1. Animals concentrate key nutrients in their bodies. In fenced wildlife reserves where nutrient input and/or retention is low, the off-site removal of animals may constitute a significant loss of nutrients for the ecosystem.2. Here we add wildlife capture and removal into the phosphorus (P) and calcium (Ca) budget for a 121,700 ha fenced game reserve located in the southern Kalahari.We then use faecal P concentrations from 11 mammal herbivores >10 kg as an indicator of potential nutrient stress in this system to investigate whether the implications of nutrient loss via off-site wildlife removal may be cause for concern.Finally, we assess the role of natural predation as a mechanism to minimise the need for wildlife removal and concomitant nutrient loss.3. During the period 2009-2018, mean loss of P and Ca via wildlife removal was 2.9 and 6.2 kg km −2 year −1 , respectively. This compares to 1.0 and 2.1 kg km −2 year −1 of P and Ca added via the provision of mineral licks. If it is assumed that natural fluxes of these elements are in steady state, then anthropogenic activities have resulted in a net deficit of 18.5 kg/km 2 of P and 40.6 kg/km 2 of Ca over the decade. 4. We found that dry season herbivore faecal P concentrations are close to or below a widely cited minimum threshold of 2,000 mg/kg, below which most vertebrates begin suffering growth and reproductive issues. Large animals were more likely to be under this threshold. Prolonged continuation of off-site wildlife removal may result in nutrient losses that can lead to long-term ecological degradation. Natural predation levels were, however, found sufficient to mitigate the need for wildlife removal and present a management strategy whereby herbivore populations can be regulated without a loss of nutrients. Synthesis and applications.We find that the capture and permanent removal of large-bodied animals from wildlife reserves can be a significant cause of nutrient loss. Over time, in sites where nutrient input and/or retention is low, this may | 1361

AbstractThe Late Quaternary extinctions of megafauna (defined as animal species >44.5 kg) reduced the dispersal of seeds and nutrients, and likely also microbes and parasites. Here we use body-mass based scaling and range maps for extinct and extant mammal species to show that these extinctions led to an almost seven-fold reduction in the movement of gut-transported microbes, such as Escherichia coli (3.3 km2/day to 0.5 km2/day). Similarly, the extinctions led to a seven-fold reduction in the mean home ranges of vector-borne pathogens (7.8 km2 to 1.1 km2). To understand the impact of this, we created an individual-based model where an order of magnitude decrease in home range increased maximum aggregated microbial mutations 4-fold after 20,000 years. We hypothesize that pathogen speciation and hence endemism increased with isolation, as global dispersal distances decreased through a mechanism similar to the theory of island biogeography. To investigate if such an effect could be found, we analysed where 145 zoonotic diseases have emerged in human populations and found quantitative estimates of reduced dispersal of ectoparasites and fecal pathogens significantly improved our ability to predict the locations of outbreaks (increasing variance explained by 8%). There are limitations to this analysis which we discuss in detail, but if further studies support these results, they broadly suggest that reduced pathogen dispersal following megafauna extinctions may have increased the emergence of zoonotic pathogens moving into human populations.

The Late Quaternary extinctions of megafauna (defined as animal species > 44.5 kg) reduced the dispersal of seeds and nutrients, and likely also microbes and parasites. Here we use body‐mass based scaling and range maps for extinct and extant mammal species to show that these extinctions led to an almost seven‐fold reduction in the movement of gut‐transported microbes, such as Escherichia coli (3.3–0.5 km2 d−1). Similarly, the extinctions led to a seven‐fold reduction in the mean home ranges of vector‐borne pathogens (7.8–1.1 km2). To understand the impact of this, we created an individual‐based model where an order of magnitude decrease in home range increased maximum aggregated microbial mutations 4‐fold after 20 000 yr. We hypothesize that pathogen speciation and hence endemism increased with isolation, as global dispersal distances decreased through a mechanism similar to the theory of island biogeography. To investigate if such an effect could be found, we analysed where 145 zoonotic diseases have emerged in human populations and found quantitative estimates of reduced dispersal of ectoparasites and fecal pathogens significantly improved our ability to predict the locations of outbreaks (increasing variance explained by 8%). There are limitations to this analysis which we discuss in detail, but if further studies support these results, they broadly suggest that reduced pathogen dispersal following megafauna extinctions may have increased the emergence of zoonotic pathogens moving into human populations.

Animals are important vectors for transporting seeds, nutrients and microbes across landscapes. However, models that quantify the magnitude of these ecosystem services across a broad range of taxa often rely on generalised mass‐based scaling parameters for gut passage time. This relationship is weak and fundamentally breaks down when considering individual species, indicating that current models may incorrectly attribute or estimate the magnitude of dispersal. We collated a large dataset of gut passage time for endothermic animals measured using undigested markers (n = 391 species). For each species, we compiled trait data, including body mass, morphology, gut physiology, diet and phylogeny. We then compared the ability of five statistical models (constant, generalised least squares, phylogenetic generalised least squares, general linear model and random forest) to estimate the time of first marker appearance (transit time; TT) and mean marker retention time (MRT) for particle and solute markers in mammals and birds separately. For mammals, we found that the inclusion of additional traits appreciably reduced the median root‐mean squared error across all markers in a leave‐one‐out cross validation. For birds, however, additional traits did not significantly improve our ability to predict gut passage time across markers. This may have occurred due to the smaller number of bird species included in our analysis or the absence of important explanatory factors such as differences in gastrointestinal morphology. Using the MRTparticle random forest model from this study, we updated two trait‐based dispersal models for seed and nutrient movement by mammals. The magnitude of dispersal in our updated predictions ranged from 66% to 176% of the original model formulation for different scenarios, highlighting the importance of gut passage time for dispersal models. Furthermore, the contribution by individual or groups of species was found sizeably altered in our updated models. Future modelling studies of dispersal by mammals, for which empirical estimates of gut passage time are absent, will benefit from predicting gut passage time using statistical models that incorporate traits including animal morphology, diet and gut physiology. A free Plain Language Summary can be found within the Supporting Information of this article.

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1.ABSTRACTBackgroundDetermining the life-history traits of extinct species is often difficult from skeletal remains alone, limiting the accuracy of studies modeling past ecosystems. However, the analysis of the degraded endogenous bacterial DNA present in paleontological fecal matter (coprolites) may enable the characterization of specific traits such as the host’s digestive physiology and diet. An issue when evaluating the microbial composition of coprolites is the degree to which the microbiome is representative of the host’s original gut community versus the changes that occur in the weeks following deposition due to desiccation. Analyses of paleontological microorganisms are also relevant in the light of recent studies linking the Late Pleistocene and Early Holocene extinctions with modern-day zoonotic pathogen outbreaks.MethodsShotgun sequencing was performed on ancient DNA (aDNA) extracted from coprolites of the Columbian mammoth (Mammuthus Columbi), Shasta ground sloth (Nothrotheriops shastensis) and paleontological bison (Bison sp.) collected from caves on the Colorado Plateau, Southwestern USA. The novel metagenomic classifier MTSv, parameterized for studies of aDNA, was used to assign bacterial taxa to sequencing reads. The resulting bacterial community of coprolites was then compared to those from modern fecal specimens of the African savannah elephant (Loxodonta africana), the brown-throated sloth (Bradypus variegatus) and the modern bison (Bison bison). Both paleontological and modern bison fecal bacterial communities were also compared to those of progressively dried cattle feces to determine whether endogenous DNA from coprolites had a microbiome signal skewed towards aerobic microorganisms typical of desiccated fecal matter.ResultsThe diversity of phyla identified from coprolites was lower than modern specimens. The relative abundance of Actinobacteria was increased in coprolites compared to modern specimens, with fewer Bacteroidetes and Euryarchaeota. Firmicutes had a reduced relative abundance in the mammoth and bison coprolites, compared to the African savanna elephants and modern bison. There was a significant separation of samples in NMDS plots based on their classification as either paleontological or modern, and to a lesser extent, based on the host species. Increasingly dried cattle feces formed a continuum between the modern and paleontological bison samples.ConclusionOur results reveal that any coprolite metagenomes should always be compared to desiccated modern fecal samples from closely related hosts fed a comparable diet to determine the degree to which the coprolite metagenome is a result of desiccation versus true dissimilarities between the modern and paleontological hosts. Also, a large-scale desiccation study including a variety of modern species may shed light on life-history traits of extinct species without close extant relatives, by establishing the proximity of coprolite metagenomes with those from dried modern samples.

Forest thinning of overgrown Western US forests is becoming more common to reduce severe fire danger. Such large changes in forest structure could impact the global carbon budget, but despite being relatively well studied, there are uncertainties on how forest thinning may impact forest carbon use efficiency, carbon allocation, and herbivore abundance. In three, quarter ha plots along a forest thinning chronosequence near Flagstaff, Az, we measured total NPP (wood, fine root, and litter), total autotrophic respiration (wood, rhizosphere, and canopy respiration) and large mammal herbivory (with camera traps and dung counts) over a 2-year period. We found strong seasonality in all carbon cycling parameters and herbivory peaking during the warm, wet monsoon period. Forest thinning increased understory NPP, herbivore abundance and small tree mortality. Carbon was produced more efficiently in the thinned stands (Carbon use efficiency -CUE = 0.63 and 0.61) versus the un-thinned stand (CUE 0.39). Unexpectedly, carbon allocated towards root growth increased in the thinned stands. Overall, GPP was similar in the two thinned sites 4.3 Mg C ha-1 year-1, but was about 30 per greater in the un-thinned site (5.68 Mg C ha-1 year-1). Overall, the thinning, and the return to a more natural pre-fire suppression landscape, increased the efficiency of the forest both in terms of carbon and animals.

Many species of large mammals were driven to extinction during the late Pleistocene and early Holocene (approx. 10,000 - 50,000 years ago), with cascading effects on the physical structure of ecosystems and the dispersal of seeds, nutrients, and microbes. However, it remains uncertain whether the parasites associated with these extinct hosts also disappeared or persisted in surviving (extant) mammals. We hypothesize that if some parasites endured, extant mammals sharing their ranges with phylogenetically similar extinct mammals would have a greater pathogen richness than expected based on current levels of host diversity. We find that the inclusion of variables related to these extinctions account for an additional 5% of deviance when modelling per-host viral and bacterial richness, compared to models run without these variables. Viral and bacterial richness for extant mammals was calculated from host-pathogen associations within the CLOVER repository. Partial dependence plots show a positive correlation between the number of extinct mammals lost and per-host viral and bacterial richness (p < 0.001 and p = 0.03, respectively). Additionally, decreasing phylogenetic distance between the extinct and extant species is associated with an increasing viral richness (p < 0.001). We discuss four mechanisms that may be driving these patterns and highlight future research to distinguish between them. Next, we use the models and IUCN range maps to identify geographic regions where viral and bacterial richness differs due to the inclusion of extinction variables. Notably, the richness of both pathogen types is increased in South America (viruses: +6.8%; bacteria: +3.1%) and decreased in Africa (viruses: -2.6%; bacteria: -13.6%), two continents known to have high and low levels of historical mammal extinctions, respectively. Viral richness is also elevated in North America (+8.6%), Europe (+5.1%), Oceania (+3.3%), and Asia (+2.3%). These results support the inclusion of extinction variables in future models of pathogen richness and may allow for improved targeting of future surveillance efforts.