Control of a Desert-Grassland Transition by a Keystone Rodent Guild

Desert landscape features influencing the microgeographic genetic structure of Nelson's pocket mouse Chaetodipus nelsoni

Elucidating the factors that drive the genetic patterns of natural populations is key in evolutionary biology, ecology and conservation. Hence, it is crucial to understand the role that environmental features play in species genetic diversity and structure. Landscape genetics measures functional connectivity and evaluates the effects of landscape composition, configuration, and heterogeneity on microevolutionary processes. Deserts constitute one of the world's most widespread biomes and exhibit a striking heterogeneity of microhabitats, yet few landscape genetics studies have been performed with rodents in deserts. We evaluated the relationship between landscape and functional connectivity, at a microgeographic scale, of the Nelson's pocket mouse Chaetodipus nelsoni in the Mapimí Biosphere Reserve (Chihuahuan desert). We used single-nucleotide polymorphisms and characterized the landscape based on on-site environmental data and from Landsat satellite images. We identified two distinct genetic clusters shaped by elevation, vegetation and soil. High elevation group showed higher connectivity in the elevated zones (1250-1350 m), with scarce vegetation and predominantly rocky soils; whereas that of Low elevation group was at <1200 m, with denser vegetation and sandy soils. These genetic patterns are likely associated with the species' locomotion type, feeding strategy and building of burrows. Interestingly, we also identified morphological differences, where hind foot size was significantly smaller in individuals from High elevation compared to Low elevation, suggesting the possibility of ecomorphs associated with habitat differences and potential local adaptation processes, which should be explored further. These findings improve our understanding of the genetics and ecology of C. nelsoni and other desert rodents.

Dryland state transitions alter trophic interactions in a predator-prey system

Environmental change is expected to alter trophic interactions and food web dynamics with consequences for ecosystem structure, function and stability. However, the mechanisms by which environmental change influences top-down and bottom-up processes are poorly documented. Here, we examined how environmental change caused by shrub encroachment affects trophic interactions in a dryland. The predator-prey system included an apex canid predator (coyote; Canis latrans), an intermediate canid predator (kit fox; Vulpes macrotis), and two herbivorous lagomorph prey (black-tailed jackrabbit, Lepus californicus; and desert cottontail, Sylvilagus audubonii) in the Chihuahuan Desert of New Mexico, USA. We evaluated alternative hypotheses for how shrub encroachment could affect habitat use and trophic interactions, including (i) modifying bottom-up processes by reducing herbaceous forage, (ii) modifying top-down processes by changing canid space use or the landscape of fear experienced by lagomorph prey and (iii) altering intraguild interactions between the dominant coyote and the intermediate kit fox. We used 7 years of camera trap data collected across grassland-to-shrubland gradients under variable precipitation to test our a priori hypotheses within a structural equation modelling framework. Lagomorph prey responded strongly to bottom-up pulses during years of high summer precipitation, but only at sites with moderate to high shrub cover. This outcome is inconsistent with the hypothesis that bottom-up effects should be strongest in grasslands because of greater herbaceous food resources. Instead, this interaction likely reflects changes in the landscape of fear because perceived predation risk in lagomorphs is reduced in shrub-dominated habitats. Shrub encroachment did not directly affect predation pressure on lagomorphs by changing canid site use intensity. However, site use intensity of both canid species was positively associated with jackrabbits, indicating additional bottom-up effects. Finally, we detected interactions between predators in which coyotes restricted space use of kit foxes, but these intraguild interactions also depended on shrub encroachment. Our findings demonstrate how environmental change can affect trophic interactions beyond traditional top-down and bottom-up processes by altering perceived predation risk in prey. These results have implications for understanding spatial patterns of herbivory and the feedbacks that reinforce shrubland states in drylands worldwide.

Activated carbon seed technologies: Innovative solutions to assist in the restoration and revegetation of invaded drylands

The demand for seed-based restoration and revegetation of degraded drylands has intensified with increased disturbance and climate change. Invasive plants often hinder the establishment of seeded species; thus, they are routinely controlled with herbicides. Herbicides used to control invasive plants may maintain soil activity and cause non-target damage to seeded species. Activated carbon (AC), which has a high adsorption of many herbicides, has been incorporated into seed pellets and coatings (seed technologies) to limit herbicide damage. Though various AC seed technologies have been examined in numerous laboratory and field studies, questions remain regarding their effectiveness and how to improve it, and what causes variation in results. We synthesized the literature on AC seed technologies for dryland restoration and revegetation to attempt to answer these questions. AC pellets compared to seed coatings were more thoroughly tested in the field and generally provide strong herbicide protection. However, greater amounts of AC in seed coatings appear to increase their effectiveness. Seed coatings show more potential for use than pellets because they are less logistically challenging to use compared to pellets, but need more field testing and refinement. Results often differ between laboratory and field studies, suggesting that field studies are critical in determining realized effects. However, seedling establishment failures from other barriers make it challenging to evaluate the effectiveness of AC seed technologies in the field. AC seed technologies are an innovative tool that with continued refinement, especially if other barriers to seedling establishment can be overcome, may improve the restoration and revegetation of degraded drylands.

Transferability of ecological forecasting models to novel biotic conditions in a long-term experimental study

Ecological forecasting models play an increasingly important role for managing natural resources and assessing our fundamental knowledge of processes driving ecological dynamics. As global environmental change pushes ecosystems beyond their historical conditions, the utility of these models may depend on their transferability to novel conditions. Because species interactions can alter resource use, timing of reproduction, and other aspects of a species' realized niche, changes in biotic conditions, which can arise from community reorganization events in response to environmental change, have the potential to impact model transferability. Using a long-term experiment on desert rodents, we assessed model transferability under novel biotic conditions to better understand the limitations of ecological forecasting. We show that ecological forecasts can be less accurate when the models generating them are transferred to novel biotic conditions and that the extent of model transferability can depend on the species being forecast. We also demonstrate the importance of incorporating uncertainty into forecast evaluation with transferred models generating less accurate and more uncertain forecasts. These results suggest that how a species perceives its competitive landscape can influence model transferability and that when uncertainties are properly accounted for, transferred models may still be appropriate for decision making. Assessing the extent of the transferability of forecasting models is a crucial step to increase our understanding of the limitations of ecological forecasts.

Effects of multiple mammalian herbivores and climate on grassland-shrubland transitions in the Chihuahuan Desert

The replacement of grasses by shrubs or bare ground (xerification) is a primary form of landscape change in drylands globally with consequences for ecosystem services. The potential for wild herbivores to trigger or reinforce shrubland states may be underappreciated, however, and comparative analyses across herbivore taxa are sparse. We sought to clarify the relative effects of domestic cattle, native rodents, native lagomorphs, and exotic African oryx (Oryx gazella) on a Chihuahuan Desert grassland undergoing shrub encroachment. We then asked whether drought periods, wet season precipitation, or interspecific grass-shrub competition modified herbivore effects to alter plant cover, species diversity, or community composition. We established a long-term experiment with hierarchical herbivore exclosure treatments and surveyed plant foliar cover over 25 years. Cover of honey mesquite (Prosopis glandulosa) proliferated, responding primarily to climate, and was unaffected by herbivore treatments. Surprisingly, cattle and African oryx exclusion had only marginal effects on perennial grass cover at their current densities. Native lagomorphs interacted with climate to limit perennial grass cover during wet periods. Native rodents strongly decreased plant diversity, decreased evenness, and altered community composition. Overall, we found no evidence of mammalian herbivores facilitating or inhibiting shrub encroachment, but native small mammals interacting with climate drove dynamics of herbaceous plant communities. Ongoing monitoring will determine whether increased perennial grass cover from exclusion of native lagomorphs and rodents slows the transition to a dense shrubland.

Trade-offs between deer herbivory and nitrogen competition alter grassland forb composition

Two of the major factors that control the composition of herbaceous plant communities are competition for limiting soil resources and herbivory. We present results from a 14-year full factorial experiment in a tallgrass prairie ecosystem that crossed nitrogen (N) addition with fencing to exclude white-tailed deer, Odocoileus virginianus, from half the plots. Deer presence was associated with only modest decreases in aboveground plant biomass (14% decrease; -45 ± 19 g m-2) with no interaction with N addition. N addition at 5.44 and 9.52 g N m-2 year-1 led to increases in biomass. There were weak increases in species richness associated with deer presence, but only for no or low added N (1 and 2 g N m-2 year-1). However, the presence of deer greatly impacted the abundances of some of the dominant perennial forb species, but not the dominant grasses. Deer presence increased the abundance of the forb Artemisia ludoviciana by 34 ± 12 SE g m-2 (94%) and decreased the forb Solidago rigida by 32 ± 13 SE g m-2 (79%). We suggest that these changes may have resulted from trade-offs in plant competitive ability for soil N versus resistance to deer herbivory. Field observations suggest deer acted as florivores, mainly consuming the flowers of susceptible forb species. The preferential consumption of flowers of forbs that seem to be superior N competitors appears to create an axis of interspecific niche differentiation. The overpopulation of white-tailed deer in many tallgrass reserves likely structures the abundance of forb species.

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

The diversity of animals identified as keystone species

Although the keystone species concept was conceived of over 50 years ago, contemporary efforts to synthesize related literature have been limited. Our objective was to create a list of keystone animal species identified in the literature and to examine the variation in the traits of species and the ecosystem influences they elicit. We documented 230 species considered keystones. A clustering analysis classified them into five archetypes based on combinations of their taxonomic class, body size, trophic level, and role (consumers, modifiers, or prey). Although conservation and public perception of keystones primarily focuses on large vertebrate consumers, our analysis reveals that researchers have defined a wide diversity of keystone species, with large variation in associated ecosystem processes. Future research may confront ambiguity in the definition of keystone status, as well as clarify the type, abundance, and quality of data required to assign the term. Identifying keystones with increased rigor would not only enrich the literature but also inform intervention to safeguard threatened keystones and their associated influences on ecosystems.

Correlation and Influence of Seasonal Variation of Diet with Gut Microbiota Diversity and Metabolism Profile of Chipmunk

Tamias Sibiricus is the only member of the genus Tamias, a significant and vigorous seed distributor and vital food for their predators. No information is known about the strict diet, gut microbiota structure, and metabolism profile of chipmunks and how they diversify seasonally. The above factors, as well as flexibility toward seasonal shifts, are critical in defining its growth rates, health, survivorship, and population stability. This study explored the diet, gut microbiota composition, and chipmunk metabolism. Additionally, the influence of different seasons was also investigated by using next-generation sequencing. Results revealed that seasons strongly affected a diet: streptophyte accounted for 37% in spring, which was lower than in summer (34.3%) and autumn (31.4%). Further, Ascomycota was observed at 43.8% in spring, which reduced to 36.6% in summer and the lowest (31.3%) in autumn. Whereas, nematodes showed maximum abundance from spring (15.8%) to summer (20.6%) and autumn (24.1%). These results signify the insectivorous nature of the chipmunk in summer and autumn. While herbivorous and fungivorous nature in spring. The DNA analysis revealed that chipmunk mainly feeds on fungi, including Aspergillus and Penicillium genus. Similar to diet composition, the microbiome also exhibited highly significant dissimilarity (p < 0.001, R = 0.235) between spring/autumn and spring/summer seasons. Proteobacteria (35.45%), Firmicutes (26.7%), and Bacteroidetes (23.59%) were shown to be the better discriminators as they contributed the most to causing differences between seasons. Moreover, PICRUSt showed that the assimilation of nutrients were also varied seasonally. The abundance of carbohydrates, lipids, nucleotides, xenobiotics, energy, terpenoids, and polyketides metabolism was higher in spring than in other seasons. Our study illustrates that seasonal reconstruction in the chipmunk diet has a significant role in shaping temporal variations in gut microbial community structure and metabolism profile.

Evolutionary and ecological patterns of scatter- and larder-hoarding behaviours in rodents

Scatter- and larder hoarding are the primary strategies of food-hoarding animals and have important implications for plant-animal interactions and plant recruitment. However, their origins and influencing factors have not been fully investigated across a wide range of taxa. Our systematic literature search amassed data for 183 seed-hoarding rodent species worldwide and tested relationships of seed-hoarding behaviours with phylogenetic signal, functional traits and environmental factors. We found that the evolution of hoarding strategies was not random in phylogeny, and scatter hoarding originated independently multiple times from larder hoarding. Rodents with higher encephalisation quotient (relative brain size), omnivorous diet (related to dependence on seeds) and inhabiting lower latitudes were disproportionately likely to scatter hoard. Despite body mass's potential relationship with competition through food defence, it was associated with food-hoarding strategy only in a few families. Our results show the need to study the community and ecological context of food-hoarding behaviours.

Niche partitioning in an assemblage of granivorous rodents, and the challenge of community-level conservation

Coexistence of competing species in the same foraging guild has long puzzled ecologists. In particular, how do small subordinate species persist with larger dominant competitors? This question becomes particularly important when conservation interventions, such as reintroduction or translocation, become necessary for the smaller species. Exclusion of dominant competitors might be necessary to establish populations of some endangered species. Ultimately, however, the goal should be to conserve whole communities. Determining how subordinate species escape competitive exclusion in intact communities could inform conservation decisions by clarifying the ecological conditions and processes required for coexistence at local or regional scales. We tested for spatial and temporal partitioning among six species of native, granivorous rodents using null models, and characterized the microhabitat of each species using resource-selection models. We found that the species’ nightly activity patterns are aggregated temporally but segregated spatially. As expected, we found clear evidence that the larger-bodied kangaroo rats drive spatial partitioning, but we also found species-specific microhabitat associations, which suggests that habitat heterogeneity is part of what enables these species to coexist. Restoration of natural disturbance regimes that create habitat heterogeneity, and selection of translocation sites without specific competitors, are among the management recommendations to consider in this case. More generally, this study highlights the need for a community-level approach to conservation and the usefulness of basic ecological data for guiding management decisions.

High-quality reference genome for an arid-adapted mammal, the banner-tailed kangaroo rat (Dipodomys spectabilis)

Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semiarid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered in the United States. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (Dipodomys spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (Dipodomys ordii and Dipodomys stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (N_e) and linking these patterns to the species’ current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.

Declines in rodent abundance and diversity track regional climate variability in North American drylands

Regional long-term monitoring can enhance the detection of biodiversity declines associated with climate change, improving future projections by reducing reliance on space-for-time substitution and increasing scalability. Rodents are diverse and important consumers in drylands, regions defined by the scarcity of water that cover 45% of Earth's land surface and face increasingly drier and more variable climates. We analyzed abundance data for 22 rodent species across grassland, shrubland, ecotone, and woodland ecosystems in the southwestern USA. Two time series (1995-2006 and 2004-2013) coincided with phases of the Pacific Decadal Oscillation (PDO), which influences drought in southwestern North America. Regionally, rodent species diversity declined 20%-35%, with greater losses during the later time period. Abundance also declined regionally, but only during 2004-2013, with losses of 5% of animals captured. During the first time series (wetter climate), plant productivity outranked climate variables as the best regional predictor of rodent abundance for 70% of taxa, whereas during the second period (drier climate), climate best explained variation in abundance for 60% of taxa. Temporal dynamics in diversity and abundance differed spatially among ecosystems, with the largest declines in woodlands and shrublands of central New Mexico and Colorado. Which species were winners or losers under increasing drought and amplified interannual variability in drought depended on ecosystem type and the phase of the PDO. Fewer taxa were significant winners (18%) than losers (30%) under drought, but the identities of winners and losers differed among ecosystems for 70% of taxa. Our results suggest that the sensitivities of rodent species to climate contributed to regional declines in diversity and abundance during 1995-2013. Whether these changes portend future declines in drought-sensitive consumers in the southwestern USA will depend on the climate during the next major PDO cycle.

Savanna Rodents’ Selective Removal of an Encroaching Plant’s Seeds Increased With Grass Biomass

In savannas across the planet, encroaching woody plants are altering ecosystem functions and reshaping communities. Seed predation by rodents may serve to slow the encroachment of woody plants in grasslands and savannas. Our goals for this study were to determine if rodents in an African savanna selectively removed seeds of an encroaching plant and if foraging activity was influenced by the local vegetation structure or by the landscape context. From trials with two species of seeds (encroacher = Dichrostachys cinerea, non-encroaching overstory tree = Senegalia nigrescens) at 64 seed stations, we recorded 1,065 foraging events by seven species of granivorous rodents. We found a strong positive relationship between rodent activity and the number of seeds removed during trials. Foraging events were dominated by rodent seed predators, with &lt;10.6% of events involving a rodent with the potential for secondary dispersal. Rodents selectively removed the seeds of the encroaching species, removing 32.6% more D. cinerea seeds compared to S. nigrescens. Additionally, rodent activity and the number of seeds removed increased at sites with more grass biomass. Our results suggest a potential mechanistic role for rodents in mitigating the spread of woody plants in grass dominated savannas.

Seed predator effects on plants: Moving beyond time-corrected proxies

We previously demonstrated that small mammals impact plant recruitment globally via size-dependent seed predation, generating a unimodal pattern across ecosystems. Chen et al. (2021) critiqued our seed removal analysis, advocating corrections for exposure time. We show such manipulations are unwarranted and argue for increased emphasis on plant recruitment metrics.

Resource selection of a montane endemic: Sex-specific differences in white-bellied voles (Microtus longicaudus leucophaeus)

Resources that an individual selects contrasted against what is available can provide valuable information regarding species-specific behavior and ecological relationships. Small mammals represent excellent study organisms to assess such relationships. Isolated populations that exist on the edge of a species’ distribution often exhibit behavioral adaptations to the extremes experienced by a species and can provide meaningful insight into the resource requirements of the species. We deployed radio transmitters in a peripheral population of the long-tailed vole (Microtus longicaudus) during the mating season. We developed models of resource selection at multiple scales (within home range and patch). We found voles generally selected areas close to water and roads and consisting of high understory vegetation primarily composed of grasses. Resource selection varied between sexes suggesting different resource needs during the breeding season. The differential resource needs of voles might be a result of the energetic requirements for reproduction and are representative of a promiscuous or polygynous mating system.

Effects of artificial light at night on the foraging behavior of an endangered nocturnal mammal

Modification of nighttime light levels by artificial illumination (artificial light at night; ALAN) is a rapidly increasing form of human disturbance that affects natural environments worldwide. Light in natural environments influences a variety of physiological and ecological processes directly and indirectly and, as a result, the effects of light pollution on species, communities and ecosystems are emerging as significant. Small prey species may be particularly susceptible to ALAN as it makes them more conspicuous and thus more vulnerable to predation by visually oriented predators. Understanding the effects of disturbance like ALAN is especially important for threatened or endangered species as impacts have the potential to impede recovery, but due to low population numbers inherent to at-risk species, disturbance is rarely studied. The endangered Stephens' kangaroo rat (SKR), Dipodomys stephensi, is a nocturnal rodent threatened by habitat destruction from urban expansion. The degree to which ALAN impacts their recovery is unknown. In this study, we examined the effects of ALAN on SKR foraging decisions across a gradient of light intensity for two types of ALAN, flood and bug lights (756 vs 300 lumen, respectfully) during full and new moon conditions. We found that ALAN decreased probability of resource patch depletion compared to controls. Moreover, lunar illumination, distance from the light source and light type interacted to alter SKR foraging. Under the new moon, SKR were consistently more likely to deplete patches under control conditions, but there was an increasing probability of patch depletion with distance from the source of artificial light. The full moon dampened SKR foraging activity and the effect of artificial lights. Our study underscores that ALAN reduces habitat suitability, and raises the possibility that ALAN may impede the recovery of at-risk nocturnal rodents.

Large-scale patterns of seed removal by small mammals differ between areas of low- versus high-wolf occupancy

Because most tree species recruit from seeds, seed predation by small-mammal granivores may be important for determining plant distribution and regeneration in forests. Despite the importance of seed predation, large-scale patterns of small-mammal granivory are often highly variable and thus difficult to predict. We hypothesize distributions of apex predators can create large-scale variation in the distribution and abundance of mesopredators that consume small mammals, creating predictable areas of high and low granivory. For example, because gray wolf (Canis lupus) territories are characterized by relatively less use by coyotes (C. latrans) and greater use by foxes (Vulpes vulpes, Urocyon cinereoargentus) that consume a greater proportion of small mammals, wolf territories may be areas of reduced small-mammal granivory. Using large-scale, multiyear field trials at 22 sites with high- and low-wolf occupancy in northern Wisconsin, we evaluated whether removal of seeds of four tree species was lower in wolf territories. Consistent with the hypothesized consequences of wolf occupancy, seed removal of three species was more than 25% lower in high-wolf-occupancy areas across 2 years and small-mammal abundance was more than 40% lower in high-wolf areas during one of two study years. These significant results, in conjunction with evidence of seed consumption in situ and the absence of significant habitat differences between high- and low-wolf areas, suggest that top-down effects of wolves on small-mammal granivory and seed survival may occur. Understanding how interactions among carnivores create spatial patterns in interactions among lower trophic levels may allow for more accurate predictions of large-scale patterns in seed survival and forest composition.

Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations

Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration.

The origin of tetrapod herbivory: effects on local plant diversity

The origin of herbivory in the Carboniferous was a landmark event in the evolution of terrestrial ecosystems, increasing ecological diversity in animals but also giving them greater influence on the evolution of land plants. We evaluate the effect of early vertebrate herbivory on plant evolution by comparing local species richness of plant palaeofloras with that of vertebrate herbivores and herbivore body size. Vertebrate herbivores became diverse and achieved a much greater range of body sizes across the Carboniferous-Permian transition interval. This coincides with an abrupt reduction in local plant richness that persists throughout the Permian. Time-series regression analysis supports a negative relationship of plant richness with herbivore richness but a positive relationship of plant richness with minimum herbivore body size. This is consistent with studies of present-day ecosystems in which increased diversity of smaller, more selective herbivores places greater predation pressures on plants, while a prevalence of larger bodied, less selective herbivores reduces the dominance of a few highly tolerant plant species, thereby promoting greater local richness. The diversification of herbivores across the Carboniferous-Permian boundary, along with the appearance of smaller, more selective herbivores like bolosaurid parareptiles, constrained plant diversity throughout the Permian. These findings demonstrate that the establishment of widespread vertebrate herbivory has structured plant communities since the late Palaeozoic, as expected from examination of modern ecosystems, and illustrates the potential for fossil datasets in testing palaeoecological hypotheses.

Attraction and Avoidance between Predators and Prey at Wildlife Crossings on Roads

Wildlife passages are currently built at roads and railway lines to re-establish connectivity. However, little is known about whether predator-prey interactions may reduce the effectiveness of the crossing structures. We evaluated the co-occurrence patterns of predator-prey species-pairs at 113 crossing structures, noting their coincidence at the same structure and/or on the same day. We built occupancy models using presence-absence matrices for three prey and five predator types obtained during 2076 passage-days of monitoring. The results indicate that predators and prey do not use passages independently. Attraction or segregation effects occurred in 20% of predator-prey species-pairs and were detected in 67% of cases with respect to same-day use. Our results show that both predator and prey species used the same structures to cross fenced roads. However, the spatial and daily patterns of crossing suggest that there were predators that attended crossings to search for prey and that prey species avoided using crossings in the presence of predators. Our results support two recommendations to avoid crossing structures losing effectiveness or becoming prey traps: (i) increase the number of wider structures to reduce the risks of predator-prey encounters and (ii) include inside them structural heterogeneity and refuges, to reduce the likelihood for predator-prey interactions.

Seed type, habitat and time of day influence post-dispersal seed removal in temperate ecosystems

Seed survival is of great importance for the performance of plant species and it is strongly affected by post-dispersal seed removal by either different animals such as granivorous species and secondary dispersers or abiotic conditions such as wind or water. The success of post-dispersal seed removal depends on seed specific traits including seed size, the presence of coats or elaiosomes, the mode of seed dispersion, and on the habitat in which seeds happen to arrive. In the present study we asked how seed traits (dehulled vs. intact; size; dispersal mode), habitat (forest vs. grassland), and time of day (night vs. day) influence post-dispersal seed removal of the four plant species Chelidonium majus, Lotus corniculatus, Tragopogon pratensis and Helianthus annuus. Seed removal experiments were performed in three regions in Hesse, Germany. The results showed different, inconsistent influences of time of day, depending on habitat and region, but consistent variation across seed types. C. majus and dehulled H. annuus seeds had the fastest removal rates. The impact of the habitat on post-dispersal seed removal was very low, only intact H. annuus seeds were removed at significantly higher rates in grasslands than in forests. Our study demonstrates consistent differences across seed types across different habitats and time: smaller seeds and those dispersed by animals had a faster removal rate. It further highlights that experimental studies need to consider seeds in their natural form to be most realistic.

Temporal changes in species composition affect a ubiquitous species' use of habitat patches

Across landscapes, shifts in species composition often co-occur with shifts in structural or abiotic habitat features, making it difficult to disentangle the role of competitors and environment on assessments of patch quality. Using over two decades of rodent community data from a long-term experiment, we show that a small, ubiquitous granivore (Chaetodipus penicillatus) shifted its use of different experimental treatments with the establishment of a novel competitor, C. baileyi. Shifts in residency, probability of movement between patches, and the arrival of new individuals in patches altered which treatment supported the highest abundances of C. penicillatus. Our results suggest that the establishment of a new species worsened the quality of the originally preferred treatment, likely by impacting resource availability. Paradoxically, the presence of the new species also increased C. penicillatus' use of the less preferred treatment, potentially through shifts in the competitive network on those plots.

Lidar Prediction of Small Mammal Diversity in Wisconsin, USA

Vegetation structure is a crucial component of habitat selection for many taxa, and airborne LiDAR (Light Detection and Ranging) technology is increasingly used to measure forest structure. Many studies have examined the relationship between LiDAR-derived structural characteristics and wildlife, but few have examined those characteristics in relation to small mammals, specifically, small mammal diversity. The aim of this study was to determine if LiDAR could predict small mammal diversity in a temperate-mixed forest community in Northern Wisconsin, USA, and which LiDAR-derived structural variables best predict small mammal diversity. We calculated grid metrics from LiDAR point cloud data for 17 plots in three differently managed sites and related the metrics to small mammal diversity calculated from five months of small mammal trapping data. We created linear models, then used model selection and multi-model inference as well as model fit metrics to determine if LiDAR-derived structural variables could predict small mammal diversity. We found that small mammal diversity could be predicted by LiDAR-derived variables including structural diversity, cover, and canopy complexity as well as site (as a proxy for management). Structural diversity and canopy complexity were positively related with small mammal diversity, while cover was negatively related to small mammal diversity. Although this study was conducted in a single habitat type during a single season, it demonstrates that LiDAR can be used to predict small mammal diversity in this location and possibly can be expanded to predict small mammal diversity across larger spatial scales.

Enemy release from the effects of generalist granivores can facilitate Bromus tectorum invasion in the Great Basin Desert

The enemy release hypothesis (ERH) of plant invasion asserts that natural enemies limit populations of invasive plants more strongly in native ranges than in non-native ranges. Despite considerable empirical attention, few studies have directly tested this idea, especially with respect to generalist herbivores. This knowledge gap is important because escaping the effects of generalists is a critical aspect of the ERH that may help explain successful plant invasions. Here, we used consumer exclosures and seed addition experiments to contrast the effects of granivorous rodents (an important guild of generalists) on the establishment of cheatgrass (Bromus tectorum) in western Asia, where cheatgrass is native, versus the Great Basin Desert, USA, where cheatgrass is exotic and highly invasive. Consistent with the ERH, rodent foraging reduced cheatgrass establishment by nearly 60% in western Asia but had no effect in the Great Basin. This main result corresponded with a region-specific foraging pattern: rodents in the Great Basin but not western Asia generally avoided seeds from cheatgrass relative to seeds from native competitors. Our results suggest that enemy release from the effects of an important guild of generalists may contribute to the explosive success of cheatgrass in the Great Basin. These findings corroborate classic theory on enemy release and expand our understanding of how generalists can influence the trajectory of exotic plant invasions.

Seedling recruitment correlates with seed input across seed sizes: implications for coexistence

Understanding controls on recruitment is critical to predicting community assembly, diversity, and coexistence. Theory posits that at mean fecundity, recruitment of highly fecund small-seeded plants should be primarily microsite limited, which is indicated by a saturating recruitment function. In contrast, species that produce fewer large seeds are more likely to be seed-limited, which is characterized by a linear recruitment function. If these patterns hold in nature, seed predation that disproportionately affects larger-seeded species can limit their establishment. We tested these predictions by comparing recruitment functions among 16 co-occurring perennial forb species that vary by over two orders of magnitude in seed size. We also assessed how postdispersal seed predation by mice influenced recruitment. We added seeds at densities from zero to three times natural fecundity of each species to undisturbed plots and examined spatial variation in recruitment by conducting experiments across 10 grassland sites that varied in productivity and resource availability. Consistent across two replicated years, most species had linear recruitment functions across the range of added seed densities, indicative of seed-limited recruitment. Depending on year, the recruitment functions of only 19-37% of target species saturated near their average fecundity, and this was not associated with seed size. Recruitment was strongly inhibited by rodent seed predation for large-seeded species but not for smaller-seeded species. Proportional recruitment was more sensitive to spatial variation in recruitment conditions across sites for some small-seeded species than for large-seeded species. These results contradict the common belief that highly fecund small-seeded species suffer from microsite-limited recruitment. Rather, they imply that, at least episodically, recruitment can be strongly correlated to plant fecundity. However, proportional recruitment of small-seeded species was inhibited at productive sites to a greater extent than large-seeded species. Results also show that in a system where the dominant granivore prefers larger seeds, low-fecundity large-seeded species can suffer from even greater seed-limited recruitment than would occur in the absence of predators.

Rodent burrow network dynamics under human-induced landscape transformation from desert to steppe in Kalmykian rangelands

Rodents play an important role in rangelands through the engineering of extensive burrow systems, which provides key habitats for many animal and plant species. We have analyzed the long-term variation in the abundance and distribution of rodent burrows in grazing ecosystems of southern Russia (Kalmykia) under the landscape change from desert to steppe caused by the drastic reduction of livestock after the collapse of the USSR in the early 1990s. We conducted burrow surveys in the "desert" (1980) and "steppe" (2017) periods on 19 3-km transects. We found considerable changes in burrow abundance and distribution, as well as evidence of desert habitat fragmentation and isolation caused by the expansion of tall-grass communities. Burrows of the open-dwelling diurnal ground squirrel (Spermophilus pygmaeus), the dominant and the keystone species during the "desert" period, almost completely disappeared from the rodent burrow network by 2017, indicating significant habitat loss. In contrast, the burrows of the folivorous social vole (Microtus socialis) which was rare in the 1980s, became abundant and ubiquitously distributed. The burrow density of the desert-dwelling psammophilous midday gerbil (Meriones meridianus) decreased, while the distances between occupied patches increased, indicating desert habitat fragmentation and loss of population connectivity. Burrows of the folivorous tamarisk gerbils (M. tamariscinus) were recorded only sporadically in both 1980 and 2017. The observed changes in the rodent burrow network, the key component of grazing ecosystems, correlate with rodent species ecology and can have long-term and important consequences for ecosystem functioning.

Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent

Gene flow in animals is limited or facilitated by different features within the landscape matrix they inhabit. The landscape representation in landscape genetics (LG) is traditionally modeled as resistance surfaces (RS), where novel optimization approaches are needed for assigning resistance values that adequately avoid subjectivity. Also, desert ecosystems and mammals are scarcely represented in LG studies. We addressed these issues by evaluating, at a microgeographic scale, the effect of landscape features on functional connectivity of the desert-dwelling Dipodomys merriami. We characterized genetic diversity and structure with microsatellites loci, estimated home ranges and movement of individuals using telemetry-one of the first with rodents, generated a set of individual and composite environmental surfaces based on hypotheses of variables influencing movement, and assessed how these variables relate to individual-based gene flow. Genetic diversity and structure results evidenced a family-induced pattern driven by first-order-related individuals, notably determining landscape genetic inferences. The vegetation cover and soil resistance optimized surface (NDVI) were the best-supported model and a significant predictor of individual genetic distance, followed by humidity and NDVI+humidity. Based on an accurate definition of thematic resolution, we also showed that vegetation is better represented as continuously (vs. categorically) distributed. Hence, with a nonsubjective optimization framework for RS and telemetry, we were able to describe that vegetation cover, soil texture, and climatic variables influence D. merriami's functional connectivity at a microgeographic scale, patterns we could further explain based on the home range, habitat use, and activity observed between sexes. We describe the relationship between environmental features and some aspects of D. merriami's behavior and physiology.

Native lagomorphs suppress grass establishment in a shrub-encroached, semiarid grassland

Shrub encroachment into arid grasslands has been associated with reduced grass abundance, increased soil erosion, and local declines in biodiversity. Livestock overgrazing and the associated reduction of fine fuels has been a primary driver of shrub encroachment in the southwestern United States, but shrublands continue to persist despite livestock removal and grassland restoration efforts. We hypothesized that an herbivory feedback from native mammals may contribute to continued suppression of grasses after the removal of livestock. Our herbivore exclusion experiment in southeastern Arizona included five treatment levels and allowed access to native mammals based on their relative body size, separating the effects of rodents, lagomorphs, and mule deer. We included two control treatments and replicated each treatment 10 times (n = 50). We introduced uniform divisions of lawn sod (Cynodon dactylon) into each exclosure for 24-hr periods prior to (n = 2) and following (n = 2) the monsoon rains and used motion-activated cameras to document herbivore visitations. In the pre-monsoon trials, treatments that allowed lagomorph access had less sod biomass relative to other treatments (p < 0.001), averaging 44% (SD 36%) and 29% (SD 45%) remaining biomass after the 24-hr trial periods. Following the onset of monsoons, differences in remaining biomass among treatments disappeared. Desert cottontails (Sylvilagus audubonii) were detected more frequently than any of the other 11 herbivore species present at the site, accounting for 83% of detections during the pre-monsoon trials. Significantly more (p < 0.001) desert cottontails were detected during the pre-monsoon trials (2,077) compared to the post-monsoon trials (174), which coincided with biomass removal from lagomorph accessible treatments. We conclude that desert cottontails are significant consumers of herbaceous vegetation in shrub-encroached arid grasslands and they, along with other native herbivores, may act as a biotic feedback contributing to the competitive advantage and persistence of shrubs.

Indirect effects of a large mammalian herbivore on small mammal populations: Context-dependent variation across habitat types, mammal species, and seasons

Multiple consumer species frequently co-occur in the same landscape and, through effects on surrounding environments, can interact in direct and indirect ways. These interactions can vary in occurrence and importance, and focusing on this variation is critical for understanding the dynamics of interactions among consumers. Large mammalian herbivores are important engineers of ecosystems worldwide, have substantial impacts on vegetation, and can indirectly affect small-mammal populations. However, the degree to which such indirect effects vary within the same system has received minimal attention. We used a 16-year-old exclosure experiment, stratified across a heterogeneous landscape, to evaluate the importance of context-dependent interactions between tule elk (Cervus canadensis nannodes) and small mammals (deer mice [Peromyscus maniculatus], meadow voles [Microtus californicus], and harvest mice [Reithrodontymys megalotis]) in a coastal grassland in California. Effects of elk on voles varied among habitats and seasons: In open grasslands, elk reduced vole numbers during fall 2013 but not summer 2014; in Lupinus-dominated grasslands, elk reduced vole numbers during summer 2014 but not fall 2013; and in Baccharis-dominated grasslands, elk had no effect on vole numbers in either season. Effects of elk on the two mice species also varied among habitats and seasons, but often in different ways from voles and each other. In fall 2013, elk decreased mice abundances in Lupinus-dominated grasslands, but not in Baccharis-dominated or open grasslands. In summer 2014, elk decreased the abundance of harvest mice consistently across habitat types. In contrast, elk increased deer-mice numbers in open grasslands but not other habitats. Within the same heterogenous study system, the influence of elk on small mammals was strongly context-dependent, varying among habitats, mammal species, and seasons. We hypothesize that such variability is common in nature and that failure to consider it may yield inaccurate findings and limit our understanding of interactions among co-occurring consumers.

Biotic resistance and disturbance: rodent consumers regulate post-fire plant invasions and increase plant community diversity

Biotic resistance and disturbance are fundamental processes influencing plant invasion outcomes; however, the role of consumers in regulating the establishment and spread of plant invaders and how disturbance modifies biotic resistance by consumers is unclear. We document that fire in combination with experimental exclusion of rodent consumers shifted a native desert shrubland to a low-diversity, invasive annual grassland dominated by Bromus tectorum (cheatgrass). In contrast, burned plots with rodents present suppressed invasion by cheatgrass and developed into a more diverse forb community. Rodents created strong biotic resistance to the establishment of aggressive plant invaders likely through seed and seedling predation, which had cascading effects on plant competition and plant community diversity. Fire mediated its positive effects on plant invaders through native plant removal and by decreasing the abundance and diversity of the rodent community. The experimental disruption of plant and consumer-mediated biotic resistance of plant invaders using fire and rodent exclusion treatments provides strong evidence that native plants and rodents are important regulators of plant invasion dynamics and plant biodiversity in our study system. While rodents conferred strong resistance to invasion in our study system, fluctuations in rodent populations due to disturbance and climatic events may provide windows of opportunity for exotic plant species to escape biotic resistance by rodent consumers and initiate invasions.

Niche opportunities for invasive annual plants in dryland ecosystems are controlled by disturbance, trophic interactions, and rainfall

Resource availability and biotic interactions control opportunities for the establishment and expansion of invasive species. Studies on biotic resistance to plant invasions have typically focused on competition and occasionally on herbivory, while resource-oriented studies have focused on water or nutrient pulses. Through synthesizing these approaches, we identify conditions that create invasion opportunities. In a nested fully factorial experiment, we examined how chronic alterations in water availability and rodent density influenced the density of invasive species in both the Mojave Desert and the Great Basin Desert after fire. We used structural equation modeling to examine the direct and mediated effects controlling the density of invasives in both deserts. In the first 2 years after our controlled burn in the Great Basin, we observed that fire had a direct effect on increasing the invasive forb Halogeton glomeratus as well as a mediated effect through reducing rodent densities and herbivory. 4 years after the burn, the invasive annual grass Bromus tectorum was suppressing Halogeton glomeratus in mammal exclusion plots. There was a clear transition from years where invasives were controlled by disturbance and trophic interactions to years were resource availability and competition controlled invasive density. Similarly, in the Mojave Desert we observed a strong early influence of trophic processes on invasives, with Schismus arabicus benefitted by rodents and Bromus rubens negatively influenced by rodents. In the Mojave Desert, post-fire conditions became less important in controlling the abundance of invasives over time, while Bromus rubens was consistently benefitted by increases in fall rainfall.

Community Assembly Theory as a Framework for Biological Invasions

Biological invasions present a global problem underlain by an ecological paradox that thwarts explanation: how do some exotic species, evolutionarily naïve to their new environments, outperform locally adapted natives? We propose that community assembly theory provides a framework for addressing this question. Local community assembly rules can be defined by evaluating how native species' traits interact with community filters to affect species abundance. Evaluation of exotic species against this benchmark indicates that exotics that follow assembly rules behave like natives, while those exhibiting novel interactions with community filters can greatly underperform or outperform natives. Additionally, advantages gained by exotics over natives following disturbance can be explained by accounting for extrinsic assembly processes that bias exotic traits toward ruderal strategies.

Granivory from native rodents and competition from an exotic invader strongly and equally limit the establishment of native grasses

Seed predation and resource competition are fundamental biotic filters that affect the assembly of plant communities, yet empirical studies rarely assess their importance relative to one another. Here, we used rodent exclosures and experimental seed additions to compare how rodent granivory and resource competition affected the net establishment of an exotic invader (Bromus tectorum) and two native bunchgrasses (Pseudoroegneria spicata and Elymus elymoides) in the Great Basin Desert, USA. Rodent granivory limited the establishment of both native grasses, but had no significant effect on B. tectorum. Competition from B. tectorum limited the establishment of both native grasses, but neither native grass imposed a significant competitive effect on B. tectorum. Interestingly, we found that rodent granivory and B. tectorum competition limited the establishment of native grasses to the same extent, suggesting that these biotic interactions may impose equally important barriers to the local establishment of P. spicata and E. elymoides. By evaluating the strength of multiple biotic interactions in simultaneous, coordinated experiments, we can understand their relative contributions to community-level patterns.