitive to projected climate changes in the region. Unburned patches occur most often in younger stands, which may be related to a greater deciduous fraction of vegetation as well as lower fuel loads compared with mature stands. The fraction of unburned patches may therefore increase in response to decreasing FRIs and increased deciduousness in the region, or these may decrease if fire weather conditions become more severe.Peer-reviewedPublisher Versio