Cryptic behavior and activity cycles of a small mammal keystone species revealed through accelerometry: a case study of Merriam's kangaroo rats (Dipodomys merriami)

BACKGROUND

Kangaroo rats are small mammals that are among the most abundant vertebrates in many terrestrial ecosystems in Western North America and are considered both keystone species and ecosystem engineers, providing numerous linkages between other species as both consumers and resources. However, there are challenges to studying the behavior and activity of these species due to the difficulty of observing large numbers of individuals that are small, secretive, and nocturnal. Our goal was to develop an integrated approach of miniaturized animal-borne accelerometry and radiotelemetry to classify the cryptic behavior and activity cycles of kangaroo rats and test hypotheses of how their behavior is influenced by light cycles, moonlight, and weather.

METHODS

We provide a proof-of-concept approach to effectively quantify behavioral patterns of small bodied (< 50 g), nocturnal, and terrestrial free-ranging mammals using large acceleration datasets by combining low-mass, miniaturized animal-borne accelerometers with radiotelemetry and advanced machine learning techniques. We developed a method of attachment and retrieval for deploying accelerometers, a non-disruptive method of gathering observational validation datasets for acceleration data on free-ranging nocturnal small mammals, and used these techniques on Merriam's kangaroo rats to analyze how behavioral patterns relate to abiotic factors.

RESULTS

We found that Merriam's kangaroo rats are only active during the nighttime phases of the diel cycle and are particularly active during later light phases of the night (i.e., late night, morning twilight, and dawn). We found no reduction in activity or foraging associated with moonlight, indicating that kangaroo rats are actually more lunarphilic than lunarphobic. We also found that kangaroo rats increased foraging effort on more humid nights, most likely as a mechanism to avoid cutaneous water loss.

CONCLUSIONS

Small mammals are often integral to ecosystem functionality, as many of these species are highly abundant ecosystem engineers driving linkages in energy flow and nutrient transfer across trophic levels. Our work represents the first continuous detailed quantitative description of fine-scale behavioral activity budgets in kangaroo rats, and lays out a general framework for how to use miniaturized biologging devices on small and nocturnal mammals to examine behavioral responses to environmental factors.

Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem

Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time-consuming methodologies and low-resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow-footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow-footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.

Multiple Anthropogenic Pressures Lead to Seed Dispersal Collapse of the Southernmost Palm Jubaea chilensis

Seed dispersal is a critical process for plant reproduction and regeneration. Successful recruitment depends on pre- and post-dispersal processes that complete a seed’s journey until becoming a new plant. However, anthropogenic stressors may disrupt the seed dispersal process at some stages, collapsing plant regeneration and hampering its long-term persistence. The Chilean palm tree Jubaea chilensis is the southernmost and the only non-tropical palm species, which currently relies on the scatter-hoarding rodent Octodon degus for seed dispersal. We assessed seed fate by measuring predation and dispersal rates through experimental fieldwork in the Palmar de Ocoa site (located within La Campana National Park) and the Palmar El Salto. We also used previous reports on seed harvest and seedling herbivory to depict the whole J. chilensis seed dispersal process and assess the relative importance of different anthropogenic pressures. We asked the following questions: (1) What is the effect of human harvesting on J. chilensis recruitment? (2) Do native and exotic rodents predate J. chilensis seeds in the same way? and (3) Does post-dispersal herbivory matter? We found that J. chilensis fruits are harvested for human consumption, reducing pre-dispersal available seeds by removing about 23 tons per season. Then, post-dispersal seeds at the Ocoa palm grove are heavily predated by exotic (Rattus rattus) and native (Octodon spp.) rodents; only 8.7% of the seeds are effectively dispersed by Octodon degus. At Palmar El Salto, 100% of the seeds were predated by Rattus rattus, precluding further analysis. Finally, 70% of the seedlings were consumed by exotic herbivores (mainly rabbits), resulting in a success rate of 1.81%. Only 7.9% of the surviving seedlings become infantile plants (4 year-old). Our assessment suggests that J. chilensis has aging populations with very few young individuals in disturbed sites to replace the old ones. For those reasons, we suggest increasing its conservation category to critically endangered as land-use change is rapidly fragmenting and shrinking the extant J. chilensis populations. We urge to take urgent actions to protect this relict palm, which otherwise may go extinct in the next decades.

Size dependency of patch departure behavior: evidence from granivorous rodents

Individual size is a major determinant of mobile organisms’ ecology and behavior. This study aims to explore whether allometric scaling principles can provide an underlying framework for general patterns of resource patch use. To this end, we used giving‐up densities (GUDs), that is, the amount of resources remaining in a patch after a forager has quit feeding, as a comparative measure of the amount of resources exploited by a forager of any given size. We specifically tested the hypothesis that size‐dependent responses to both internal (energy requirement) and external (risk management) forces may have an effect on GUDs. We addressed this topic by conducting an extensive meta‐analysis of published data on granivorous rodents, including 292 GUD measurements reported in 25 papers. The data set includes data on 22 granivorous rodent species belonging to three taxonomic suborders (Castorimorpha, Myomorpha, and Sciuromorpha) and spans three habitat types (desert, grassland, and forest). The observations refer to both patches subject to predation risk and safe patches. Pooling all data, we observed positive allometric scaling of GUDs with average forager size (scaling exponent = 0.45), which explained 15% of overall variance in individual GUDs. Perceived predation risk during foraging led to an increase in GUDs independently of forager size and taxonomy and of habitat type, which explained an additional 12% of overall GUD variance. The size scaling exponent of GUDs is positive across habitat types and taxonomic suborders of rodents. Some variation was observed, however. The scaling coefficients in grassland and forest habitat types were significantly higher than in the desert habitat type. In addition, Sciuromorpha and Myomorpha exhibited a more pronounced size scaling of GUDs than Castorimorpha. This suggests that different adaptive behaviors may be used in different contexts and/or from different foragers. With body size being a fundamental ecological descriptor, research into size scaling of GUDs may help to place patch‐use observations in a broader allometric framework.

Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey plants; (ii) how these effects vary with climatic context (here, seasonality in rainfall); and (iii) the extent to which behavioural responses of small mammals are contingent upon small-mammal density. We tested the effects of a diverse LMH community on small-mammal habitat use using 4 years of spatially explicit small-mammal trapping and vegetation data from the UHURU Experiment, a replicated set of LMH exclosures in semi-arid Kenyan savanna. Small-mammal habitat use was positively associated with tree density and negatively associated with bare (unvegetated) patches in all plots and seasons. In the presence of LMH, and especially during the dry season, small mammals consistently selected tree cover and avoided bare patches. In contrast, when LMH were excluded, small mammals were weakly associated with tree cover and did not avoid bare patches as strongly. These behavioural responses of small mammals were largely unaffected by changes in small-mammal density associated with LMH exclusion. Our results show that LMH indirectly affect small-mammal behaviour, and that these effects are influenced by climate and can arise via density-independent mechanisms. This raises the possibility that anthropogenic LMH declines might interact with changing patterns of rainfall to alter small-mammal distribution and behaviour, independent of numerical responses by small mammals to these perturbations. For example, increased rainfall in East Africa (as predicted in many recent climate-model simulations) may relax constraints on small-mammal distribution where LMH are rare or absent, whereas increased aridity and/or drought frequency may tighten them.

Remote Cameras Reveal Experimental Artifact in a Study of Seed Predation in a Semi-Arid Shrubland

Granivorous animals may prefer to predate or cache seed of certain plant species over others. Multiple studies have documented preference for larger, non-native seed by granivores. To accomplish this, researchers have traditionally used indirect inference by relating patterns of seed removal to the species composition of the granivorous animal community. To measure seed removal, researchers present seed to granivorous animals in the field using equipment intended to exclude certain animal taxa while permitting access to others. This approach allows researchers to differentiate patterns of seed removal among various taxa (e.g., birds, small mammals, and insects); however, it is unclear whether the animals of interest are freely using the exclusion devices, which may be a hindrance to discovering the seed dishes. We used video observation to perform a study of seed predation using a custom-built, infrared digital camera and recording system. We presented native and non-native seed mixtures in partitioned Petri dishes both within and outside of exclusion cages. The exclusion cages were intended to allow entrance by rodent taxa while preventing entrance by rabbits and birds. We documented all seed removal visits by granivorous animals, which we identified to the genus level. Genera exhibited varying seed removal patterns based on seed type (native vs. non-native) and dish type (open vs. enclosed). We documented avoidance of the enclosed dishes by all but one rodent taxa, even though these dishes were intended to be used freely by rodents. This suggests that preference for non-native seed occurs differentially among granivorous animals in this system; however, interpretation of these nuanced results would be difficult without the benefit of video observation. When feasible, video observation should accompany studies using in situ equipment to ensure incorrect assumptions do not lead to inappropriate interpretation of results.

Ecology, distribution, and predictive occurrence modeling of Palmer’s chipmunk (Tamias palmeri): a high-elevation small mammal endemic to the Spring Mountains in southern Nevada, USA

Although montane sky islands surrounded by desert scrub and shrub steppe comprise a large part of the biological diversity of the Basin and Range Province of southwestern North America, comprehensive ecological and population demographic studies for high-elevation small mammals within these areas are rare. Here, we examine the ecology and population parameters of the Palmer’s chipmunk (Tamias palmeri) in the Spring Mountains of southern Nevada, and present a predictive GIS-based distribution and probability of occurrence model at both home range and geographic spatial scales. Logistic regression analyses and Akaike Information Criterion model selection found variables of forest type, slope, and distance to water sources as predictive of chipmunk occurrence at the geographic scale. At the home range scale, increasing population density, decreasing overstory canopy cover, and decreasing understory canopy cover contributed to increased survival rates.

Diet of a sigmodontine rodent assemblage in a Peruvian montane forest

Knowledge of feeding habits of small rodents is necessary for understanding food webs, trophic structure, and plant-animal interactions in Neotropical forests. Despite several studies that have investigated community structure and feeding behavior of rodents, large gaps remain in our understanding of their guild occupancy. Our objective was to investigate the diets of 7 species of small (< 100g) sympatric sigmodontine rodents in a high (3,500 m) Andean montane rainforest in Peru. We qualitatively and quantitatively assessed diet items in fecal samples from livetrapped rodents from 2009 to 2012. Frequency data for 4 diet categories indicated that all 7 species of rodents contained 4 diet categories in fecal samples: arthropods (88%), remains of leaves and fibers from plants (61%), intact seeds (with or without fruit pulp; 50%), and mycorrhizal spores (45%). Omnivory was found to be a strategy used by all species, although contingency table analysis revealed significant differences among and within species in diet categories. Cluster analysis showed 2 main groupings: that of the Thomasomys spp. plus Calomys sorellus group which included high amounts of intact seeds and plant parts in their fecal samples, and those of the genera Akodon, Microryzomys, Oligoryzomys, which included a greater proportion of arthropods in their fecal samples, but still consumed substantial amounts of fruit and plant parts. Intact seed remains from at least 17 plant species (9 families) were found in fecal samples. We concluded that this assemblage of sigmodontine rodents is omnivorous but that they likely play an important role as frugivores and in seed dispersal in tropical montane forests in Peru. El conocimiento de los hábitos alimenticios de roedores pequeños es necesario para comprender cadenas alimenticias, estructura trófica, e interacciones planta-animal en los bosques neotropicales. A pesar de que numerosos estudios han investigado la estructura de comunidades y el comportamiento de forrajeo en roedores, aún existen grandes vacíos en nuestra comprensión de sus gremios tróficos. Nuestro objetivo fue investigar las dietas de siete especies de pequeños (< 100 g) roedores sigmodontinos simpátricos en un bosque montano andino a 3.500] m en Perú. Cualitativamente y cuantitativamente evaluamos la dieta en muestras fecales de roedores capturados entre el 2009 y el 2012. Datos de frecuencia para cuatro categorías de dieta indicaron que las siete especies de roedores consumieron cuatro categorías de dieta: artrópodos (88%), pedazos de hojas y fibras de plantas (61%), semillas intactas (con o sin pulpa de frutos; 50%), y esporas de micorrizas (45%). Omnivoría fue la estrategia utilizada por todas las especies, aunque el análisis con tablas de contingencia reveló diferencias significativas entre y dentro de especies en categorías de dieta. El análisis de agrupación presentó 2 grupos principales: el grupo Thomasomys spp. y Calomys sorellus, que incluye una gran proporción de semillas intactas, y partes de plantas en las muestras fecales y el grupo que incluye los géneros Akodon, Microryzomys y Oligoryzomys, el cual incluyó una proporción mayor de artrópodos en sus muestras fecales, pero con niveles altos de semillas intactas. Semillas intactas de al menos 17 especies de plantas (9 familias) fueron encontradas en las muestras fecales. Concluimos que este ensamble de roedores sigmodontinos es omnívoro y que probablemente las especies juegan un rol importante como frugívoros y en la dispersión de semillas en los bosques montanos tropicales en el Perú.

Mechanisms driving postfire abundance of a generalist mammal

Changes in vertebrate abundance following disturbance are commonly attributed to shifts in food resources or predation pressure, but underlying mechanisms have rarely been tested. We examined four hypotheses for the commonly reported increase in abundance of deer mouse ( Peromyscus maniculatus (Wagner, 1845)) following forest fires: source–sink dynamics, decreased predation, increased food resources, and increased foraging efficiency. We found that reproduction of deer mouse was considerably higher in burned versus unburned forests and survival did not differ between habitats, indicating that burned forests were not sink habitats. Comparable survival also suggested that predation rates were similar between habitats. Increased reproduction in burned versus unburned forest suggested better resource conditions, but abundance of seeds and arthropods (the primary food resources for mice) either did not differ between habitats or were higher overall in unburned forest. Foraging experiments indicated that seed removal from depots was substantially higher in burned versus unburned forests after controlling for mouse density. Additionally, in both habitats, mice were captured more often in open microhabitats and the odds of individual insect removal increased with decreasing cover during certain sampling periods. Of the four hypotheses tested, greater foraging efficiency provided the best explanation for elevated populations of deer mouse. However, predation risk may have influenced foraging success.

Effects of more frequent and prolonged El Niño events on life-history parameters of the degu, a long-lived and slow-reproducing rodent

Global climate change (GCC) can have profound effects on species whose ecology is governed primarily by climatic factors. The ecology of small mammals inhabiting semiarid Chile is strongly affected by the El Niño Southern Oscillation (ENSO). During La Niña events in this area, dry conditions prevail and species may disappear from the thorn-scrub habitat. Conversely, El Niño events bring high rainfall, and associated pulses of food trigger small-mammal population increases. We used capture-mark-recapture to study responses of the degu (Octodon degus), a dominant small mammal, to variation in rainfall over 18 years. In response to a recent trend toward wetter conditions, degus reached record-high densities and maintained more stable numbers in the area. Underlying mechanisms involved variation in adult survival, juvenile persistence, and fecundity linked to rainfall changes during consecutive years (i.e., rainfall phases). During prolonged droughts, degus had low survival and produced fewer offspring, with low persistence. Following high rainfall, these parameters reversed; consecutive wet years resulted in further increases. Weak declines in fecundity and adult survival and high persistence of juveniles explained delayed responses to deteriorating conditions in initial dry years. If GCC leads to increased frequency of El Niño events, we anticipate greater numerical dominance of degus in semiarid Chile and possible range expansion. Furthermore, degus have strong impacts on other small mammal and some plant species, are important prey species, and are agricultural pests and disease reservoirs. Hence, GCC has the potential to dramatically influence their ecology in northern Chile and to have cascading effects on other components of this system.

Weed-biocontrol insects reduce native-plant recruitment through second-order apparent competition

Small-mammal seed predation is an important force structuring native-plant communities that may also influence exotic-plant invasions. In the intermountain West, deer mice (Peromyscus maniculatus) are prominent predators of native-plant seeds, but they avoid consuming seeds of certain widespread invasives like spotted knapweed (Centaurea maculosa). These mice also consume the biological-control insects Urophora spp. introduced to control C. maculosa, and this food resource substantially increases deer mouse populations. Thus, mice may play an important role in the invasion and management of C. maculosa through food-web interactions. We examined deer mouse seed predation and its effects on seedling emergence and establishment of a dominant native grass, Pseudoroegneria spicata, and forb, Balsamorhiza sagittata, in C. maculosa-invaded grasslands that were treated with herbicide to suppress C. maculosa or left untreated as controls. Deer mice readily took seeds of both native plants but removed 2-20 times more of the larger B. sagittata seeds than the smaller P. spicata seeds. Seed predation reduced emergence and establishment of both species but had greater impacts on B. sagittata. The intensity of seed predation corresponded with annual and seasonal changes in deer mouse abundance, suggesting that abundance largely determined mouse impacts on native-plant seeds. Accordingly, herbicide treatments that reduced mouse abundance by suppressing C. maculosa and its associated biocontrol food subsidies to mice also reduced seed predation and decreased the impact of deer mice on B. sagittata establishment. These results provide evidence that Urophora biocontrol agents may exacerbate the negative effects of C. maculosa on native plants through a form of second-order apparent competition-a biocontrol indirect effect that has not been previously documented. Herbicide suppressed C. maculosa and Urophora, reducing mouse populations and moderating seed predation on native plants, but the herbicide's direct negative effects on native forb seedlings overwhelmed the indirect positive effect of reducing deer mouse seed predation. By manipulating this four-level food chain, we illustrate that host-specific biological control agents may impact nontarget plant species through food-web interactions, and herbicides may influence management outcomes through indirect trophic interactions in addition to their direct effects on plants.

Indirect effects of prey swamping: differential seed predation during a bamboo masting event

Resource pulses often involve extraordinary increases in prey availability that "swamp" consumers and reverberate through indirect interactions affecting other community members. We developed a model that predicts predator-mediated indirect effects induced by an epidemic prey on co-occurring prey types differing in relative profitability/preference and validated our model by examining current-season and delayed effects of a bamboo mass seeding event on seed survival of canopy tree species in mixed Patagonian forests. The model shows that predator foraging behavior, prey profitability, and the scale of prey swamping influence the character and strength of short-term indirect effects on various alternative prey. When in large prey-swamped patches, nonselective predators decrease predation on all prey types. Selective predators, instead, only benefit prey of similar quality to the swamping species, while very low or high preference prey remain unaffected. Negative indirect effects (apparent competition) may override such positive effects (apparent mutualism), especially for highly preferred prey, when prey-swamped patches are small enough to allow predator aggregation and/or predators show a reproductive numerical response to elevated food supply. Seed predation patterns during bamboo (Chusquea culeou) masting were consistent with predicted short-term indirect effects mediated by a selective predator foraging in large prey-swamped patches. Bamboo seeds and similarly-sized Austrocedrus chilensis (ciprés) and Nothofagus obliqua (roble) seeds suffered lower predation in bamboo flowered than nonflowered patches. Predation rates on the small-seeded Nothofagus dombeyi (coihue) and the large-seeded Nothofagus alpina (rauli) were independent of bamboo flowering. Indirect positive effects were transient; three months after bamboo seeding, granivores preyed heavily upon all seed types, irrespective of patch flowering condition. Moreover, one year after bamboo seeding, predation rates on the most preferred seed (rauli) was higher in flowered than in nonflowered patches. Despite rapid predator numerical responses, short-term positive effects can still influence community recruitment dynamics because surviving seeds may find refuge beneath the litter produced by bamboo dieback. Together, our theoretical analysis and experiments indicate that indirect effects experienced by alternative prey during and after prey-swamping episodes need not be universal but can change across a prey quality spectrum, and they critically depend on predator-foraging rules and the spatial scale of swamping.

Microhabitat use and foraging behaviour of Sminthopsis youngsoni (Marsupialia:Dasyuridae) in arid central Australia

In this study, fluorescent pigment tracking was used to determine the microhabitat use and foraging behaviour of a small insectivorous marsupial, Sminthopsis youngsoni (the lesser hairy-footed dunnart), in the dunefields of the Simpson Desert, south-western Queensland. In total, 25 successful trails were traced over the duration of this study, between March 1996 and April 1998. Nocturnal foraging trails were identified, then the distance travelled by the dunnart through each microhabitat type (nine in all) was measured and accumulated for each trail and compared with surrounding available microhabitats along control trails. This provided an index of selectivity of microhabitat use. Terrestrial invertebrates were collected from both actual and control trails to measure food availability. Dunnarts strongly selected open microhabitats when foraging, with the periphery of spinifex hummocks (up to 20 cm from the edge of a spinifex hummock) being favoured. Spinifex itself was avoided unless shelter was sought (i.e. immediately after release). Potential invertebrate prey captured along the actual trails travelled by dunnarts tended to occur in greater numbers and were larger than those captured along the control trails, indicating that dunnarts can accurately locate resource-rich areas in which to forage. Clearly, the foraging strategies used by this species enable it to successfully exploit patchy and unpredictable food resources, thereby ensuring its continued persistence and relative abundance in an unstable environment.