Small mammal responses to environmental change: integrating past and present dynamics

Far away from home? Ancient DNA shows the presence of bicolored shrew (Crocidura leucodon) in Bronze Age Denmark

An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6× coverage). Phylogenetic analyses determined this specimen as a bicolored shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.

Tectonic extension and paleoelevation influence mammalian diversity dynamics in the Basin and Range Province of western North America

Landscape properties have a profound influence on the diversity and distribution of biota, with present-day biodiversity hot spots occurring in topographically complex regions globally. Complex topography is created by tectonic processes and further shaped by interactions between climate and land-surface processes. These processes enrich diversity at the regional scale by promoting speciation and accommodating increased species richness along strong environmental gradients. Synthesis of the mammalian fossil record and a geophysical model of topographic evolution of the Basin and Range Province in western North America enable us to directly quantify relationships between mammal diversity and landscape dynamics over the past 30 million years. We analyze the covariation between tectonic history (extensional strain rates, paleotopography, and ruggedness), global temperature, and diversity dynamics. Mammal species richness and turnover exhibit stronger responses to rates of change in landscape properties than to the specific properties themselves, with peaks in diversity coinciding with high tectonic strain rates and large changes in elevation across spatial scales.

Shrew Communities in Mediterranean Agro-Ecosystems of Central Greece: Associations with Crop Types, Land Uses, and Soil Parameters

Shrew communities play a crucial role in a diverse range of natural, urban, and agricultural ecosystems. We used Barn owl diet analysis as the ideal proxy to assess small-mammal distribution patterns on large spatial scales. More than 10,000 pellets were analyzed from Thessaly, the largest agricultural prefecture located in central Greece. A total of more than 29,000 prey items were identified, one of the largest datasets used in similar analyses in Europe. Three discrete shrew species were present in Thessaly agricultural plains, central Greece (Güldenstädt's shrew Crocidura gueldenstaedtii, Bi-coloured shrew Crocidura leucodon, and Pygmy white-toothed shrew Suncus etruscus), which comprised a total of 7452 shrews, representing 25.64% of the total small-mammals' dataset. C. gueldenstaedtii and S. etruscus demonstrated strong associations with heavy argillaceous-clay soils and Vertisol soil types, whereas S. etruscus was also associated with non-irrigated land and non-intensive cultivated plots. C. leucodon demonstrated no significant associations to any environmental gradient and demonstrated habitat plasticity, most possibly shaped by existing resources and competition. Our study highlights the important insights gained from Barn owl diet analysis in respect of small-mammal assemblages on broad geographical scales, and the inclusion of soil parameters as drivers of habitat suitability and distribution patterns for small-mammal responses.

High variation in handling times confers 35-year stability to predator feeding rates despite community change

Historical resurveys of ecological communities are important for placing the structure of modern ecosystems in context. Rarely, however, are snapshot surveys alone sufficient for providing direct insight into the rates of the ecological processes underlying community functioning, either now or in the past. In this study, I used a statistically reasoned observational approach to estimate the feeding rates of a New Zealand intertidal predator, Haustrum haustorium, using diet surveys performed at several sites by Robert Paine in 1968-1969 and by me in 2004. Comparisons between time periods reveal a remarkable consistency in the predator's prey-specific feeding rates, which contrasts with the changes I observed in prey abundances, the predator's body-size distribution, and the prey's proportional contributions to the predator's apparent diet. Although these and additional changes in the predator's per-capita attack rates seem to show adaptive changes in its prey preferences, they do not. Rather, feeding-rate stability is an inherently statistical consequence of the predator's high among-prey variation in handling times which determine the length of time that feeding events will remain detectable to observers performing diet surveys. Though understudied, similarly high among-prey variation in handling (or digestion) times is evident in many predator species throughout the animal kingdom. The resultant disconnect between a predator's apparent diet and its actual feeding rates suggests that much of the temporal, biogeographic, and seemingly context-dependent variation that is often perceived in community structure, predator diets, and food-web topology may be of less functional consequence than assumed. Qualitative changes in ecological pattern need not represent qualitative changes in ecological process.

Anthropogenically-induced range expansion as an invasion front in native species: An example in North American flying squirrels

Biological invasions are typically framed as non-native species impacting the populations of native species or ecosystems. However, in a changing world, taxonomically similar native species that were previously parapatric or allopatric may become increasingly sympatric over short time periods (<100 years). In the context of climate change in the Northern Hemisphere, this may have a negative impact on northern species whose ranges are being invaded by southern species. To highlight factors that may influence invasion fronts in native species, I use two species of North American flying squirrels, small-bodied nocturnal arboreal Sciurids, as an example. I discuss what factors may enable or limit the expansion of southern flying squirrels (SFS; Glaucomys fuscus) into northern flying squirrel (NFS; Glaucomys sabrinus) habitat and potential impacts that anthropogenically-induced factors have on range shift dynamics. The range expansion of SFS may impact NFS via resource competition, hybridization, and parasite-mediation. Factors potentially enabling the expansion of SFS into NFS habitat include anthropogenic habitat disturbance and climate change, wherein historical land-use (i.e., logging) alters forest composition increasing habitat suitability for SFS and a warming climate allows SFS to expanded their ranges northward into colder regions. Shifts in forest species composition from historical logging may interact with a warming climate to enable SFS to quickly expand their range. Factors limiting SFS expansion include thermoregulation limitations and absence of potential food and denning resources. The factors influencing the dynamics between these two species may be applicable to the shifting ranges of other taxonomically and functionally similar native species in the context of a rapidly changing world in the Anthropocene.

Small Mammal Diversity Changes in a Baltic Country, 1975-2021: A Review

The structure and diversity of small mammal (SM) communities over the long term may show the influences of climate change, landscape changes and local disturbances. We review published data regarding SM trapping and owl pellet analysis from Lithuania (the most southerly of the three Baltic States, Northern Europe), covering the period 1975-2021. Over decades, we analysed trends in the diversity of SM communities and the proportions of species and proportions of trophic groups. The large increase in granivores, from 6.9% in 1975-1980 to 45.4% in 2011-2020 and 54.7% in 2021, coincided with a decrease in omnivores and insectivores. The proportion of herbivores increased less notably. At the species level, significant decreases in the proportions of M. arvalis, C. glareolus and S. araneus were accompanied by notable increases in the proportions of A. flavicollis and A. agrarius, the latter from 1.0% in 1975-1980 to 25.3% in 2021. Concluding, two periods were identified, specifically before the 1990s and subsequently. In the second period, in the aftermath of land-use changes within the country in 1990, diversity increased, and dominance decreased, a situation that has not subsequently changed. Not excluding the concomitant effects of climate change, we relate these patterns to the alterations in habitat and anthropogenic impact.

Spatiotemporal impacts of the Anthropocene on small mammal communities, and the role of small biological preserves in maintaining biodiversity

The multi-faceted impacts of the Anthropocene are increasingly modifying natural ecosystems and threatening biodiversity. Can small protected spaces conserve small mammal diversity across spatial and temporal scales of human impact? We identified small mammal remains from modern raptor pellets and Holocene archeological sites along a human modification gradient in the San Francisco Bay Area, CA and evaluated alpha and beta diversity across sites and time periods. We found that Shannon diversity, standardized species richness, and evenness decrease across modern sites based on level of human modification, with no corresponding change between Holocene sites. Additionally, the alpha diversity of modern sites with moderate and high levels of human modification was significantly lower than the diversity of modern sites with low levels of human modification as well as all Holocene sites. On the other hand, the small mammal communities from Jasper Ridge Biological Preserve, a small protected area, retain Holocene levels of alpha diversity. Jasper Ridge has also changed less over time in terms of overall community composition (beta diversity) than more modified sites. Despite this, Holocene and Anthropocene communities are distinct regardless of study area. Our results suggest that small mammal communities today are fundamentally different from even a few centuries ago, but that even relatively small protected spaces can partially conserve native faunal communities, highlighting their important role in urban conservation.

Factors influencing range contraction of a rodent herbivore in a steppe grassland over the past decades

Climate warming and human disturbance are known to be key drivers in causing range contraction of many species, but quantitative assessment on their distinctive and interactive effects on local disappearance is still rare.

In this study, we examined the association of climate warming and human disturbance stressors with local disappearance probability of Brandt's voles (Lasiopodomys brandtii) in a steppe grassland in northern China.

We used logistic generalized additive models to quantify the relationship between local disappearance probability of Brandt's voles and environmental variables. The year following the last observation year was used to estimate the disappearance threshold of Brandt's voles. We projected the distribution change of Brandt's voles under future climate warming scenarios.

We found climate warming attributed to local disappearance and range contraction for southern populations of Brandt's voles from 1971 to 2020. Human stressors and high vegetation coverage increased the probability of local disappearance of voles in years of abundant precipitation. The southern boundary retreated northward at a speed of 99.0 km per decade with the temperature rise of 0.36°C. The disappearance threshold of maximum air temperature of Brandt's voles in the warmest month (27.50 ± 1.61°C) was similar to the lower critical temperature of its thermal neutral zone.

Our study suggests that the rapid climate change over the past decades contributed to the range contraction of its southern boundary of this keystone species in the steppe grassland of China. It is necessary to take actions to preserve the isolated populations of Brandt's voles from the effects of accelerated climate change and human disturbance.

Patterns and Predictors of Small Mammal Phylogenetic and Functional Diversity in Contrasting Elevational Gradients in Kenya

Mountains of the Afrotropics are global biodiversity hotspots and centers of speciation and endemism; however, very few studies have focused on the phylogenetic and functional dimensions of Afromontane small mammals. We investigated the patterns and mechanisms of small mammal phylogenetic and functional diversity and assembly along elevational gradients in Mount Kenya, the second highest mountain in Africa, and a contrasting low mountain range, Chyulu Hills. We sampled 24 200-m interval transects in both sites; 18 in Mt. Kenya (9 each in the windward side, Chogoria, and the leeward side, Sirimon) and 6 in Chyulu. We extracted the mitochondrial Cytochrome b gene to reconstruct a time-calibrated species tree for estimating phylogenetic diversity indices [phylogenetic richness (PD), mean nearest taxon distance (PDMNTD), and nearest taxon index (PDNTI)]. A functional trait data set was compiled from the field-recorded measurements and published data sets for estimating functional diversity indices [functional richness (FD), mean nearest taxon distance (FDMNTD), and nearest taxon index (FDNTI)]. Several environmental variables representing water-energy availability, primary habitat productivity, and topographic heterogeneity were used to estimate the predictive power of abiotic conditions on diversity variances using generalized linear and generalized additive regression models. The PD and FD peaked around mid-elevations in Mt. Kenya, unimodally increased or decreased in Chogoria and Sirimon, and monotonically increased in Chyulu. The divergence and community structure indices—PDMNTD, FDMNTD, and PDNTI and FDNTI—were relatively weakly associated with elevation. Overall, the tendency of assemblages to be phylogenetically and functionally closely related than expected by chance decreased with elevation in Mt. Kenya but increased in Chyulu. Across the indices, the annual precipitation and topographic ruggedness were the strongest predictors in Mt. Kenya, evapotranspiration and temperature seasonality were the strongest predictors in Chyulu, while temperature seasonality and terrain ruggedness overlapped as the strongest predictors in Chogoria and Sirimon in addition to annual precipitation in the latter and normalized difference vegetation index in the former. The observed contrasting trends in diversity distribution and the strongest predictors between elevational gradients are integral to the sustainable management of the high faunal biodiversity in tropical Afromontane ecosystems.

Shrinkage of body size in rodents as a strategy of populations under anthropogenic conditions (results of 50 years of study of rodent populations)

Based on results of 50 years of continuous observations of populations of the pine vole (Microtus subterraneus de Selys-Longchamps, 1836) and yellow-necked wood mouse (Sylvaemus flavicollis Melchior, 1834), the phenomenon of reducing body size of individuals was revealed, particularly a significant reduction in body dimensions and body mass. The research was conducted at the Kaniv Nature Reserve covering various stages of the local ecosystem's existence under anthropogenic impact. Four cycles of density dynamics of two populations are chosen for comparison of their characteristics. The first three cycles correspond to qualitatively different periods in the existence of the protected ecosystem and populations of the studied species, whereas the last cycle reflects the current situation. It has been established that the tendency to decrease body dimensions is also characteristic for other rodent species, its manifestations are observed for 35 years, and the scale gradually increases. By fatness indexes, individuals of the pine vole on average lose 23.3% and yellow-necked wood mice lose 16.7% of the former values. It was shown that the level of reduce in exterior parameters is always greater in females than in males, and in the group of breeding adults it can reach 32%. It has been found that the phenomenon also applies to juveniles, whose fatness decreases by an average of 21%. The phenomenon occurs against the background of violations of various aspects of population dynamics, which allows it to be associated with anthropogenic changes in the environment. It is suggested that shrinking can be realized by various mechanisms. First, as a result of mortality, the largest individuals and reproductive females with their greatest energy needs fall out of the population, and, second, the growth and weight gain of young animals is slower. As a result, the decrease in external parameters of individuals reduces their specific energy needs and allows them to better survive under adverse conditions. From these points of view, reducing body dimensions can be considered as a specific population strategy to maintain ecological balance.

The effects of formalin fixation and fluid storage on stable isotopes in rodent hair

Stable isotopes are increasingly being used to unlock the wealth of information contained in specimens preserved in museum collections. However, preservation methods that employ formalin may confound ecological interpretations. To quantify the effects of formalin fixation and subsequent fluid storage in ethanol on the isotopic signatures of small mammal hair, we analyzed δ 13C and δ 15N values from specimens of seven rodent species that were sampled repeatedly both before and after varying lengths of formalin fixation (1–11 days) and ethanol storage (1–6 years). We supplemented these data with a 2-week fixation experiment using deer mice (Peromyscus maniculatus) in which no ethanol storage was employed. As expected, preservation in formalin and ethanol had no discernable effect on δ 15N values. In contrast, specimen δ 13C values decreased in a saturating fashion during formalin fixation and over subsequent years of fluid storage in ethanol. On the basis of models that we fit to these time series, we estimate the long-term effect of fixation and storage on δ 13C values to be −0.92‰ after 4 years. This biologically relevant shift in δ 13C values should be accounted for when inferring the diets of species from fluid-stored museum collections and when comparing across specimens with different preservation histories.

Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.

Lost in a sagebrush sea: comparative genetic assessment of an isolated montane population of Tamias amoenus

The montane sky islands of the Great Basin are characterized by unique, isolated habitats and communities that likely are vulnerable to extirpation with environmental change. A subspecies of yellow pine chipmunk, the Humboldt yellow pine chipmunk (Tamias amoenus celeris), is associated with the whitebark and limber pine forests of the Pine Forest Range (PFR) in Nevada. We sampled T. amoenus and least chipmunks (T. minimus) from the isolated PFR and compared genetic diversity between these populations and more “mainland” populations, including other subspecies of chipmunks. Given the high frequency of hybridization in Tamias, we tested for hybridization between T. amoenus and T. minimus in the PFR. We examined phylogenetic relationships, population divergence and diversity, and screened populations for a common pathogen, Borrelia hermsii, to gain insight into population health. We found T. amoenus of the PFR are closely related to T. amoenus in the Warner Mountains and Sierra Nevada, but maintain substantively lower genetic variation. Microsatellite analyses show PFR T. amoenus are highly genetically differentiated from other populations. In contrast, PFR T. minimus had higher genetic diversity that was comparable to the other T. minimus population we sampled. Pathogen screening revealed that T. amoenus carried higher pathogen loads than T. minimus in the PFR, although the prevalence of infection was similar to other Tamias populations. Our assessment of habitat associations suggests that the Humboldt yellow pine chipmunk almost entirely is restricted to the conifer systems of the PFR, while least chipmunks are prevalent in the other forests. Our work highlights the need for continued conservation and research efforts to identify how response to environmental change can be facilitated in isolated species and habitats.

Historical Landscape Use of Migratory Caribou: New Insights From Old Antlers

Accumulations of shed caribou antlers (Rangifer tarandus) are valuable resources for expanding the temporal scope with which we evaluate seasonal landscape use of herds. Female caribou shed their antlers within days of giving birth, thus marking calving ground locations. Antler geochemistry (87Sr/86Sr) reflects the isotopic signature of regions used during antler growth, thereby providing data on a second component of seasonal landscape use. Here, we evaluate shed caribou antlers from the Coastal Plain of the Arctic National Wildlife Refuge, Alaska. The Central and Eastern regions of the Coastal Plain are calving grounds for the Porcupine Caribou Herd, while the Western Coastal Plain supports calving by the Central Arctic Herd. We found that antler 87Sr/86Sr from the Central and Eastern Coastal Plain were isotopically indistinguishable, while antler 87Sr/86Sr from the Western Coastal Plain was significantly smaller. For each region, we compared isotopic data for “recent” antlers, which overlap the bulk of standardized state and federal caribou monitoring (early 1980s and younger), with “historical” antlers shed in years predating these records (from the 1300s to the 1970s). For Porcupine Herd females calving in the Arctic Refuge, comparisons of antler 87Sr/86Sr through time indicate that summer ranges have been consistent since at least the 1960s. However, changes between historical and recent antler 87Sr/86Sr for the Central Arctic Herd indicate a shift in summer landscape use after the late 1970s. The timing of this shift is coincident with multiple factors including increased infrastructural development in their range related to hydrocarbon extraction. Accumulations of shed caribou antlers and their isotope geochemistry extend modern datasets by decades to centuries and provide valuable baseline data for evaluating potential anthropogenic and other influences on caribou migration and landscape use.

Markers for genetic change

Background and aims

Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question.

Methods

We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined.

Results

The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders.

Conclusions

Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.

Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies

The application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.

Parasites and wildlife in a changing world: The vector-host- pathogen interaction as a learning case

In the Anthropocene context, changes in climate, land use and biodiversity are considered among the most important anthropogenic factors affecting parasites-host interaction and wildlife zoonotic diseases emergence. Transmission of vector borne pathogens are particularly sensitive to these changes due to the complexity of their cycle, where the transmission of a microparasite depends on the interaction between its vector, usually a macroparasite, and its reservoir host, in many cases represented by a wildlife vertebrate. The scope of this paper focuses on the effect of some major, fast-occurring anthropogenic changes on the vectorial capacity for tick and mosquito borne pathogens. Specifically, we review and present the latest advances regarding two emerging vector-borne viruses in Europe: Tick-borne encephalitis virus (TBEV) and West Nile virus (WNV). In both cases, variation in vector to host ratio is critical in determining the intensity of pathogen transmission and consequently infection hazard for humans. Forecasting vector-borne disease hazard under the global change scenarios is particularly challenging, requiring long term studies based on a multidisciplinary approach in a One-Health framework.

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.

A semiarid fruit agroecosystem as a conservation-friendly option for small mammals in an anthropized landscape in Mexico

Many studies have addressed the potential of low-input agroecosystems for biological conservation. However, most have been carried out on annual agroecosystems in temperate, developed countries. As agricultural surface will increase and natural protected areas alone will not warrant the conservation of biodiversity, it is crucial to include different types of agroecosystems in research and conservation efforts. In Mexico, perennial, low-input, fruit-oriented nopal orchards (Opuntia spp.), one of the few crops suitable for semiarid areas, are the 10th out of 61 most important fruit crops grown in the country. We assessed their value for conservation in an anthropized landscape by comparing their rodent assemblages with those in adjacent habitats and determined the influence of the latter on the rodent communities inside them. We live-trapped rodents in 12 orchards and adjacent natural xeric shrubland, grassland, and cropland. We captured 19 different species, of which 17 used the orchards. Four are Mexican endemics. Orchards have higher α diversity, species richness, and abundance than cropland and grassland and are not different from shrubland. The dominant rodent species are the same in orchards and shrubland, and where these two meet they integrate into one habitat. Within-habitat quality is a critical driver of the composition and diversity of rodent communities in the orchards studied, and the neighboring habitats do not modify them substantially. Increasing within-patch heterogeneity beyond a certain level is at the expense of habitat integrity and produces small-scale fragmentation reducing habitat quality. At a landscape scale, orchards contribute importantly to regional rodent diversity compared with other land use types, and appear to increase habitat connectivity between patches of shrubland. Orchards' higher α diversity would give them higher ecological resilience and make them better suited than grassland and cropland to contribute to the conservation of local biota. Nopal orchards should be considered conservation allies and incorporated in regional conservation plans. Regrettably, their future is unwarranted as producers face low revenues and lack of governmental support. Our confirmation that orchards have an important, positive impact on biodiversity can be used as a strong argument to lobby for incentives to safeguard this environmental friendly, low-input agroecosystem.

Biodiversity and Topographic Complexity: Modern and Geohistorical Perspectives

Topographically complex regions on land and in the oceans feature hotspots of biodiversity that reflect geological influences on ecological and evolutionary processes. Over geologic time, topographic diversity gradients wax and wane over millions of years, tracking tectonic or climatic history. Topographic diversity gradients from the present day and the past can result from the generation of species by vicariance or from the accumulation of species from dispersal into a region with strong environmental gradients. Biological and geological approaches must be integrated to test alternative models of diversification along topographic gradients. Reciprocal illumination among phylogenetic, phylogeographic, ecological, paleontological, tectonic, and climatic perspectives is an emerging frontier of biogeographic research.

High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones

RATIONALE

Microfaunal skeletal remains can be sensitive indicators of the contemporary ecosystem in which they are sampled and are often recovered in owl pellets in large numbers. Species identification of these remains can be obtained using a range of morphological criteria established for particular skeletal elements, but typically dominated by a reliance on cranial characters. However, this can induce biases under different environmental and taphonomic conditions. The aim of this research was to develop a high-throughput method of objectively identifying rodent remains from archaeological deposits using collagen fingerprinting, most notably the identification of rats from other myomorph rodents as a means to identify disturbances in the archaeofauna through the presence of invasive taxa not contemporary with the archaeological deposits.

METHODS

Collagen was extracted from complete microfaunal skeletal remains in such a manner as to leave the bones morphologically intact (i.e., weaker concentration of acid than previously used over shorter length of time). Acid-soluble collagen was then ultrafiltered into ammonium bicarbonate and digested with trypsin prior to dilution in the MALDI matrix and acquisition of peptide mass fingerprints using a matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer.

RESULTS

Collagen fingerprinting was able to distinguish between Rattus, Mus, Apodemus and Micromys at the genus level; at the species level, R. rattus and R. norvegicus could be separated whereas A. flavicollis and A. sylvaticus could not. A total of 12,317 archaeological microvertebrate samples were screened for myomorph signatures but none were found to be invasive rats (Rattus) or mice (Mus). Of the contemporary murine fauna, no harvest mice (Micromys) were identified and only 24 field mouse (Apodemus) discovered.

CONCLUSIONS

As a result, no evidence of recent bioturbation could be inferred from the faunal remains of these archaeological deposits. More importantly this work presents a method for high-throughput screening of specific taxa and is the first application of collagen fingerprinting to microfaunal remains of archaeological specimens.

Energy flow and functional compensation in Great Basin small mammals under natural and anthropogenic environmental change

Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities--particularly the spread of nonnative annual grasslands--has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management.