Widespread Treponema pallidum Infection in Nonhuman Primates, Tanzania.

We investigated Treponema pallidum infection in 8 nonhuman primate species (289 animals) in Tanzania during 2015-2017. We used a serologic treponemal test to detect antibodies against the bacterium. Infection was further confirmed from tissue samples of skin-ulcerated animals by 3 independent PCRs (polA, tp47, and TP_0619). Our findings indicate that T. pallidum infection is geographically widespread in Tanzania and occurs in several species (olive baboons, yellow baboons, vervet monkeys, and blue monkeys). We found the bacterium at 11 of 14 investigated geographic locations. Anogenital ulceration was the most common clinical manifestation; orofacial lesions also were observed. Molecular data show that nonhuman primates in Tanzania are most likely infected with T. pallidum subsp. pertenue-like strains, which could have implications for human yaws eradication.

Savanna chimpanzees adjust sleeping nest architecture in response to local weather conditions.

OBJECTIVES: Great ape nests are hypothesized to aid safe, secure sleep via providing thermoregulation or protection from predators and vectors. We aimed to describe and investigate variation in chimpanzee nest architecture across two populations in response to local weather conditions. MATERIALS AND METHODS: We experimentally tested whether nests provide insulation by measuring heat loss within and outside nests, and took detailed measurements of the number, size, and type of materials used in nest building across two dry-habitat research sites (Fongoli, Senegal, and Issa, Tanzania). We tested application of principal components analysis (PCA) to extract composite quantitative measures of the key components of shape and architecture, before testing how PCs vary across populations with overnight weather conditions that reflect hypothesized thermoregulatory function. RESULTS: Heat loss is greater and occurs faster outside of nests. PCA allowed meaningful comparison of nests within and between sites. Nest variation at both sites revealed chimpanzees built thicker nests in cooler conditions and used more broken branches and support in moister conditions. Chimpanzees in Fongoli used more lining and mattress material in colder conditions, whilst in Issa nest depth and support branch size were larger in windier conditions. DISCUSSION: Shape and architectural measures reflected insulation and stability of nest structure. Chimpanzees in Fongoli and Issa may achieve the same functional goals by adjusting nest shape and architecture in different ways. These results suggest that wild chimpanzees show flexible building techniques in response to local, overnight weather conditions in making an insulating and stable, supportive platform for sleep.

Phase Separation of Binary Charged Particle Systems with Small Size Disparities using a Dusty Plasma.

The phase separation in binary mixtures of charged particles has been investigated in a dusty plasma under microgravity on parabolic flights. A method based on the use of fluorescent dust particles was developed that allows us to distinguish between particles of slightly different size. A clear trend towards phase separation even for smallest size (charge) disparities is observed. The diffusion flux is directly measured from the experiment and uphill diffusion coefficients have been determined.

Ion-wake-mediated particle interaction in a magnetized-plasma flow.

The interaction forces between dust grains in a flowing plasma are strongly modified by the formation of ion wakes. Here, we study the interparticle forces mediated by ion wakes in the presence of a strong magnetic field parallel to the ion flow. For increasing magnetic flux densities a continuous decay of the interaction force is observed. This transition occurs at parameters, where the ion cyclotron frequency starts to exceed the ion plasma frequency, which is in agreement with theoretical predictions. The modification of the interparticle forces is important for the understanding of the structure and dynamics of magnetized dusty plasmas.

Instantaneous normal mode analysis of melting of finite dust clusters.

The experimental melting transition of finite two-dimensional dust clusters in a dusty plasma is analyzed using the method of instantaneous normal modes. In the experiment, dust clusters are heated in a thermodynamic equilibrium from a solid to a liquid state using a four-axis laser manipulation system. The fluid properties of the dust cluster, such as the diffusion constant, are measured from the instantaneous normal mode analysis. Thereby, the phase transition of these finite clusters is approached from the liquid phase. From the diffusion constants, unique melting temperatures have been assigned to dust clusters of various sizes that very well reflect their dynamical stability properties.

Molecular diversity of entodiniomorphid ciliate Troglodytella abrassarti and its coevolution with chimpanzees.

The entodiniomorphid ciliate Troglodytella abrassarti is a colonic mutualist of great apes. Its host specificity makes it a suitable model for studies of primate evolution. We explored molecular diversity of T. abrassarti with regard to large geographical distribution and taxonomic diversity of its most common host, the chimpanzee. We found a very low diversification of T. abrassarti in chimpanzees across Africa. Distribution of two types of T. abrassarti supports evolutionary separation of the Western chimpanzee, P. t. verus, from populations in Central and East Africa. Type I T. abrassarti is probably a derived form, which corresponds with the Central African origin of chimpanzees and a founder event leading to P. t. verus. Exclusivity of the respective types of T. abrassarti to Western and Central/Eastern chimpanzees corroborates the difference found between an introduced population of presumed Western chimpanzees on Rubondo Island and an autochthonous population in mainland Tanzania. The identity of T. abrassarti from Nigerian P. t. ellioti and Central African chimpanzees suggests their close evolutionary relationship. Although this contrasts with published mtDNA data, it corroborates current opinion on the exclusive position of P. t. verus within the chimpanzee phylogeny. The type of T. abrassarti occurring in Central and East African common chimpanzee was confirmed also in bonobos. This may point to the presence of an ancestral Type II found throughout the Lower Guinean rainforest dating back to the common Pan ancestor. Alternatively, the molecular uniformity of T. abrassarti may imply a historical overlap of the species' distribution ranges.

Responses of chimpanzees to a recently dead community member at Gombe National Park, Tanzania.

Chimpanzee responses to the death of a group member have rarely been observed in the wild and most instances involve infant deaths. One of the very few detailed accounts of a group's response to the death of an adult community member is from Gombe National Park, Tanzania, where Teleki [Folia Primatologica 20:81-94, 1973] observed the responses of 16 chimpanzees to an accidental death, none of whom touched the body. Now, almost 40 years later, we report on the behaviors of 16 (different) Gombe individuals to the recently dead body of an adult female community member. In stark contrast to Teleki's account, we observed individual chimpanzees' responses to range from curious observation and passive investigation (e.g. smelling and grooming) to the shaking, dragging, and frustrated beating of the body. Variation across demographic groups is described and may reflect individuals' past experience with death. The implications of our observations are discussed in the context of core morbidity traits shared between humans and chimpanzees.

Wave spectra of two-dimensional dusty plasma solids and liquids.

Brownian dynamics simulations were carried out to study wave spectra of two-dimensional dusty plasma liquids and solids for a wide range of wavelengths. The existence of a longitudinal dust-thermal mode was confirmed in simulations, and a cutoff wave number in the transverse mode was measured. Dispersion relations, resulting from simulations, were compared with those from analytical theories, such as the random-phase approximation (RPA), the quasilocalized charged approximation (QLCA), and the harmonic approximation (HA). An overall good agreement between the QLCA and simulations was found for wide ranges of states and wavelengths after taking into account the direct thermal effect in the QLCA, while for the RPA and HA, good agreement with simulations was found in the high and low-temperature limits, respectively.

Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates.

In our most recent study, we found that in Tanzania infection with Treponema pallidum (TP) subsp. pertenue (TPE) is present in four different monkey species. In order to gain information on the diversity and epidemiological spread of the infection in Tanzanian nonhuman primates (NHP), we identified two suitable candidate genes for multi-locus sequence typing (MLST). We demonstrate the functionality of the MLST system in invasively and non-invasively collected samples. While we were not able to demonstrate frequent interspecies transmission of TPE in Tanzanian monkeys, our results show a clustering of TPE strains according to geography and not host species, which is suggestive for rare transmission events between different NHP species. In addition to the geographic stability, we describe the relative temporal stability of the strains infecting NHPs and identified multi-strain infection. Differences between TPE strains of NHP and human origin are highlighted. Our results show that antibiotic resistance does not occur in Tanzanian TPE strains of NHP origin.

Probing a dusty magnetized plasma with self-excited dust-density waves.

A cloud of nanodust particles is created in a reactive argon-acetylene plasma. It is then transformed into a dusty magnetized argon plasma. Plasma parameters are obtained with the dust-density wave diagnostic introduced by Tadsen et al. [Phys. Plasmas 22, 113701 (2015)10.1063/1.4934927]. A change from an open to a cylindrically enclosed nanodust cloud, which was observed earlier, can now be explained by a stronger electric confinement if a vertical magnetic field is present. Using two-dimensional extinction measurements and the inverse Abel transform to determine the dust density, a redistribution of the dust with increasing magnetic induction is found. The dust-density profile changes from being peaked around the central void to being peaked at an outer torus ring resulting in a hollow profile. As the plasma parameters cannot explain this behavior, we propose a rotation of the nanodust cloud in the magnetized plasma as the origin of the modified profile.

DNA recovery from wild chimpanzee tools.

Most of our knowledge of wild chimpanzee behaviour stems from fewer than 10 long-term field sites. This bias limits studies to a potentially unrepresentative set of communities known to show great behavioural diversity on small geographic scales. Here, we introduce a new genetic approach to bridge the gap between behavioural material evidence in unhabituated chimpanzees and genetic advances in the field of primatology. The use of DNA analyses has revolutionised archaeological and primatological fields, whereby extraction of DNA from non-invasively collected samples allows researchers to reconstruct behaviour without ever directly observing individuals. We used commercially available forensic DNA kits to show that termite-fishing by wild chimpanzees (Pan troglodytes schweinfurthii) leaves behind detectable chimpanzee DNA evidence on tools. We then quantified the recovered DNA, compared the yield to that from faecal samples, and performed an initial assessment of mitochondrial and microsatellite markers to identify individuals. From 49 termite-fishing tools from the Issa Valley research site in western Tanzania, we recovered an average of 52 pg/µl chimpanzee DNA, compared to 376.2 pg/µl in faecal DNA extracts. Mitochondrial DNA haplotypes could be assigned to 41 of 49 tools (84%). Twenty-six tool DNA extracts yielded >25 pg/µl DNA and were selected for microsatellite analyses; genotypes were determined with confidence for 18 tools. These tools were used by a minimum of 11 individuals across the study period and termite mounds. These results demonstrate the utility of bio-molecular techniques and a primate archaeology approach in non-invasive monitoring and behavioural reconstruction of unhabituated primate populations.

Food mechanical properties and isotopic signatures in forest versus savannah dwelling eastern chimpanzees.

Chimpanzees are traditionally described as ripe fruit specialists with large incisors but relatively small postcanine teeth, adhering to a somewhat narrow dietary niche. Field observations and isotopic analyses suggest that environmental conditions greatly affect habitat resource utilisation by chimpanzee populations. Here we combine measures of dietary mechanics with stable isotope signatures from eastern chimpanzees living in tropical forest (Ngogo, Uganda) and savannah woodland (Issa Valley, Tanzania). We show that foods at Issa can present a considerable mechanical challenge, most saliently in the external tissues of savannah woodland plants compared to their tropical forest equivalents. This pattern is concurrent with different isotopic signatures between sites. These findings demonstrate that chimpanzee foods in some habitats are mechanically more demanding than previously thought, elucidating the broader evolutionary constraints acting on chimpanzee dental morphology. Similarly, these data can help clarify the dietary mechanical landscape of extinct hominins often overlooked by broad C3/C4 isotopic categories.

Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds.

The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we consider the microbes and arthropods found in chimpanzee beds, relative to the surrounding environment (n = 41 and 15 beds, respectively). Based on the study of human homes, we hypothesized that the microbes found in chimpanzee beds would be less diverse than those on nearby branches and leaves and that their beds would be primarily composed of body-associated organisms. However, we found that differences between wet and dry seasons and elevation above sea level explained nearly all of the observed variation in microbial diversity and community structure. While we can identify the presence of a chimpanzee based on the assemblage of bacteria, the dominant signal is that of environmental microbes. We found just four ectoparasitic arthropod specimens, none of which appears to be specialized on chimpanzees or their structures. These results suggest that the life to which chimpanzees are exposed while in their beds is predominately the same as that of the surrounding environment.

CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.

Allometry and Ecology of the Bilaterian Gut Microbiome.

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction.IMPORTANCE The intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification.

Stochastic heating of a single Brownian particle by charge fluctuations in a radio-frequency produced plasma sheath.

The Brownian motion of a single particle in the plasma sheath is studied to separate the effect of stochastic heating by charge fluctuations from heating by collective effects. By measuring the particle velocities in the ballistic regime and by carefully determining the particle mass from the Epstein drag it is shown that for a pressure of 10 Pa, which is typical of many experiments, the proper kinetic temperature of the Brownian particle remains close to the gas temperature and rises only slightly with particle size. This weak effect is confirmed by a detailed model for charging and charge fluctuations in the sheath. A substantial temperature rise is found for decreasing pressure, which approximately shows the expected scaling with p(-2). The system under study is an example for non-equilibrium Brownian motion under the influence of white noise without corresponding dissipation.

Numerity of a socially housed hamadryas baboon (Papio hamadryas) and a socially housed squirrel monkey (Saimiri sciureus).

To extend a study conducted by E. M. Brannon and H. S. Terrace (1998, 2000), the authors trained 1 hamadryas baboon (Papio hamadryas) and 1 squirrel monkey (Saimiri sciureus) to respond to stimuli representing the numerosities 1-4 in ascending order. When tested with novel stimuli of the same numerosities, both subjects' performance appeared to be based on the numerical attributes of stimuli. Subjects were then tested on their ability to order pairs of numerosities derived from the values 1-9. Both subjects successfully ordered pairs that included the untrained numerosities 5-9 regardless of the total surface area of numerosities. Accuracy and latency of responding also showed numerical distance and magnitude effects. Numerosity was a salient cue to both subjects, suggesting that these 2 families of primates perceive ordinal relations. The outcome shows that cognitive studies of this type can be effectively conducted with socially housed animals.

Collisional and collisionless expansion of Yukawa balls.

The expansion of Yukawa balls is studied by means of molecular dynamics simulations of collisionless and collisional situations. High computation speed was achieved by using the parallel computing power of graphics processing units. When the radius of the Yukawa ball is large compared to the shielding length, the expansion process starts with the blow-off of the outermost layer. A rarefactive wave subsequently propagates radially inward at the speed of longitudinal phonons. This mechanism is fundamentally different from Coulomb explosions, which employ a self-similar expansion of the entire system. In the collisionless limit, the outer layers carry away most of the available energy. The simulations are compared with analytical estimates. In the collisional case, the expansion process can be described by a nonlinear diffusion equation that is a special case of the porous medium equation.

Melting scenarios for three-dimensional dusty plasma clusters.

The melting transition of finite three-dimensional dust clouds (Yukawa balls) from a solid-like to a liquid-like state is systematically studied with high spatial and temporal resolution of the individual grains by means of stereoscopy. Two different melting scenarios are reported: Melting is induced first by an increase of plasma power, and second by laser-induced heating. The experiments confirm that melting starts with a loss of orientational correlation, followed by a loss of the radial order upon further heating. While the plasma-power melting is driven via the ion wakefield, laser heating provides a more equilibrium scenario. The internal loss of correlations is well captured by the triple correlation function (TCF) which is insensitive to particle exchanges and the rotation of the cluster as a whole. The critical Coulomb coupling parameter for N=35 is determined as Γ(crit)≈570. The experimental findings are in good agreement with thermodynamic Monte Carlo simulations.

Self-diffusion in 2D dusty-plasma liquids: numerical-simulation results.

We perform Brownian dynamics simulations for studying the self-diffusion in two-dimensional (2D) dusty-plasma liquids, in terms of both mean-square displacement and the velocity autocorrelation function (VAF). Superdiffusion of charged dust particles has been observed to be the most significant at an infinitely small damping rate gamma for intermediate coupling strength, where the long-time asymptotic behavior of VAF is found to be the product of t;{-1} and exp(-gammat). The former represents the prediction of early theories in 2D simple liquids and the latter the VAF of a free Brownian particle. This leads to a smooth transition from superdiffusion to normal diffusion, and then to subdiffusion with an increase of the damping rate. These results well explain the seemingly contradictory observations scattered in recent classical molecular dynamics simulations and experiments of dusty plasmas.