Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA.

Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.

Climate change leads to increasing population density and impacts of a key island invader.

The considerable threats of invasive rodents to island biodiversity are likely to be compounded by climate change. Forecasts for such interactions have been most pronounced for the Southern Ocean islands where ameliorating conditions are expected to decrease thermal and resource restrictions on rodents. Firm evidence for changing rodent populations in response to climate change, and demonstrations of associated impacts on the terrestrial environment, are nonetheless entirely absent for the region. Using data collected over three decades on sub-Antarctic Marion Island, we tested empirically whether mouse populations have changed through time and whether these changes can be associated significantly with changing abiotic conditions. Changes in invertebrate populations, which have previously been attributed to mouse predation, but with little explicit demographic analysis, were also examined to determine whether they can be associated with changing mouse populations. The total number of mice on the island at annual peak density increased by 430.0% between 1979-1980 and 2008-2011. This increase was due to an advanced breeding season, which was robustly related to the number of precipitation-free days during the non-breeding season. Mice directly reduced invertebrate densities, with biomass losses of up to two orders of magnitude in some habitats. Such invertebrate declines are expected to have significant consequences for ecosystem processes over the long term. Our results demonstrate that as climate change continues to create ameliorating conditions for invasive rodents on sub-Antarctic islands, the severity of their impacts will increase. They also emphasize the importance of rodent eradication for the restoration of invaded islands.

Color Doppler ultrasound-guided PTBD with and without metal stent implantation by endoscopic control: prospective success and early adverse event rates.

OBJECTIVE: There are just a few reports on Color Doppler Ultrasound-guided PTBD with and without metal stent implantation by endoscopic control. Ultrasound guidance facilitates percutaneous bile duct access and avoids severe adverse events. Internal biliary drainage rate in PTBD should be as high as possible as endoscopic ultrasound-guided cholangiodrainage (EUCD) offers internal drainage regularly. We report our prospective study analyzing success, internal drainage and adverse event rates. MATERIALS AND METHODS: Between June 2009 and November 2014 overall 63 PTBDs were performed prospectively in 37 patients (18 m, 19f; age on average: 72 years) with benign (9 %) and malignant (91 %) bile duct obstruction. Ultrasound was used in combination with fluoroscopic guidance. Whenever possible, primary or early secondary metal stent implantation via PTBD by endoscopic control was performed as a one step-procedure. RESULTS: 38 of 41 (93 %) initial PTBDs (in four patients PTBD was performed twice) were successful. 22 of 63 PTBDs were follow-up examinations with different interventions. In 34 of 38 successful (89 %) PTBDs, an internal drainage (or metal stent) was implanted. 12 metal stent implantations via PTBD were performed under endoscopic control. Just 2 (5 %) permanent external drainages were inserted. In 63 performed PTBDs 5 (7.9 %) early major adverse events (no severe intrahepatic bleeding) were documented and treated without any procedure related death. When metal stent implantation was performed via PTBD no adverse event was documented. CONCLUSION: Color Doppler guided PTBD is an effective and safe method for biliary drainage avoiding severe adverse events. Primary or early secondary metal stent implantation via PTBD reduces complication risks additionally. Endoscopic control of stent implantation via PTBD is helpful for optimal stent placement.

Protecting and connecting landscapes stabilizes populations of the Endangered savannah elephant.

The influence of protected areas on the growth of African savannah elephant populations is inadequately known. Across southern Africa, elephant numbers grew at 0.16% annually for the past quarter century. Locally, much depends on metapopulation dynamics-the size and connections of individual populations. Population numbers in large, connected, and strictly protected areas typically increased, were less variable from year to year, and suffered less from poaching. Conversely, populations in buffer areas that are less protected but still connected have more variation in growth from year to year. Buffer areas also differed more in their growth rates, likely due to more threats and dispersal opportunities in the face of such dangers. Isolated populations showed consistently high growth due to a lack of emigration. This suggests that "fortress" conservation generally maintains high growth, while anthropogenic-driven source-sink dynamics within connected conservation clusters drive stability in core areas and variability in buffers.

Derivation of free energy expressions for tube models from coarse-grained slip-link models.

We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)] by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)] can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)] starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)]. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)]. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical formulation of tube models. The next step will be to formulate the dynamics of the primitive-path conformation and the entanglement density along the primitive path. Now that the free energy is known, statistical mechanics can be employed for this purpose.

Mapping potential connections between Southern Africa's elephant populations.

Southern Africa spans nearly 7 million km2 and contains approximately 80% of the world's savannah elephants (Loxodonta africana) mostly living in isolated protected areas. Here we ask what are the prospects for improving the connections between these populations? We combine 1.2 million telemetry observations from 254 elephants with spatial data on environmental factors and human land use across eight southern African countries. Telemetry data show what natural features limit elephant movement and what human factors, including fencing, further prevent or restrict dispersal. The resulting intersection of geospatial data and elephant presences provides a map of suitable landscapes that are environmentally appropriate for elephants and where humans allow elephants to occupy. We explore the environmental and anthropogenic constraints in detail using five case studies. Lastly, we review all the major potential connections that may remain to connect a fragmented elephant metapopulation and document connections that are no longer feasible.

Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology.

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.

Thermodynamically consistent incorporation of entanglement spatial fluctuations in the slip-link model.

We evaluate the thermodynamic consistency of the anisotropic mobile slip-link model for entangled flexible polymers. The level of description is that of a single chain, whose interactions with other chains are coarse grained to discrete entanglements. The dynamics of the model consist of the motion of entanglements through space and of the chain through the entanglements, as well as the creation and destruction of entanglements, which are implemented in a mean-field way. Entanglements are modeled as discrete slip links, whose spatial positions are confined by quadratic potentials. The confinement potentials move with the macroscopic velocity field, hence the entanglements fluctuate around purely affine motion. We allow for anisotropy of these fluctuations, described by a set of shape tensors. By casting the model in the form of the general equation for the nonequilibrium reversible-irreversible coupling from nonequilibrium thermodynamics, we show that (i) since the confinement potentials contribute to the chain free energy, they must also contribute to the stress tensor, (ii) these stress contributions are of two kinds: one related to the virtual springs connecting the slip links to the centers of the confinement potentials and the other related to the shape tensors, and (iii) these two kinds of stress contributions cancel each other if the confinement potentials become anisotropic in flow, according to a lower-convected evolution of the confinement strength or, equivalently, an upper-convected evolution of the shape tensors of the entanglement spatial fluctuations. In previous publications, we have shown that this cancellation is necessary for the model to obey the stress-optical rule and the Green-Kubo relation, and simultaneously to agree with plateau modulus predictions of multichain models and simulations.

The 2020 elephant die-off in Botswana.

The cause of deaths of 350 elephants in 2020 in a relatively small unprotected area of northern Botswana is unknown, and may never be known. Media speculations about it ignore ecological realities. Worse, they make conjectures that can be detrimental to wildlife and sometimes discredit conservation incentives. A broader understanding of the ecological and conservation issues speaks to elephant management across the Kavango-Zambezi Transfrontier Conservation Area that extends across Botswana, Namibia, Angola, Zambia, and Zimbabwe. Our communication addresses these. Malicious poisoning and poaching are unlikely to have played a role. Other species were unaffected, and elephant carcases had their tusks intact. Restriction of freshwater supplies that force elephants to use pans as a water source possibly polluted by blue-green algae blooms is a possible cause, but as yet not supported by evidence. No other species were involved. A contagious disease is the more probable one. Fences and a deep channel of water confine these elephants' dispersal. These factors explain the elephants' relatively high population growth rate despite a spell of increased poaching during 2014-2018. While the deaths represent only ~2% of the area's elephants, the additive effects of poaching and stress induced by people protecting their crops cause alarm. Confinement and relatively high densities probably explain why the die-off occurred only here. It suggests a re-alignment or removal of fences that restrict elephant movements and limits year-round access to freshwater.

Species inequality in scientific study.

Some conservationists argue for a focused effort to protect the most critically endangered species, and others suggest a large-scale endeavor to safeguard common species across large areas. Similar arguments are applicable to the distribution of scientific effort among species. Should conservation scientists focus research efforts on threatened species, common species, or do all species deserve equal attention? We assessed the scientific equity among 1909 mammals, birds, reptiles, and amphibians of southern Africa by relating the number of papers written about each species to their status on the International Union for Conservation of Nature Red List. Threatened large mammals and reptiles had more papers written about them than their nonthreatened counterparts, whereas threatened small mammals and amphibians received less attention than nonthreatened species. Threatened birds received an intermediate amount of attention in the scientific literature. Thus, threat status appears to drive scientific effort among some animal groups, whereas other factors (e.g., pest management and commercial interest) appear to dictate scientific investment in particular species of other groups. Furthermore, the scientific investment per species differed greatly between groups-the mean number of papers per threatened large mammal eclipsed that of threatened reptiles, birds, small mammals, and amphibians by 2.6-, 15-, 216-, and more than 500-fold, respectively. Thus, in the eyes of science, all species are not created equal. A few species commanded a great proportion of scientific attention, whereas for many species information that might inform conservation is virtually nonexistent.

Daily rhythms of body temperature and heat production of sibling Mastomys species from different ecosystems--the response to photoperiod manipulations.

We compared body temperature (T(b)) and metabolic rates, measured as oxygen consumption (VO(2)), daily rhythms of two sibling species of the genus Mastomys. We also studied their responses to long day (16L: 8D, LD) and short day (8L: 16D, SD) photoperiod manipulations at a constant ambient temperature of 26+1 degrees C. We noted significant differences in T(b) and VO(2) daily rhythm patterns, under SD and LD-acclimation between the sibling species. These differences explain adaptation to the climatic conditions that prevail in the different ecosystems where these species live. To the best of our knowledge, this is the first time that physiological differences between the two siblings are measured by using chronobiological methods.

Partial migration in savanna elephant populations distributed across southern Africa.

Migration is an important, but threatened ecological process. Conserving migration requires the maintenance of functional connectivity across sufficiently large areas. Therefore, we need to know if, where and why species migrate. Elephants are highly mobile and can travel long distances but we do not know if they migrate. Here, we analysed the movement trajectories of 139 savanna elephants (Loxodonta africana) within eight clusters of protected areas across southern Africa to determine if elephants migrate, and if so, where, how and why they migrate. Only 25 of these elephants migrated. Elephants are a facultative partially migratory species, where only some individuals in a population migrate opportunistically, and not every year. Elephants migrated between distinct seasonal ranges corresponding to southern Africa's dry and wet seasons. The timing of wet season migrations was associated with the onset of rainfall and the subsequent greening up of forage. Conversely, the duration, distance, and the timing of dry season migrations varied idiosyncratically. The drivers of elephant migration are likely a complex interaction between individual traits, density, and the distribution and availability of resources. Despite most migrations crossing administrative boundaries, conservation networks provided functional space for elephants to migrate.

Correction: Pattern or process? Evaluating the peninsula effect as a determinant of species richness in coastal dune forests.

[This corrects the article DOI: 10.1371/journal.pone.0173694.].

Savanna elephants maintain homeothermy under African heat.

To conserve body water, mammals may reduce evaporative water loss by storing heat, allowing core body temperature to rise more than usual during the day, and to fall more than usual during the cooler night, so demonstrating heterothermy. It has been proposed that elephants are heterothermic, but body temperature never has been measured in elephants over 24 h at environmental temperatures higher than body temperature, where elephants would have to rely on evaporative cooling to maintain homeothermy. We used ingested temperature data loggers to record core temperature of four partly free-ranging savanna elephants exposed to high solar radiation and environmental temperatures that exceeded core temperature (> 36 °C) in their natural habitat. The elephants maintained core temperature at an average 36.6 °C within narrow daily limits of about 1.3 °C. While mean 24-h core temperature increased with maximum air temperature, it did not increase with mean air temperature. Maximum and minimum daily core temperatures also did not change with maximum air temperatures. As a result, core temperature range remained constant despite large variations in daily air temperatures. Contrary to the view that elephants exhibit heterothermy to cope with heat, savanna elephants in their natural habitat with access to adequate resources of food and water, and able to use thermoregulatory behaviour, maintained homeothermy.

Involvement of the CD95 (APO-1/Fas) receptor and ligand system in Helicobacter pylori-induced gastric epithelial apoptosis.

Helicobacter pylori infection is associated with chronic gastritis, peptic ulceration, and gastric carcinoma. The potential role of CD95-mediated apoptosis was investigated in a panel of gastric biopsies obtained from patients with H. pylori-associated chronic gastritis (n = 29) and with noninfected normal mucosa (n = 10). Immunohistochemistry revealed increased CD95 receptor expression in epithelial and lamina propria cells in chronic gastritis. By in situ hybridization, CD95 ligand mRNA was absent or low in normal mucosa but expressed at high levels in lamina propria lymphocytes and, unexpectedly, in epithelial cells in chronic gastritis. Apoptotic cells were rare in normal mucosa but were observed regularly in chronic gastritis in close proximity to CD95 ligand mRNA expression throughout the epithelial and lamina propria cells. In a functional analysis gastric epithelial cell lines were incubated with supernatants of H. pylori. Treatment with the cytotoxic isolate H. pylori 60190 but not with the noncytotoxic isolate Tx30a upregulated CD95 in up to 50% of gastric epithelial cells and induced apoptosis in these cells. H. pylori-induced apoptosis was partially prevented by blocking CD95, demonstrating the functional role of the CD95 system. These findings suggest that H. pylori-associated chronic gastritis involves apoptosis of gastric epithelial cells by activation of the CD95 receptor and ligand system.

Pattern or process? Evaluating the peninsula effect as a determinant of species richness in coastal dune forests.

The peninsula effect predicts that the number of species should decline from the base of a peninsula to the tip. However, evidence for the peninsula effect is ambiguous, as different analytical methods, study taxa, and variations in local habitat or regional climatic conditions influence conclusions on its presence. We address this uncertainty by using two analytical methods to investigate the peninsula effect in three taxa that occupy different trophic levels: trees, millipedes, and birds. We surveyed 81 tree quadrants, 102 millipede transects, and 152 bird points within 150 km of coastal dune forest that resemble a habitat peninsula along the northeast coast of South Africa. We then used spatial (trend surface analyses) and non-spatial regressions (generalized linear mixed models) to test for the presence of the peninsula effect in each of the three taxa. We also used linear mixed models to test if climate (temperature and precipitation) and/or local habitat conditions (water availability associated with topography and landscape structural variables) could explain gradients in species richness. Non-spatial models suggest that the peninsula effect was present in all three taxa. However, spatial models indicated that only bird species richness declined from the peninsula base to the peninsula tip. Millipede species richness increased near the centre of the peninsula, while tree species richness increased near the tip. Local habitat conditions explained species richness patterns of birds and trees, but not of millipedes, regardless of model type. Our study highlights the idiosyncrasies associated with the peninsula effect-conclusions on the presence of the peninsula effect depend on the analytical methods used and the taxon studied. The peninsula effect might therefore be better suited to describe a species richness pattern where the number of species decline from a broader habitat base to a narrow tip, rather than a process that drives species richness.

A systematic review of elephant impact across Africa.

Contradictory findings among scientific studies that address a particular issue may impede the conversion of science to management implementation. A systematic review of peer-reviewed studies to generate a single outcome may overcome this problem. The contentious topic of the impact that a megaherbivore such as the savanna elephant have for other species and their environment can benefit from such an approach. After some 68 years, 367 peer-reviewed papers covered the topic and 51 of these papers provided sufficient data to be included in a meta-analysis. We separated the direct impact that elephants had on trees and herbs from the indirect effects on other vertebrates, invertebrates, and soil properties. Elephants have an impact on tree structure and abundance but no overall negative cascading effects for species that share space with them. Primary productivity explained a small amount of variation of elephant impact on vegetation. Elephant numbers (density), study duration, rainfall, tree cover, and the presence of artificial water and fences failed to describe patterns of impact. We conclude that published information do not support the calls made for artificially manipulating elephant numbers to ameliorate elephant impact, and call for the management of space use by elephants to maintain savanna heterogeneity.

Savanna elephant numbers are only a quarter of their expected values.

Savannas once constituted the range of many species that human encroachment has now reduced to a fraction of their former distribution. Many survive only in protected areas. Poaching reduces the savanna elephant, even where protected, likely to the detriment of savanna ecosystems. While resources go into estimating elephant populations, an ecological benchmark by which to assess counts is lacking. Knowing how many elephants there are and how many poachers kill is important, but on their own, such data lack context. We collated savanna elephant count data from 73 protected areas across the continent estimated to hold ~50% of Africa's elephants and extracted densities from 18 broadly stable population time series. We modeled these densities using primary productivity, water availability, and an index of poaching as predictors. We then used the model to predict stable densities given current conditions and poaching for all 73 populations. Next, to generate ecological benchmarks, we predicted such densities for a scenario of zero poaching. Where historical data are available, they corroborate or exceed benchmarks. According to recent counts, collectively, the 73 savanna elephant populations are at 75% of the size predicted based on current conditions and poaching levels. However, populations are at <25% of ecological benchmarks given a scenario of zero poaching (~967,000)-a total deficit of ~730,000 elephants. Populations in 30% of the 73 protected areas were <5% of their benchmarks, and the median current density as a percentage of ecological benchmark across protected areas was just 13%. The ecological context provided by these benchmark values, in conjunction with ongoing census projects, allow efficient targeting of conservation efforts.

Coping with heat: behavioural and physiological responses of savanna elephants in their natural habitat.

Most of southern Africa's elephants inhabit environments where environmental temperatures exceed body temperature, but we do not know how elephants respond to such environments. We evaluated the relationships between apparent thermoregulatory behaviour and environmental, skin and core temperatures for tame savanna elephants (Loxodonta africana) that were free-ranging in the hot parts of the day, in their natural environment. Environmental temperature dictated elephant behaviour within a day, with potential consequences for fine-scale habitat selection, space use and foraging. At black globe temperatures of ~30°C, elephants adjusted their behaviour to reduce environmental heat load and increase heat dissipation (e.g. shade use, wetting behaviour). Resting, walking and feeding were also influenced by environmental temperature. By relying on behavioural and autonomic adjustments, the elephants maintained homeothermy, even at environmental temperatures exceeding 40°C. Elephants clearly have the capacity to deal with extreme heat, at least in environments with adequate resources of forage, water and shade. Future conservation actions should provide for the thermoregulatory, resource and spatial needs of elephants.