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opencc-zeroDec 2022View details →

Airborne eDNA documents a diverse and ecologically complex tropical bat and other mammal community

Environmental (e)DNA has rapidly become a powerful biomonitoring tool, particularly in aquatic ecosystems. This approach has not been as widely adopted in terrestrial communities where the methods of vertebrate eDNA collection have varied from the use of secondary collectors such as blood-feeding parasites and spider webs to washing surfaces of leaves and soil sampling. Recent studies have demonstrated the potential of direct collection of eDNA from air sampling, but none have tested how effective airborne eDNA sampling might be in a biodiverse environment. We used three prototype samplers to actively sample a mixed neotropical bat community in a partially controlled environment. We assess whether airborne eDNA can accurately characterize a high-diversity community with skewed abundances and to determine if filter design impacts DNA collection and taxonomic recovery. Our study provides evidence for the accuracy of airborne eDNA as a detection tool and highlights its potential for monitoring high-density, diverse assemblages such as bat roosts. Analysis of air samples recovered >91% of the species present and some limited relationship between species abundance and read count. Our data suggest this method can accurately depict a diverse mixed mammal community, particularly when the location is contained (e.g., a roost, den or burrow) but also highlights the potential for secondary transfer of eDNA material on clothing and equipment. Our results also demonstrate that simple, inexpensive, battery-operated homemade air samplers can collect an abundance of eDNA from the air, opening the opportunity for sampling in remote environments.

opencc-zeroDec 2022View details →

Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity

Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.

opencc-by-4.0Dec 2022View details →

Global variation in unique and redundant mammal functional diversity across the daily cycle

(1) Data S1: Excel file consisting of ‘1_Data’ Trait data containing both missing values and imputed data, with data sources as a ‘2_Metadata’ sheet in the excel file. Activity patterns were extracted from our recently compiled database for mammals (Cox et al., 2021). ‘3_Updated activity patterns’: Here, we updated activity patterns for 109 species and provide data sources. We also now consider that the African forest elephant (Loxodonta cyclotis) is a separate species to the African savannah elephant (Loxodonta africana). (2) README.md file describing Data S1 (3) Supplementary information in the form of appendixes, figures and tables

opencc-by-nc-4.0Mar 2021View details →

Figure 2 in Mammal diversity among vertical strata and the evaluation of a survey technique in a central Amazonian forest

Figure 2. Species accumulation curve for (A) sampling effort (camera trap days) and (B) completeness of vertical strata.

opencc-by-nc-4.0Mar 2021View details →

Figure 1 in Mammal diversity among vertical strata and the evaluation of a survey technique in a central Amazonian forest

Figure 1. Locations of the nine paired camera traps located in the Cuieiras Biological Reserve, Brazil. F represents the floor stratum and C represents the canopy stratum.

opencc-zeroJan 2023View details →

Differential effects of ecosystem engineering by the superb lyrebird Menura novaehollandiae and herbivory by large mammals on floristic regeneration and structure in wet eucalypt forests

Ecosystem engineers that modify soil and ground-layer properties exert a strong influence on vegetation communities in ecosystems worldwide. Understanding the interactions between animal engineers and vegetation is challenging when in the presence of large herbivores, as many vegetation communities are simultaneously affected by both engineering and herbivory. The superb lyrebird Menura novaehollandiae, an ecosystem engineer in wet forests of south-eastern Australia, extensively modifies litter and soil on the forest floor. The aim of this study was to disentangle the impacts of engineering by lyrebirds and herbivory by large mammals on the composition and structure of ground-layer vegetation. We carried out a two-year, manipulative exclusion experiment in the Central Highlands of Victoria, Australia. We compared three treatments: fenced plots with simulated lyrebird foraging; fenced plots excluding herbivores and lyrebirds; and open controls. This design allowed assessment of the relative impacts of engineering and herbivory on germination rates, seedling density, vegetation cover and structure, and community composition. Engineering by lyrebirds enhanced the germination of seeds in the litter layer. After two years, more than double the number of germinants were present in 'engineered' than 'non-engineered' plots. Engineering did not affect the density of seedlings, but herbivory had strong detrimental effects. Herbivory also reduced the floristic richness and structural complexity (< 0.5 m) of forest vegetation, including the cover of herbs. Neither process altered the floristic composition of the vegetation within the 2-year study period. Ecosystem engineering by lyrebirds and herbivory by large mammals both influence the structure of forest-floor vegetation. The two-fold increase in seeds stimulated to germinate by engineering may contribute to the evolutionary adaptation of plants by allowing greater phenotypic expression and selection than would otherwise occur. Over long timescales, engineering and herbivory likely combine to maintain a more-open forest floor conducive to ongoing ecosystem engineering by lyrebirds.

opencc-zeroFeb 2023View details →

Habitat and not topographic heterogeneity constrains the range sizes of African mammals

Aim: The extinction risks of species are influenced by their geographical range sizes, as species with smaller ranges are more likely to go extinct following disturbance events. Theoretically, heterogeneous landscapes can maintain small-ranged species, because they facilitate the coexistence of taxa that are each constrained to distinct abiotic conditions. However, we do not fully understand whether this process is more attributable to variation in habitat types (habitat heterogeneity) or physical elevations (topographic heterogeneity) across landscapes. Here, we compare the influences of habitat versus topographic heterogeneity on mammalian range sizes in Africa. Location: Africa. Taxon: Mammalia. Methods: We built a phylogenetic generalized least squares model to predict the range sizes of 1033 mammalian species from their functional traits and abiotic conditions. We assessed how the performance of the model changed when we incorporated measures of the local habitat and, separately, topographic heterogeneity that species experience. Results: Habitat and topographic heterogeneity are weakly correlated across Africa (ρ = 0.14). Habitat heterogeneity is inversely related to range size (model coefficient = −0.88). Incorporating habitat heterogeneity significantly decreased the model's AICc, increased its likelihood and increased the proportion of variance that is explained in the range sizes of species. Conversely, topographic heterogeneity is not significantly related to range size and had no impact on the model's AICc, likelihood or predictive performance. This contrast between habitat and topographic heterogeneity is particularly prevalent in carnivorous mammalian clades. Results at multiple spatial resolutions differed minimally. Main Conclusions: Our findings advance ecological theory by demonstrating that a landscape's variation in habitats, and not in elevations, relates inversely with mammalian range size and therefore facilitates the coexistence of small-ranged mammals. Conservation efforts in regions of high habitat heterogeneity will be critical to prevent extinctions in Africa's biodiverse mammalian species.

opencc-zeroFeb 2023View details →

Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals

Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of the latter two revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-western Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples for calibration of the molecular clock. We found that across the three species, divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat to the interglacial environments. In European narrow-headed voles, we identified multiple time-structured mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

opencc-zeroFeb 2023View details →

Bridging the gap: Optimising connectivity solutions for an arboreal gliding mammal

Connectivity modelling tools are important for developing mitigation strategies to alleviate negative impacts on animal movement caused by road networks. Arboreal gliding mammals are especially vulnerable to road widening as they are unable to cross gaps beyond their gliding capacity. However, there are limitations of conventional raster-based modelling techniques when applied on this group. We developed and applied a new model that quantifies the changes in connectivity for an arboreal gliding species, the Sunda colugo, in Singapore using information on species-specific glide performance through a vector-based GIS approach. We also incorporated a genetic algorithm to determine optimal locations for sets of glide poles that could be installed to improve connectivity. Expectedly, connectivity was heavily impacted by the road widening works, with a 93.3% decrease in the total number of feasible glide paths connecting roadside trees. Nine glide poles installed during the construction phase of the project were initially uninformed by the connectivity model and they provided 26 additional connections only. Comparatively, the top nine pole locations identified through the genetic algorithm provided 247 additional connections, almost 10 times more than the amount supplied by the initial nine glide pole locations determined through qualitative methods. The multi-objective capacity of the genetic algorithm also reduced large connectivity gaps post-development, with simulated glide poles increasing the percentage of pixels covered with connectivity from 16.1% to 27.7%. Synthesis and applications: Our model fills a knowledge gap in connectivity modelling for arboreal gliding mammals whose movements are affected by varying habitat alterations. We demonstrated that locations of mitigation structures greatly influence the success of mitigation efforts and the locations can be optimized by incorporating the glide performance of the species into the genetic algorithm. Given limited conservation resources, this approach would benefit managers in formulating cost-effective efforts for arboreal gliding mammals.

opencc-zeroMar 2023View details →

Dataset from: Exaptation and vulnerability to introduced mammal herbivores on Balearic endemic flora

Aim: How introduced mammal herbivores affect insular flora is still under study. Also, disentangling which particular traits, that plants might develop from exaptations, are functional to avoid herbivory remains mainly unknown. This study aims to assess if the flora of continental islands with historic native herbivores has exapted to the introduction of new mammal herbivores and to predict the potential vulnerability of endemic species from islands where mammal herbivores have not been introduced yet. Location: Balearic Islands Taxon: 96 Balearic endemic plant species Methods: We investigated whether the endemic flora on continental islands maintains functional traits that resist introduced mammal herbivores by analysing the chemical and morphological traits related to plant resistance of five individuals per species (n=480). Also, we measured plant-size variables to assess plant escape strategies. Overall, we combined these traits with the accessibility to goats. Predictive models were generated for species that inhabit islands where goats have not been introduced to assess their potential vulnerability. Results: Endemic species may defend against new herbivores (e.g., goats) if they contain highly toxic compounds (alkaloids, glycosides, coumarins), spinescent and urticating structures, or specific plant architecture (low plant size, high specific leaf area). If such traits are absent, the species may become extinct—unless they inhabit areas inaccessible to goats. On continental islands, some endemic species are expected to resist the introduction of herbivores, while others may be significantly affected. Main conclusions: Part of the endemic flora may have previously adapted to ancient herbivores on the islands. Even though the ancient connection with the mainland, these traits may allow the plants to resist the presence of introduced herbivores. However, non-exapted species could be threatened by the introduction of non-native ungulates.

opencc-zeroMar 2023View details →

Small mammal granivory as a biotic filter for tree establishment beyond elevation range boundaries

Trees often experience migration lags in their response to rapidly changing climate. Preferential granivory by nocturnal small mammals has the potential to create lags by reducing germination success beyond range edges. To determine how granivory may limit establishment of trees beyond their range margins, we conducted a seed choice experiment which offered seeds of five regionally dominant tree species to small mammals within distinct forest communities across a 400m elevational gradient on four mountains in the northeastern United States. Multinomial logistic mixed effects models were used to (a) quantify seed preference of each species across the elevational gradient and (b) assess relationships between seed preference and abiotic variables. A separate seed dispersal experiment was used to compare the probability of seed consumption versus seed caching. The low-elevation temperate tree species Fagus grandifolia and Acer saccharum had an equally high probability of granivory within and beyond their range margins (~40% and ~20%, respectively). Generally, seed preference was positively correlated with seed mass and nutrient content regardless of elevation. Our seed dispersal experiment revealed that seeds were 3× more likely to be consumed than cached, suggesting that small mammals can potentially decrease germination success. Overall, temperate tree species with either high seed mass or nutritional value may experience substantial granivory beyond their range margin, partially explaining the observed lag between tree dispersal and climate change. Thus, granivory is vital to consider when modeling future tree species distributions under various climate change scenarios.

Data for: Small reductions in cargo vessel speed dramatically reduce noise impacts to marine mammals

Global reductions in the underwater radiated noise levels from cargo vessels are needed to reduce increasing cumulative impacts to marine wildlife. We use a vessel exposure simulation model to examine how reducing vessel source levels through slowdowns and technological modifications can lessen impacts on marine mammals. We show that the area exposed to ship noise reduces dramatically with moderate source level reductions that can be readily achieved with small reductions in speed. Moreover, slowdowns reduce all impacts to marine mammals despite the longer time that a slower vessel takes to pass an animal. We conclude that cumulative noise impacts from the global fleet can be reduced immediately by slowdowns. This solution requires no modification to ships and is scalable – from local speed reductions in sensitive areas to ocean basins. Speed reductions can be supplemented by routing vessels away from critical habitats and by technological modifications to reduce vessel noise.

Supporting isotopic data for: Amino acid isotope analysis reveals variation in gut microbial contribution to host protein metabolism in a wild small mammal community

Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ13C) and nitrogen (δ15N) isotope analysis, we estimated the proportional contributions of essential amino acids (AAESS) synthesized by gut microbes to five co-occurring desert rodents representing herbivorous, omnivorous, and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (Dipodomys spp.) routed a substantial proportion (~40–50%) of their AAESS from gut microbes, while higher trophic level omnivores (Peromyscus spp.) and insectivores (Onychomys arenicola) obtained most of their AAESS (~58%) from plant-based energy channels but still received ~20% of their AAESS from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals.

Rapid reduction of Paraoxonase expression followed by inactivation across semiaquatic mammals suggests adaptive benefit of gene loss

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of function; loss of protein function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages – Pon1 became a pseudogene at least six times independently in aquatic and semiaquatic mammals with clear genetic lesions, such as stop codons and frameshifts. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and blood plasma activity across four major aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We also observed in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing for accumulation of disrupting mutations. The recurrent and rapid loss of Pon1 even suggests that it is adaptive in aquatic mammals. Accordingly, we examined diving and dietary traits across pinniped species as potential driving forces of Pon1 loss. We found that loss is best correlated with diving activity and is likely the result of selective pressures associated with hypoxia and hypoxia-induced inflammation.

The Mammal Dental Metrics Database: a compilation of fossil and extant mammal tooth measurements

Fossil relative abundance data in combination with specimen-level measurements can reveal community-level changes underpinning long-term ecological and evolutionary dynamics. However relative abundance data is not consistently reported in the paleontological literature, and measurement data is presented in individual studies in varying formats. Here, we compiled dental measurements (tooth crown length, width, and height) from the paleontological literature (or otherwise available sources) in a single database, simultaneously permitting analyses of size and relative abundance for the fossil record. This first version of the database focuses on large mammals and on the African and Arabian Neogene fossil record. Measurements of teeth of extant species were also collected. Each row gives the available measurements for a single tooth. Specimens with multiple teeth reported are divided among several rows. Taxonomic information was entered largely as given in the original source, without standardization or revision of taxonomic identifications. Geographic, stratigraphic, and assemblage information was also collected for fossil specimens, and specimens were assigned to individual 'computational localities' (normally combinations of geological unit and location) that can be treated as paleo-communities (metacommunities). Numeric ages and geographic and geological information for these localities are given in a corresponding spreadsheet. Sources are given for all measurement and age data. This dataset provides a powerful new resource for investigations of changes in relative abundance, body mass, or mass-abundance distributions in the fossil record.

opencc-zeroJun 2023View details →

From seed dispersal service to reproductive collapse: density-dependent outcome of a palm-mammal interaction

Interspecific ecological interactions are inherently context-dependent. They may vary in both magnitude and sign depending on the biotic and abiotic conditions, depicting a mutualism-antagonism continuum. However, how population abundances and the activity of interacting species modulate these interactions remains underexplored. Here, we chose the interaction between the Mediterranean palm Chamaerops humilis and the feral goat Capra hircus in Mallorca (Balearic Islands, Spain). We selected three study plots with low, intermediate and high intensities of goat activity where we characterized palm distribution, seed rain, seed predation, and early palm recruitment during two consecutive years. Since goats can cause both costs (e.g. florivory) and benefits (e.g. seed dispersal) to C. humilis performance, we investigated the following three questions: (1) Does the spatial distribution of adult palms vary depending on the intensity of goat activity? (2) Does the intensity of goat activity influence seed rain and its potential spatial association with adult palms? (3) To what extent does the intensity of goat activity determine post-dispersal events such as seed predation and seedling emergence? We found that adult palms showed a more clumped and complex distribution (double-cluster process) in plots with low and intermediate goat activity compared to that with high goat activity (simple-cluster process). In the low goat activity plot, dispersed seeds were spatially aggregated around adult palms, showing twice insect-seed predation and nearly three times lower seed germination success than those in the intermediate goat activity plot. Palm seed dispersal and recruitment were almost nil in the high goat activity plot due to heavy consumption of palm inflorescences and developing fruits by goats. Our findings demonstrate how the net outcome of plant-animal interactions can change from mutualism to antagonism, from reproductive service to reproductive collapse, depending on the abundance and the activity of the interacting species.

opencc-by-4.0Jun 2023View details →

Data for Multidimensional diversity drives stability of mammal communities with large carnivores in temperate forests

R code and data for Multidimensional diversity drives stability of mammal communities with large carnivores in temperate forests

opencc-by-4.0Jun 2023View details →

Is bedding material a more effective thermal insulator than trap cover for small mammal trapping? A field experiment

This dataset is currently part of a manuscript undergoing a review process in the Journal of Thermal Biology. The manuscript compares the thermal insulation provided by a cover, bedding, and a combination of both when applied to small mammal traps. Treatments were tested in two different environmental conditions, one where temperature is more stable (near the sea coast), and another where temperature fluctuations are more severe (in the Pyrenees). The first sheet contains the data collected from four Sherman traps placed in an outside terrace. One trial lasted four days, and a second trial lasted two days. Temperature (ºC) and relative humidity (%) were recorded every 10 minutes with data loggers (Elitech RC-51) situated inside each trap. Traps were assigned to a treatment as follows: Cover (CV), trap with only the PVC cover; Bedding (BD): Trap with water-proof cotton wool inside; Cover+Bedding (CV+BD): trap with the cover and with water-proof cotton wool inside; Control (CN), a conventional trap; Another logger was placed outside to have measures of air temperature (Air). In the case of BD treatment, data-loggers were placed inside the cotton. The second sheet contains the data collected from three traps of three different models: Sherman, Longworth, and Heslinga. To avoid ethical concerns related with keeping wild animals trapped for long periods of time, we placed hand-warmer heat pads (Terratherm) – with up to 12 hours of warmth – within traps to simulate endothermic metabolism generated by a trapped small mammal (Kearney et al., 2011; Griffiths et al., 2017). Despite the covers being designed for Sherman traps, in the trials we also included two other commercial traps used in the SEMICE monitoring programme (Torre et al., 2018), Longworth (Longworth Scientific Instrument Co., Oxford, UK), and Heslinga (<a href="http://www.heslingatraps.eu/">www.heslingatraps.eu</a>) for thermal insulation capacity comparisons. The experiments were conducted in two contrasting climatic areas in Barcelona province (coastal, 22 m.a.s.l, and Pyrenees, 650 m.a.s.l), to expand the range of temporal and spatial variation in winter temperatures. We performed 63 trials combining three trap models and three treatments. Traps were placed in similar conditions and submitted to the same CN, BD and CV+BD treatments cited above. The CV treatment (trap with only the PVC cover) was excluded from the second experiment due to its poor performance in retaining temperature and humidity, as demonstrated in the first experimental session (see ‘Results’ section). Furthermore, the CV treatment does not represent a common treatment in small mammal trapping studies. Inside each trap we placed a temperature data logger (iButton, Thermochron) protected within an aluminium mesh, an ideal material to house the small temperature loggers (Orrock and Connolly, 2016). In the Bedding treatments, the mesh was placed inside the cotton. Temperature was recorded continuously every five minutes. To avoid direct heat exchange between the heat pad and the data logger, we placed the heat pad at the end of the trap close to the back door, as far away from the data logger as possible. To quantify the heat output of the heat pads through time, we placed a data logger below a hand warmer in six different trials, recording temperatures every five minutes during a 12-hour period. All experiments were conducted during winter 2021.

opencc-zeroJun 2023View details →

Data from: Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals

Differences in the bacteria inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analyzed the gut microbiomes of 14 sympatric small-mammal species in a semi-arid African savanna, hypothesizing that there would be a strong phylosymbiosis pattern associated with the different body sizes and diets of the mammalian lineages present. Consistent with phylosymbiosis, microbiome dissimilarity increased with phylogenetic distance among hosts, ranging from congeneric sets of mice and hares that did not differ significantly in microbiome composition to species from different taxonomic orders that had almost no gut bacteria in common. While phylosymbiosis was detected among just the 11 species of rodents, it was substantially weaker than comparisons involving all 14 species together. In contrast, microbiome diversity and composition were generally more strongly correlated with body size, dietary breadth, and dietary overlap in comparisons restricted to rodents than in those including all lineages. The starkest divides in microbiome composition thus reflected the broad evolutionary divergence of hosts, regardless of body size or dietary composition, while subtler microbiome differences reflected variation in ecologically important traits between closely related hosts. Strong phylosymbiotic patterns arose deep in the phylogeny, and ecological filters that promote functional differentiation of cooccurring host species may disrupt or obscure this pattern near the tips.