Moose in our neighborhood: Does perceived hunting risk have cascading effects on tree performance in vicinity of roads and houses?

Like large carnivores, hunters both kill and scare ungulates, and thus might indirectly affect plant performance through trophic cascades. In this study, we hypothesized that intensive hunting and enduring fear of humans have caused moose and other forest ungulates to partly avoid areas near human infrastructure (perceived hunting risk), with positive cascading effects on recruitment of trees. Using data from the Norwegian forest inventory, we found decreasing browsing pressure and increasing tree recruitment in areas close to roads and houses, where ungulates are more likely to encounter humans. However, although browsing and recruitment were negatively related, reduced browsing was only responsible for a small proportion of the higher tree recruitment near human infrastructure. We suggest that the apparently weak cascading effect occurs because the recorded browsing pressure only partly reflects the long‐term browsing intensity close to humans. Accordingly, tree recruitment was also related to the density of small trees 5–10 years earlier, which was higher close to human infrastructure. Hence, if small tree density is a product of the browsing pressure in the past, the cascading effect is probably stronger than our estimates suggest. Reduced browsing near roads and houses is most in line with risk avoidance driven by fear of humans (behaviorally mediated), and not because of excessive hunting and local reduction in ungulate density (density mediated).     

An assessment of terminology for intraspecific diversity in fishes,with a focus on “ecotypes” and “life histories”

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., “PST”), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life‐history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life‐history traits. Life history is generally used in organismal‐ and ecology‐based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic‐ and evolution‐based journals. “Satellite species” is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life‐history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

The terminology used to describe intraspecific diversity is varied and often used ambiguously. “Ecotype” was originally used to describe patterns in genes and ecology, and recent studies employing this term tend to report a genetic basis in ISD. By contrast, “life history” describes biological parameters that affect demography, and this term tends to be used in organismal‐ and ecology‐based journals.     

The traits of “trait ecologists”: An analysis of the use of trait and functional trait terminology

Trait and functional trait approaches have revolutionized ecology improving our understanding of community assembly, species coexistence, and biodiversity loss. Focusing on traits promotes comparability across spatial and organizational scales, but terms must be used consistently. While several papers have offered definitions, it remains unclear how ecologists operationalize “trait” and “functional trait” terms. Here, we evaluate how researchers and the published literatures use these terms and explore differences among subdisciplines and study systems (taxa and biome). By conducting both a survey and a literature review, we test the hypothesis that ecologists’ working definition of “trait” is adapted or altered when confronting the realities of collecting, analyzing and presenting data. From 486 survey responses and 712 reviewed papers, we identified inconsistencies in the understanding and use of terminology among researchers, but also limited inclusion of definitions within the published literature. Discrepancies were not explained by subdiscipline, system of study, or respondent characteristics, suggesting there could be an inconsistent understanding even among those working in related topics. Consistencies among survey responses included the use of morphological, phonological, and physiological traits. Previous studies have called for unification of terminology; yet, our study shows that proposed definitions are not consistently used or accepted. Sources of disagreement include trait heritability, defining and interpreting function, and dealing with organisms in which individuals are not clearly recognizable. We discuss and offer guidelines for overcoming these disagreements. The diversity of life on Earth means traits can represent different features that can be measured and reported in different ways, and thus, narrow definitions that work for one system will fail in others. We recommend ecologists embrace the breadth of biodiversity using a simplified definition of “trait” more consistent with its common use. Trait‐based approaches will be most powerful if we accept that traits are at least as diverse as trait ecologists.     

Non-indigenous ungulates as a threat to biodiversity

Non-indigenous ungulate species pose a problem for conservation. They can be socially and economically valuable, but are also potentially harmful to biodiversity. Therefore, their introduction requires an explicit assessment of risk relative to benefit. To conduct such risk assessments, information regarding the impacts of non-indigenous ungulates on biodiversity is required. Here, we review the available evidence for the biodiversity impacts of non-indigenous ungulates. Hybridization, exploitation and apparent competition, vegetation impacts, predation, facilitation, trophic cascades and soil system functioning were assessed using a hierarchical set of criteria for the strength of the evidence. Strong evidence was lacking for risks posed by competition. Numerous reports exist of hybridization in captivity between ungulate species that normally do not co-occur, but conclusive evidence for introgression in the wild was restricted to one case. Strong evidence (using exclosure experiments) for the impacts of introduced ungulates on vegetation structure and composition was found and in some cases introduced ungulates caused the extirpation of plant species. Predation by Sus scrofa is a substantial threat to island faunas and systems, and impacts on soil system functioning elsewhere have also been found. Facilitation by ungulates has been shown to be substantial in promoting invasive plant species. By contrast, little evidence exists for apparent competition. The largest impacts from introduced ungulates are likely to be in cases where they perform novel functions in the new environment. However, to determine which types of impacts are likely to be most problematic, further evidence is required, ideally from well-designed field experiments.     

High‐throughput sequencing outperforms traditional morphological methods in Blue Catfish diet analysis and reveals novel insights into diet ecology

Blue Catfish Ictalurus furcatus are an invasive, yet economically important species in the Chesapeake Bay. However, their impact on the trophic ecology of this system is not well understood. In order to provide in‐depth analysis of predation by Blue Catfish, we identified prey items using high‐throughput DNA sequencing (HTS) of entire gastrointestinal tracts from 134 samples using two genetic markers, mitochondrial cytochrome c oxidase I (COI) and the nuclear 18S ribosomal RNA gene. We compared our HTS results to a more traditional “hybrid” approach that coupled morphological identification with DNA barcoding. The hybrid study was conducted on additional Blue Catfish samples (n = 617 stomachs) collected from the same location and season in the previous year. Taxonomic representation with HTS vastly surpassed that achieved with the hybrid methodology in Blue Catfish. Significantly, our HTS study identified several instances of at‐risk and invasive species consumption not identified using the hybrid method, supporting the hypothesis that previous studies using morphological methods may greatly underestimate consumption of critical species. Finally, we report the novel finding that Blue Catfish diet diversity inversely correlates to daily flow rates, perhaps due to higher mobility and prey‐seeking behaviors exhibited during lower flow.     

Putting the brakes on phagocytosis: “don't‐eat‐me” signaling in physiology and disease

Timely removal of dying or pathogenic cells by phagocytes is essential to maintaining host homeostasis. Phagocytes execute the clearance process with high fidelity while sparing healthy neighboring cells, and this process is at least partially regulated by the balance of “eat‐me” and “don''t‐eat‐me” signals expressed on the surface of host cells. Upon contact, eat‐me signals activate “pro‐phagocytic” receptors expressed on the phagocyte membrane and signal to promote phagocytosis. Conversely, don''t‐eat‐me signals engage “anti‐phagocytic” receptors to suppress phagocytosis. We review the current knowledge of don''t‐eat‐me signaling in normal physiology and disease contexts where aberrant don''t‐eat‐me signaling contributes to pathology.     

What Cues Do Ungulates Use to Assess Predation Risk in Dense Temperate Forests?

Anti-predator responses by ungulates can be based on habitat features or on the near-imminent threat of predators. In dense forest, cues that ungulates use to assess predation risk likely differ from half-open landscapes, as scent relative to sight is predicted to be more important. We studied, in the Białowieża Primeval Forest (Poland), whether perceived predation risk in red deer (Cervus elaphus) and wild boar (Sus scrofa) is related to habitat visibility or olfactory cues of a predator. We used camera traps in two different set-ups to record undisturbed ungulate behavior and fresh wolf (Canis lupus) scats as olfactory cue. Habitat visibility at fixed locations in deciduous old growth forest affected neither vigilance levels nor visitation rate and cumulative visitation time of both ungulate species. However, red deer showed a more than two-fold increase of vigilance level from 22% of the time present on control plots to 46% on experimental plots containing one wolf scat. Higher vigilance came at the expense of time spent foraging, which decreased from 32% to 12% while exposed to the wolf scat. These behavioral changes were most pronounced during the first week of the experiment but continuous monitoring of the plots suggested that they might last for several weeks. Wild boar did not show behavioral responses indicating higher perceived predation risk. Visitation rate and cumulative visitation time were not affected by the presence of a wolf scat in both ungulate species. The current study showed that perceived predation risk in red deer and wild boar is not related to habitat visibility in a dense forest ecosystem. However, olfactory cues of wolves affected foraging behavior of their preferred prey species red deer. We showed that odor of wolves in an ecologically equivalent dose is sufficient to create fine-scale risk factors for red deer.     

Feeding ecology and diet of the southern geladas (Theropithecus gelada obscurus) in human‐modified landscape,Wollo, Ethiopia

Studying the dietary flexibility of primates that live in human‐modified environments is crucial for understanding their ecological adaptations as well as developing management and conservation plans. Southern gelada (Theropithecus gelada obscurus) is an endemic little‐known subspecies of gelada that inhabits human‐modified landscapes in the northern central highlands of Ethiopia. During an 18‐month period, we conducted this intensive study in an unprotected area of a human‐modified landscape at Kosheme in Wollo to investigate the feeding ecology of southern geladas and their dietary responses to seasonal variations. We quantified the monthly and seasonal diet data from a band of southern geladas using instantaneous scan sampling method at 15‐min intervals, and green grass phenology and availability using visual inspection from the randomly selected permanent plots. The overall average diet of southern geladas at Kosheme constituted grass blades 55.4%, grass undergrounds 13.2%, grass bulbs 5.6%, grass seeds 5.4%, herb leaves 4.0, fruits 7.3%, and cereal crops 5.6%. Grass blade consumption increased with increasing green grass availability, while underground food consumption increased with decreasing green grass availability, and vice versa. Southern geladas spent significantly more time feeding on the grass blades and herb leaves and significantly less time on bulbs during the wet season than the dry season. Underground grass items (rhizomes and corms) were not consumed during the wet season, but made up 22.3% of the dry season diet. Thus, although grass blades are staple diet items for geladas, underground diet items are important “fallback foods” at Kosheme. Our result shows insights into the dietary flexibility southern geladas adopt to cope with human‐modified landscapes of the north‐central Ethiopian Highlands. Thus, the study contributes to a better understanding of how changing environments shape primate ecology and evolution.     

Landscape of fear in Europe: wolves affect spatial patterns of ungulate browsing in Białowieża Primeval Forest,Poland

Large carnivores can either directly influence ungulate populations or indirectly affect their behaviour. Knowledge from European systems, in contrast to North American systems, on how this might lead to cascading effects on lower trophic levels is virtually absent. We studied whether wolves Canis lupus via density‐mediated and behaviorally‐mediated effects on their ungulate prey species influence patterns of browsing and tree regeneration inside the Bia?owie?a National Park, Poland. Browsing intensity of tree saplings (height class < 150 cm), irrespective of tree species or forest type, was lower inside a wolf core area (50.5%) where predator presence is highest, than in the remainder of the wolf pack’s home range (58.3%). Additionally, browsing intensity was reduced when the amount of coarse woody debris (CWD), which can act as a ?ungulate escape impediment?, increased (within 5‐m radius) inside the wolf core area. No relationship existed outside the core area. As a result, the proportion of trees growing out of herbivore control increased more strongly with increasing amount of CWD inside compared to outside the wolf core area. This suggests that next to direct effects of wolves on ungulate density caused by a higher predation pressure inside the core area, risk effects are important and are enhanced by habitat characteristics. These results indicate that behaviorally‐mediated effects of predators on prey can become more important than density‐mediated effects in affecting lower trophic levels. This is the first study we are aware of, that shows CWD can create fine‐scale risk effects on ungulates with the potential for cascading effects of large predators on patterns of tree regeneration for a European forest system. This knowledge broadens the discussion on how the impact of large predators on ecosystem functioning depends on the physical landscape, by illustrating these effects for a system which largely contrasts in this respect to the North American systems.     

“Protein aggregates” contain RNA and DNA,entrapped by misfolded proteins but largely rescued by slowing translational elongation

All neurodegenerative diseases feature aggregates, which usually contain disease‐specific diagnostic proteins; non‐protein constituents, however, have rarely been explored. Aggregates from SY5Y‐APP_Sw neuroblastoma, a cell model of familial Alzheimer''s disease, were crosslinked and sequences of linked peptides identified. We constructed a normalized “contactome” comprising 11 subnetworks, centered on 24 high‐connectivity hubs. Remarkably, all 24 are nucleic acid‐binding proteins. This led us to isolate and sequence RNA and DNA from Alzheimer''s and control aggregates. RNA fragments were mapped to the human genome by RNA‐seq and DNA by ChIP‐seq. Nearly all aggregate RNA sequences mapped to specific genes, whereas DNA fragments were predominantly intergenic. These nucleic acid mappings are all significantly nonrandom, making an artifactual origin extremely unlikely. RNA (mostly cytoplasmic) exceeded DNA (chiefly nuclear) by twofold to fivefold. RNA fragments recovered from AD tissue were ~1.5‐to 2.5‐fold more abundant than those recovered from control tissue, similar to the increase in protein. Aggregate abundances of specific RNA sequences were strikingly differential between cultured SY5Y‐APP_Sw glioblastoma cells expressing APOE3 vs. APOE4, consistent with APOE4 competition for E‐box/CLEAR motifs. We identified many G‐quadruplex and viral sequences within RNA and DNA of aggregates, suggesting that sequestration of viral genomes may have driven the evolution of disordered nucleic acid‐binding proteins. After RNA‐interference knockdown of the translational‐procession factor EEF2 to suppress translation in SY5Y‐APP_Sw cells, the RNA content of aggregates declined by >90%, while reducing protein content by only 30% and altering DNA content by ≤10%. This implies that cotranslational misfolding of nascent proteins may ensnare polysomes into aggregates, accounting for most of their RNA content.     

Lesser of Two Evils? Foraging Choices in Response to Threats of Predation and Parasitism

Predators have documented post-encounter (density-mediated) effects on prey but their pre-encounter impacts, including behavioural alterations, can be substantial as well. While it is increasingly evident that this “ecology of fear” is important to understand for natural enemy-victim relationships, fear responses of hosts to the threat of infection by a parasite are relatively unknown. We examined larval amphibian (Lithobates pipiens) foraging choices by experimentally manipulating the presence of cues relating to predator (larval odonate) or parasite (the trematode Ribeiroia ondatrae) threats. Tadpoles avoided foraging where predator or parasite cues were present; however, they did not treat these as equal hazards. When both threats were simultaneously present, tadpoles strongly preferred to forage under the threat of parasitism compared to predation, likely driven by their relative lethality in our study. Our results indicate that altered spatial use is an important anti-parasite behaviour, and demonstrate that parasite avoidance can affect foraging in a manner similar to predators, warranting greater study of the pre-encounter effects of this enemy type.     

Ancestral ecological regime shapes reaction to food limitation in the Least Killifish,Heterandria formosa

Populations with different densities often show genetically based differences in life histories. The divergent life histories could be driven by several agents of selection, one of which is variation in per‐capita food levels. Its relationship with population density is complex, as it depends on overall food availability, individual metabolic demand, and food‐independent factors potentially affecting density, such as predation intensity. Here, we present a case study of two populations of a small live‐bearing freshwater fish, one characterized by high density, low predation risk, low overall food availability, and presumably low per‐capita food levels, and the other by low density, high predation risk, high overall food availability, and presumably high per‐capita food levels. Using a laboratory experiment, we examined whether fish from these populations respond differently to food limitation, and whether size at birth, a key trait with respect to density variation in this species, is associated with any such differential responses. While at the lower food level growth was slower, body size smaller, maturation delayed, and survival reduced in both populations, these fitness costs were smaller in fish from the high‐density population. At low food, only 15% of high‐density fish died, compared to 75% of low‐density fish. This difference was much smaller at high food (0% vs. 15% mortality). The increased survival of high‐density fish may, at least partly, be due to their larger size at birth. Moreover, being larger at birth enabled fish to mature relatively early even at the lower food level. We demonstrate that sensitivities to food limitation differ between study populations, consistent with selection for a greater ability to tolerate low per‐capita food availability in the high‐density population. While we cannot preclude other agents of selection from operating in these populations simultaneously, our results suggest that variation in per‐capita food levels is one of those agents.     

Meta‐analysis shows that environmental DNA outperforms traditional surveys,but warrants better reporting standards

1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”
2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.
3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.
4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods‐based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.

     

The formation of “mega‐flocks” depends on vegetation structure in montane coniferous forests of Taiwan

A mixed‐species bird flock is a social assemblage where two or more bird species are moving together while foraging and might benefit from increased foraging efficiency and antipredator vigilance. A “mega‐flock,” which includes flocking species from different vegetation strata, often exhibits high species diversity. Mechanisms for the formation of mega‐flocks have not yet been explored. In this study, we evaluated the influence of vegetation structure and bird species diversity in driving the occurrence of mega‐flocks. We investigated the composition of mixed‐species flocks, local bird communities, and vegetation structure in five vegetation types of two high‐elevation sites in central Taiwan. Mega‐flocks occurred more frequently in pine woodland than later successional stages of coniferous forests. However, species richness/diversity of local bird communities increased along successional stages. Therefore, vegetation variables exhibit more influence on the occurrence of mega‐flocks than local bird communities. Besides foliage height diversity, understory coverage also showed positive effects on flock size of mixed‐species flocks. Our results indicated that pine woodlands with more evenly distributed vegetation layers could facilitate the interactions of canopy and understory flocks and increase the formation of mega‐flocks and thus the complexity of mixed‐species flocks.     

Vertebrate predators have minimal cascading effects on plant production or seed predation in an intact grassland ecosystem

The strength of trophic cascades in terrestrial habitats has been the subject of considerable interest and debate. We conducted an 8-year experiment to determine how exclusion of vertebrate predators, ungulates alone (to control for ungulate exclusion from predator exclusion plots) or none of these animals influenced how strongly a three-species assemblage of rodent consumers affected plant productivity. We also examined whether predator exclusion influenced the magnitude of post-dispersal seed predation by mice. Both ungulates and rodents had strong direct effects on graminoid biomass. However, rodent impacts on plant biomass did not differ across plots with or without predators and/or ungulates. Deer mice removed more seeds from seed depots on predator exclusion plots, suggesting trait-mediated indirect effects of predators, but this short-term behavioural response did not translate into longer-term impacts on seed survival. These results suggest that vertebrate predators do not fundamentally influence primary production or seed survival in our system.     

gauseR: Simple methods for fitting Lotka‐Volterra models describing Gause’s “Struggle for Existence”

Point 1: The ecological models of Alfred J. Lotka and Vito Volterra have had an enormous impact on ecology over the past century. Some of the earliest—and clearest—experimental tests of these models were famously conducted by Georgy Gause in the 1930s. Although well known, the data from these experiments are not widely available and are often difficult to analyze using standard statistical and computational tools.Point 2: Here, we introduce the gauseR package, a collection of tools for fitting Lotka‐Volterra models to time series data of one or more species. The package includes several methods for parameter estimation and optimization, and includes 42 datasets from Gause''s species interaction experiments and related work. Additionally, we include with this paper a short blog post discussing the historical importance of these data and models, and an R vignette with a walk‐through introducing the package methods. The package is available for download at github.com/adamtclark/gauseR.Point 3: To demonstrate the package, we apply it to several classic experimental studies from Gause, as well as two other well‐known datasets on multi‐trophic dynamics on Isle Royale, and in spatially structured mite populations. In almost all cases, models fit observations closely and fitted parameter values make ecological sense.Point 4: Taken together, we hope that the methods, data, and analyses that we present here provide a simple and user‐friendly way to interact with complex ecological data. We are optimistic that these methods will be especially useful to students and educators who are studying ecological dynamics, as well as researchers who would like a fast tool for basic analyses.     

“Third‐wave” cognitive and behavioral therapies and the emergence of a process‐based approach to intervention in psychiatry

For decades, cognitive and behavioral therapies (CBTs) have been tested in randomized controlled trials for specific psychiatric syndromes that were assumed to represent expressions of latent diseases. Although these protocols were more effective as compared to psychological control conditions, placebo treatments, and even active pharmacotherapies, further advancement in efficacy and dissemination has been inhibited by a failure to focus on processes of change. This picture appears now to be evolving, due both to a collapse of the idea that mental disorders can be classified into distinct, discrete categories, and to the more central attention given to processes of change in newer, so‐called “third‐wave” CBTs. Here we review the context for this historic progress and evaluate the impact of these newer methods and models, not as protocols for treating syndromes, but as ways of targeting an expanded range of processes of change. Five key features of “third‐wave” therapies are underlined: a focus on context and function; the view that new models and methods should build on other strands of CBT; a focus on broad and flexible repertoires vs. an approach to signs and symptoms; applying processes to the clinician, not just the client; and expanding into more complex issues historically more characteristic of humanistic, existential, analytic, or system‐oriented approaches. We argue that these newer methods can be considered in the context of an idiographic approach to process‐based functional analysis. Psychological processes of change can be organized into six dimensions: cognition, affect, attention, self, motivation and overt behavior. Several important processes of change combine two or more of these dimensions. Tailoring intervention strategies to target the appropriate processes in a given individual would be a major advance in psychiatry and an important step toward precision mental health care.