Roles for non-human primate-associated phage diversity in improving medicine and public health

Mammals harbor trillions of microorganisms and understanding the ecological and evolutionary processes structuring these ecosystems may provide insights relevant to public health and medicine. Comparative studies with our closest living relatives, non-human primates, have provided first insights into their rich bacteriophage communities. Here, I discuss how this phage diversity can be useful for combatting antibiotic-resistant infections and understanding disease emergence risk. For example, some primate-associated phages show a pattern suggesting a long-term co-divergence with their primate superhosts—co-diverging phages may be more likely to exhibit a narrow host range and thus less useful for phage therapy. Captive primates lose their natural phageome, which is replaced by human-associated phages making phages an exciting tool for studying rates of microorganism transmission at human–wildlife interfaces. This commentary tackles avenues for selecting phages for therapeutic interventions based on their ecological and evolutionary history, while discussing frameworks to allow primate-associated phages to be incorporated into the arsenal of clinicians.Peer Reviewe

A 40-year evaluation of drivers of African rainforest change

Background: Tropical forests are repositories of much of the world’s biodiversity and are critical for mitigation of climate change. Yet, the drivers of forest dynamics are poorly understood. This is in large part due to the lack of long-term data on forest change and changes in drivers. Methodology: We quantify changes in tree abundance, diversity, and stand structure along transects first enumerated in 1978 and resampled 2019 in Kibale National Park, Uganda. We tested five predictions. First, based on the purported role of seed dispersal and herbivory and our quantification of changes in the abundance of frugivores and herbivores, we tested two predictions of how faunal change could have influenced forest composition. Second, based on an evaluation of life history strategies, we tested two predictions concerning how the forest could have changed following disturbance that happened prior to written history. Finally, based on a 50-year climate record, we evaluate the possible influence of climate change on forest dynamics. Results: More trees were present on the assessed transects in 2019 (508) than in 1978 (436), species richness remained similar, but diversity declined as the number of dominant species increased. Rainfall increased by only 3 mm over the 50 years but this had not significant effect on forest changes measured here. Annual average monthly maximum temperature increased significantly by 1.05 °C over 50 years. The abundance of frugivorous and folivorous primates and elephants increased over the 50 years of monitoring. Neither the prediction that an increase in abundance of seed dispersing frugivores increases the abundance of their preferred fruiting tree species, nor that as an increase in folivore abundance causes a decline in their preferred species were supported. As predicted, light-demanding species decreased in abundance while shade-tolerant species increased as expected from Kibale being disturbed prior to historical records. Finally, while temperature increased over the 50 years, we found no means to predict a priori how individual species would respond. Conclusions: Our study revealed subtle changes in the tree community over 40 years, sizable increases in primate numbers, a substantial increase in the elephant population and an increase in local temperature. Yet, a clear picture of what set of interactions impact the change in the tree community remains elusive. Our data on tree life-history strategies and frugivore/herbivore foraging preferences suggest that trees species are under opposing pressures

What is the predictive power of the colobine protein-to-fiber model and its conservation value?

Predicting variation in animal abundance across time and space has proven very difficult; however, a model exists to predict the biomass of small folivorous primates that has considerable correlative support. This model suggests that the protein-to-fiber ratio of leaves in a habitat can predict folivore biomass. Here we present an experimental test of this protein-to-fiber model to assess if the number of infant monkeys per female and group size can be predicted based on the leaf chemistry of a habitat. We expected regenerating forest in Kibale National Park, Uganda to have leaves with higher concentrations of crude protein and lower concentrations of fiber than old-growth forest trees, and consequently, we expected a greater number of infants per female in the folivorous red colobus (Procolobus rufomitratus) with access to this area. As predicted, regenerating forests did have trees with leaves with high concentrations of protein and low concentrations of fiber, but there was no corresponding change in the demographic structure of red colobus groups. We also tested whether energy was a potential determinant of these parameters, but found no evidence for its importance. Our findings support recent studies that are critical of the protein-to-fiber model, which lead us to question the model’s generality, particularly for conservation and management

Consistency of Social Interactions in Sooty Mangabeys and Chimpanzees

Predictability of social interactions can be an important measure for the social complexity of an animal group. Predictability is partially dependent on how consistent interaction patterns are over time: does the behavior on 1 day explain the behavior on another? We developed a consistency measure that serves two functions: detecting which interaction types in a dataset are so inconsistent that including them in further analyses risks introducing unexplained error; and comparatively quantifying differences in consistency within and between animal groups. We applied the consistency measure to simulated data and field data for one group of sooty mangabeys (Cercocebus atys atys) and to groups of Western chimpanzees (Pan troglodytes verus) in the Taï National Park, Côte d'Ivoire, to test its properties and compare consistency across groups. The consistency measures successfully identified interaction types whose low internal consistency would likely create analytical problems. Species-level differences in consistency were less pronounced than differences within groups: in all groups, aggression and dominance interactions were the most consistent, followed by grooming; spatial proximity at different levels was much less consistent than directed interactions. Our consistency measure can facilitate decision making of researchers wondering whether to include interaction types in their analyses or social networks and allows us to compare interaction types within and between species regarding their predictability.Peer Reviewe

Radial migration in galactic disks caused by resonance overlap of multiple patterns: Self-consistent simulations

We have recently identified a new radial migration mechanism resulting from the overlap of spiral and bar resonances in galactic disks. Here we confirm the efficiency of this mechanism in fully self-consistent, Tree-SPH simulations, as well as high-resolution pure N-body simulations. In all barred cases we clearly identify the effect of spiral-bar resonance overlap by measuring a bimodality in the changes of angular momentum in the disk, dL, whose maxima are near the bar's corotation and outer Lindblad resonance. This contrasts with the smooth distribution of dL for a simulation with no stable bar present, where strong radial migration is induced by multiple spirals. The presence of a disk gaseous component appears to increase the rate of angular momentum exchange by about 20%. The efficiency of this mechanism is such that galactic stellar disks can extend to over 10 scale-lengths within 1-3 Gyr in both Milky Way size and low-mass galaxies (circular velocity ~100 km/s). We also show that metallicity gradients can flatten in less than 1 Gyr rendering mixing in barred galaxies an order of magnitude more efficient than previously thought.Comment: replaced with accepted version: 5 pages, 5 figures (one new figure added), minor change

Prokaryote genome fluidity is dependent on effective population size

Many prokaryote species are known to have fluid genomes, with different strains varying markedly in accessory gene content through the combined action of gene loss, gene gain via lateral transfer, as well as gene duplication. However, the evolutionary forces determining genome fluidity are not yet well understood. We here for the first time systematically analyse the degree to which this distinctive genomic feature differs between bacterial species. We find that genome fluidity is positively correlated with synonymous nucleotide diversity of the core genome, a measure of effective population size Ne. No effects of genome size, phylogeny or homologous recombination rate on genome fluidity were found. Our findings are consistent with a scenario where accessory gene content turnover is for a large part dictated by neutral evolution

Census of Self-Obscured Massive Stars in Nearby Galaxies with Spitzer: Implications for Understanding the Progenitors of SN 2008S-Like Transients

A new link in the causal mapping between massive stars and potentially fatal explosive transients opened with the 2008 discovery of the dust-obscured progenitors of the luminous outbursts in NGC 6946 and NGC 300. Here we carry out a systematic mid-IR photometric search for massive, luminous, self-obscured stars in four nearby galaxies: M33, NGC 300, M81, and NGC 6946. For detection, we use only the 3.6 micron and 4.5 micron IRAC bands, as these can still be used for multi-epoch Spitzer surveys of nearby galaxies (=<10 Mpc). We combine familiar PSF and aperture-photometry with an innovative application of image subtraction to catalog the self-obscured massive stars in these galaxies. In particular, we verify that stars analogous to the progenitors of the NGC 6946 (SN 2008S) and NGC 300 transients are truly rare in all four galaxies: their number may be as low as ~1 per galaxy at any given moment. This result empirically supports the idea that the dust-enshrouded phase is a very short-lived phenomenon in the lives of many massive stars and that these objects constitute a natural extension of the AGB sequence. We also provide mid-IR catalogs of sources in NGC 300, M81, and NGC 6946.Comment: 21 pages, 15 figures, 11 tables. Accepted by ApJ on April 12, 2010. High resolution figures and full length versions of tables 6, 8 and 10 can be accessed at http://www.astronomy.ohio-state.edu/~khan/redstars

The Chandra Local Volume Survey: The X-ray Point Source Catalog of NGC 300

We present the source catalog of a new Chandra ACIS-I observation of NGC 300 obtained as part of the Chandra Local Volume Survey. Our 63 ks exposure covers ~88% of the D25 isophote (R~6.3 kpc) and yields a catalog of 95 X-ray point sources detected at high significance to a limiting unabsorbed 0.35-8 keV luminosity of ~10^36 erg s^-1. Sources were cross-correlated with a previous XMM-Newton catalog, and we find 75 "X-ray transient candidate" sources that were detected by one observatory, but not the other. We derive an X-ray scale length of 1.7+/-0.2 kpc and a recent star formation rate of 0.12 Msun yr^-1, in excellent agreement with optical observations. Deep, multi-color imaging from the Hubble Space Telescope, covering ~32% of our Chandra field, was used to search for optical counterparts to the X-ray sources, and we have developed a new source classification scheme to determine which sources are likely X-ray binaries, supernova remnants, and background AGN candidates. Finally, we present the X-ray luminosity functions (XLFs) at different X-ray energies, and we find the total NGC 300 X-ray point source population to be consistent with other late-type galaxies hosting young stellar populations (<50 Myr). We find XLF of sources associated with older stellar populations has a steeper slope than the XLF of X-ray sources coinciding with young stellar populations, consistent with theoretical predictions.Comment: 23 pages, 13 figures. Accepted to Ap

The ACS Nearby Galaxy Survey Treasury

The ACS Nearby Galaxy Survey Treasury (ANGST) is a systematic survey to establish a legacy of uniform multi-color photometry of resolved stars for a volume-limited sample of nearby galaxies (D<4 Mpc). The survey volume encompasses 69 galaxies in diverse environments, including close pairs, small & large groups, filaments, and truly isolated regions. The galaxies include a nearly complete range of morphological types spanning a factor of ~10^4 in luminosity and star formation rate. The survey data consists of images taken with ACS on HST, supplemented with archival data and new WFPC2 imaging taken after the failure of ACS. Survey images include wide field tilings covering the full radial extent of each galaxy, and single deep pointings in uncrowded regions of the most massive galaxies in the volume. The new wide field imaging in ANGST reaches median 50% completenesses of m_F475W=28.0 mag, m_F606W=27.3 mag, and m_F814W=27.3 mag, several magnitudes below the tip of the red giant branch (TRGB). The deep fields reach magnitudes sufficient to fully resolve the structure in the red clump. The resulting photometric catalogs are publicly accessible and contain over 34 million photometric measurements of >14 million stars. In this paper we present the details of the sample selection, imaging, data reduction, and the resulting photometric catalogs, along with an analysis of the photometric uncertainties (systematic and random), for both the ACS and WFPC2 imaging. We also present uniformly derived relative distances measured from the apparent magnitude of the TRGB.Comment: 54 pages, including 24 pages of figures and 16 pages of tables. Project website and data available at http://www.nearbygalaxies.org/ . Data is also available through MAST. Scheduled to appear in the Astrophysical Journal Supplements. (Replaced to fix several figures that were damaged during compression