A novel noninvasive genetic survey technique for small mammals

Noninvasive genetic surveys, often conducted by collecting fecal samples, have become a popular tool for surveying wildlife, but have primarily been applied to species with large and conspicuous scat. Although many small mammals are threatened, endangered, or data deficient, noninvasive genetic surveys have rarely been applied due to the challenges of detecting their inconspicuous fecal pellets. As part of a broader study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), we developed a noninvasive genetic survey technique for the community of small mammals in their putative range. We designed bait stations to passively collect fecal samples from rodents, and developed a multiplex primer set that amplified unique fragment sizes for salt marsh harvest mice and four other sympatric species. We tested the primer set on positive controls and on fecal pellets collected from bait stations at two regularly monitored field sites known to have very different densities of salt marsh harvest mice. The multiplex amplified DNA from all five species, even when all five species were present in a single sample. A positive species identification was made for all field-collected samples, and 43% of these field-collected samples had multispecies detections. The combination of bait stations and genetic species identification proved to be an effective means of noninvasively surveying small mammals in potential salt marsh harvest mouse habitat. The sampling technique should be applicable to a wide variety of small mammals in other systems.

Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.

A synthesis of Mexican mammalogy in Therya: the first 10 years!

Mammalogy as a discipline was pursued in Mexico since the mid-17th century.  However, Mexican researchers were involved primarily in the mid-20th century, when national scientific journals were established to emphasize research on mammals.  In 2010, the Asociación Mexicana de Mastozoología, A. C., initiated the journal Therya.  Therya has now completed its first decade of publication, and in this work, we analyze the articles and scientific notes published in Therya, focused on the studies of mammals in Mexican territory, including researchers and institutions, to describe the path that mammalogy has taken in recent years in Mexico.  This synthesis therefore serves as a frame of reference for future mammalogy studies.  We compiled all papers published in Therya during the period 2010-2019.  We built a database gathering information from these publications such as authors, institutions and states of origin, study areas, capture methods, topics and taxa studied.  We excluded from the analyses research outside of Mexico.  We did a descriptive statistics analysis including mean, proportions, percentage and trends for each and all the sections.  Therya has published 181 articles and 52 scientific notes on mammals distributed in Mexico.  The majority of authors and institutions were from Mexico City.  The states of southeastern Mexico were the most used as a study area, particularly Oaxaca and Chiapas.  The orders Carnivora and Cetartiodactyla were the most studied, mainly using indirect methods.  Trapping methods were most commonly used for small mammals.  The least studied orders were Eulipotyphla, Cingulata, and Pilosa.  The most studied topics are ecology, diversity, conservation and distribution.  Therya has become one of the most important journals about mammal research in Mexico.  Research in mammalogy, as reflected in the pages of Therya, is based in academic institutions with the metropolitan area of Mexico City, reflecting the institutional infrastructure and age, and possibly institutional budgetary factors.  The southeast portion of the country is well studied due to the existence of regional institutions, as well as to the concentration of high biodiversity.  The least studied regions of Mexico may be the result of a reduced number of research groups and social insecurity.  Much research is focused on small mammals, making Sherman traps and mist nets the most used trapping methods; carnivores and cetartiodactyls are the most studied groups, using indirect study methods reducing study costs and effort.  Ecology, diversity and distribution are the most studied topics, these studies allow the development of management plans.

Small mammal assemblage composition and habitat associations across an elevational gradient in southern California

Elevational gradients coincide with expansive climatic gradients and diverse plant and animal communities. We evaluated the small mammal assemblages in eight distinct vegetation types across an elevational gradient in southern California, the Deep Canyon Transect, to determine how assemblage composition changes across the gradient and to identify species with similar habitat associations. Livetrapping efforts (4,800 trap-nights) yielded 1,097 captures of 713 individuals, representing 14 heteromyid and cricetid species. Heteromyids dominated the six lower-elevation vegetation types (< 1,300 m a.s.l.), whereas cricetids dominated the upper end of the gradient. Richness and diversity exhibited bimodal responses to elevation, which do not conform to mid-domain effect null predictions. Canonical correspondence analysis revealed that 75% of the variation in small mammal abundances was explainable by habitat characteristics, and cluster analysis grouped small mammals into three ecologically distinct groups based on their habitat associations. One contained only Chaetodipus penicillatus, while the others were comprised of low- and high-elevation species, respectively. The low-elevation species exhibit unusual levels of sympatry (and syntopy) among closely related species of pocket mice (Chaetodipus). Further efforts should investigate the mechanisms of coexistence for Chaetodipus species with nearly identical associations and seasonal effects on richness and diversity. Repeated surveys of entire gradients such as the Deep Canyon Transect will help refine our understanding of temporal dynamics of community assemblage and diversity.

Demography of the salt marsh harvest mouse (Reithrodontomys raviventris halicoetes) and associated rodents in tidal and managed wetlands

Suisun Marsh (Solano County, California) is the largest contiguous marsh remaining on the West Coast of the United States, and makes up approximately 10% of the wetlands remaining in the San Francisco Estuary. Suisun Marsh has been safeguarded from development through the operation of over 100 privately owned waterfowl hunting clubs, which manage for diked waterfowl habitat. However, this management—and the subsequent loss of tidal influence—has been considered harmful for some species, including the endangered salt marsh harvest mouse (SMHM; Reithrodontomys raviventris). To determine the value of tidal wetlands relative to those managed for waterfowl, we performed periodic surveys for rodents in managed and tidal wetlands over 5 years, and used capture-mark-recapture analyses to estimate demographic parameters and abundance for the three most common rodents—the northern SMHM (R. r. halicoetes), the western harvest mouse (a sympatric native species; R. megalotis, WHM), and the house mouse (a sympatric invasive species; Mus musculus). Wetland type had no effect on detection, temporary emigration, or survival for any of these species. However, fecundity and population growth for all three species were affected by an interaction of season and wetland type, although none of these parameters was consistently superior in either habitat type. Estimated abundance of SMHM and Mus was similar in both wetland types, whereas WHM were more abundant in managed wetlands. Salt marsh harvest mice also showed no affinity for any microhabitat characteristics associated with tidal wetlands. Managed wetlands in Suisun Marsh support SMHM and Mus equally, and abundances of WHM were greater than in tidal wetlands, suggesting managed wetlands may be superior in terms of supporting native rodents. As climate change and sea level rise are predicted to threaten coastal marshes, these results suggest the recovery strategy for SMHM could incorporate managed wetlands.

Advances in population ecology and species interactions in mammals

The study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.

BioTIME: A database of biodiversity time series for the Anthropocene

MOTIVATION

The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

MAIN TYPES OF VARIABLES INCLUDED

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

SPATIAL LOCATION AND GRAIN

BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

TIME PERIOD AND GRAIN

BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

MAJOR TAXA AND LEVEL OF MEASUREMENT

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

SOFTWARE FORMAT

.csv and .SQL.

Enhanced facilitation at the extreme end of the aridity gradient in the Atacama Desert: a community-level approach

Plant facilitation is now recognized as an important process in severe environments. However, there is still no agreement on how facilitation changes as conditions become increasingly severe. The classic stress gradient hypothesis (SGH) predicts a monotonic increase in facilitation, which rises in frequency as conditions approach the extreme end of the environmental gradient. However, few studies have evaluated the validity of the SGH at the community level, the level at which it was formulated. Moreover, few studies have tested the SGH at either extreme of the gradient, and very few have excluded the effect of livestock on community response to stress. In line with the SGH, we hypothesized that several spatial pattern summary statistics would change monotonically from the least to the most arid sites, indicating increasingly aggregated patterns. In this study, we performed an evaluation of the SGH both within communities of shrub species and across a large portion of the Atacama Desert, and we isolated the abiotic component of the SGH. Our environmental gradient covered an extreme aridity gradient (< 20-130 mm annual precipitation). To perform point pattern analysis, we established 13 sites with environmental conditions representing four distinct levels of this gradient. Further, we conducted species co-occurrence analyses at 19 sites along the gradient. Both sets of analyses showed stronger positive spatial associations among plants at the most extreme end of the gradient. This was true regardless of whether we included all individuals, only small individuals located around large ones, or individuals in species pairs. Moreover, species tended to show greater co-occurrence as environmental severity increased. This increase in aggregation in the plant community seems to correlate with an increase in the strength of positive interspecific interactions, rather than greater clustering within each species. These monotonic increases in species co-occurrence and spatial association in more severe environments are consistent with some of the predictions of SGH, and collectively these results suggest that as the climate becomes more arid, positive species pairs interactions tend to be prevalent in the community.

Status and challenges for conservation of small mammal assemblages in South America

South America spans about 44° latitude, covers almost 18 million km(2) , and is second only to Africa in continental mammal species richness. In spite of this richness, research on the status of this fauna and on the nature and magnitude of contemporary threats remains limited. Distilling threats to this diverse fauna at a continental scale is challenging, in part because of the limited availability of rigorous studies. Recognizing this constraint, we summarize key threats to small mammals in South America, emphasizing the roles of habitat loss and degradation, direct persecution, and the increasing threat of climate change. We focus on three regional 'case studies': the tropical Andes, Amazonia and adjacent lowland regions, and the southern temperate region. We close with a brief summary of recent findings at our long-term research site in north-central Chile as they pertain to projected threats to this fauna. Habitat alteration is a pervasive threat that has been magnified by market forces and globalization (e.g. extensive agricultural development in Amazonia), and threatens increasing numbers of populations and species. Climate change poses even greater threats, from changes in rainfall and runoff regimes and resulting changes in vegetative structure and composition to secondary influences on fire dynamics. It is likely that many changes have yet to be recognized, but existing threats suggest that the future may bring dramatic changes in the distribution of many mammal taxa, although it is not clear if key habitat elements (vegetation) will respond as rapidly as climatic factors, leading to substantial uncertainty. Climate change is likely to result in 'winners' and 'losers' but available information precludes detailed assessment of which species are likely to fall into which category. In the absence of long-term monitoring and applied research to characterize these threats more accurately, and to develop strategies to reduce their impacts, managers already are being faced with daunting challenges. As the line between 'pure' and 'applied' research blurs in the face of converging interests of scientists and society we hope that solutions to these critical issues will be incorporated in addressing anticipated conservation crises.

Cascading effect of economic globalization on human risks of scrub typhus and tick-borne rickettsial diseases

The increase in global travel and trade has facilitated the dissemination of disease vectors. Globalization can also indirectly affect vector-borne diseases through the liberalization of cross-border trade, which has far-reaching, worldwide effects on agricultural practices and may in turn influence vectors through the modification of the ecological landscape. While the cascading effect of economic globalization on vector-borne diseases, sometimes acting synergistically with regional agricultural policy, could be substantial and have significant economic, agricultural, and public health implications, research into this remains very limited. We evaluated how abandonment of rice paddies in Taiwan after joining the World Trade Organization, along with periodic plowing, an agricultural policy to reduce farm pests in abandoned fields can unexpectedly influence risks to diseases transmitted by ticks and chiggers (larval trombiculid mites), which we collected from their small-mammal hosts. Sampling was limited to abandoned (fallow) and plowed fields due to the challenge of trapping small mammals in flooded rice paddies. Striped field mice (Apodemus agrarius) are the main hosts for both vectors. They harbored six times more ticks and three times more chiggers in fallow than in plowed plots. The proportion of ticks infected with Rickettsia spp. (etiologic agent of spotted fever) was three times higher in fallow plots, while that of Orientia tsutsugamushi (scrub typhus) in chiggers was similar in both treatments. Fallow plots had more ground cover and higher vegetation than plowed ones. Moreover, ticks and chiggers in both field types were dominated by species known to infest humans. Because ticks and chiggers should exhibit very low survival in flooded rice paddies, we propose that farm abandonment in Taiwan, driven by globalization, may have inadvertently led to increased risks of spotted fever and scrub typhus. However, periodic plowing can unintentionally mitigate vector burdens. Economic globalization can have unexpected consequences on disease risk through modification of the agricultural landscape, but the outcome may also be influenced by agricultural policies, calling for further research on vector-borne diseases and their control from broader perspectives.

Extreme climatic events change the dynamics and invasibility of semi-arid annual plant communities

Extreme climatic events represent disturbances that change the availability of resources. We studied their effects on annual plant assemblages in a semi-arid ecosystem in north-central Chile. We analysed 130 years of precipitation data using generalised extreme-value distribution to determine extreme events, and multivariate techniques to analyse 20 years of plant cover data of 34 native and 11 exotic species. Extreme drought resets the dynamics of the system and renders it susceptible to invasion. On the other hand, by favouring native annuals, moderately wet events change species composition and allow the community to be resilient to extreme drought. The probability of extreme drought has doubled over the last 50 years. Therefore, investigations on the interaction of climate change and biological invasions are relevant to determine the potential for future effects on the dynamics of semi-arid annual plant communities.

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.

Population dynamics of two sympatric rodents in a variable environment: rainfall, resource availability, and predation

Precipitation plays an important role in the dynamics of species found in arid and semiarid environments. However, population fluctuations generally are driven by a combination of multiple factors whose relative contribution may vary through time and among species. We monitored fluctuations of species in three trophic levels for >17 years at a semiarid community in north-central Chile. The region is strongly affected by the El Niño Southern Oscillation, resulting in high variation in rainfall that triggers dramatic changes in food resource availability, with strong effects on upper trophic levels. We focused our analyses on the role played by endogenous and exogenous (climatic) factors on the dynamics of two important rodent species in the community, Octodon degus and Phyllotis darwini. We documented population fluctuations of several orders of magnitude in response to wet and dry episodes of different strength and duration. P. darwini reached similar maximum densities, regardless of the duration of high-rainfall events, whereas O. degus showed additive effects of multiple wet years. Time series diagnostic tools revealed oscillations with a 5-year periodicity in rainfall, which may be the cause of the same periodicity and a weak second-order signal observed in the rodent dynamics. However, the dynamics of both rodent species were dominated by strong first-order processes, suggesting an important role of direct density dependence. Intraspecific competition, expressed as the ratio of rodent density/rainfall (or food resources) explained more than two-thirds of the variation in the population rate of change, whereas less than one-third was explained by lagged rainfall (or food resources). We detected no significant effects of predation. Our results contribute to a growing number of examples of dynamics governed by the combined effect of density dependence and climatic forcing. They also reveal strong bottom-up regulation that may be common in other arid environments.

The ecology and macroecology of mammalian home range area

Although many studies employ allometric relationships to demonstrate possible dependence of various traits on body mass, the relationship between home range size and body mass has been perhaps the most difficult to understand. Early studies demonstrated that carnivorous species had larger home ranges than herbivorous species of similar mass. These studies also argued that scaling relations (e.g., slopes) of the former were steeper than those of the latter and explained this in terms of the distribution of food resources, which are more uniformly distributed for most herbivores than for carnivores. In contrast to these studies, we show that scaling relations of home ranges for carnivorous mammals do not differ significantly from those of herbivorous and omnivorous species and that all three exhibit slopes that are significantly steeper than predicted on the basis of energetic requirements. We also demonstrate that home range size is constrained to fit within a polygonal constraint space bounded by lines representing energetic and/or biophysical limitations, which suggests that the log-linear relationship between home range area and mass may not be the appropriate function to compare against the energetically predicted slopes of 0.75 or 1.0. It remains unclear, however, why the slope of the relationship between home range area and body mass, whether based on raw data or on constraint lines, always exceeds that predicted by the energetic needs hypothesis.

Threat of hantavirus pulmonary syndrome to field biologists working with small mammals

Field biologists should use personal protective equipment appropriate for their activities.

Low risk for hantavirus pulmonary syndrome (HPS) has been reported among biologists engaged in fieldwork with rodents. The overall probability of acquiring HPS when working with rodents appears to be 1 in 1,412 (0.00071). Nonetheless, a causal link between HPS and lack of personal protective equipment (PPE) use is suggested by some investigators. However, supporting data are incomplete and consequently misleading. A recent HPS case was assumed to be acquired during rodent-handling activities, although substantial peridomestic exposure was evident. Regulatory groups interpret inadequate data as evidence of the need for rigorous PPE, which can hamper field research and instructional efforts. PPE recommendations should be reviewed and revised to match the risk associated with different types of fieldwork with small mammals.