Mobile genes in the human microbiome are structured from global to individual scales.

Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.

Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity.

Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.

Applications of Bayesian approach in modelling risk of malaria-related hospital mortality.

BACKGROUND: Malaria is a major public health problem in Malawi, however, quantifying its burden in a population is a challenge. Routine hospital data provide a proxy for measuring the incidence of severe malaria and for crudely estimating morbidity rates. Using such data, this paper proposes a method to describe trends, patterns and factors associated with in-hospital mortality attributed to the disease. METHODS: We develop semiparametric regression models which allow joint analysis of nonlinear effects of calendar time and continuous covariates, spatially structured variation, unstructured heterogeneity, and other fixed covariates. Modelling and inference use the fully Bayesian approach via Markov Chain Monte Carlo (MCMC) simulation techniques. The methodology is applied to analyse data arising from paediatric wards in Zomba district, Malawi, between 2002 and 2003. RESULTS AND CONCLUSION: We observe that the risk of dying in hospital is lower in the dry season, and for children who travel a distance of less than 5 kms to the hospital, but increases for those who are referred to the hospital. The results also indicate significant differences in both structured and unstructured spatial effects, and the health facility effects reveal considerable differences by type of facility or practice. More importantly, our approach shows non-linearities in the effect of metrical covariates on the probability of dying in hospital. The study emphasizes that the methodological framework used provides a useful tool for analysing the data at hand and of similar structure.

Scenario planning with linked land-sea models inform where forest conservation actions will promote coral reef resilience.

We developed a linked land-sea modeling framework based on remote sensing and empirical data, which couples sediment export and coral reef models at fine spatial resolution. This spatially-explicit (60 × 60 m) framework simultaneously tracks changes in multiple benthic and fish indicators as a function of land-use and climate change scenarios. We applied this framework in Kubulau District, Fiji, to investigate the effects of logging, agriculture expansion, and restoration on coral reef resilience. Under the deforestation scenario, models projected a 4.5-fold sediment increase (>7,000 t. yr-1) coupled with a significant decrease in benthic habitat quality across 1,940 ha and a reef fish biomass loss of 60.6 t. Under the restoration scenario, models projected a small (<30 t. yr-1) decrease in exported sediments, resulting in a significant increase in benthic habitat quality across 577 ha and a fish biomass gain of 5.7 t. The decrease in benthic habitat quality and loss of fish biomass were greater when combining climate change and deforestation scenarios. We evaluated where land-use change and bleaching scenarios would impact sediment runoff and downstream coral reefs to identify priority areas on land, where conservation or restoration could promote coral reef resilience in the face of climate change.

An assessment of an environmental gradient using coral geochemical records, Whitsunday Islands, Great Barrier Reef, Australia.

Coral cores were collected along an environmental and water quality gradient through the Whitsunday Island group, Great Barrier Reef (Australia), for trace element and stable isotope analysis. The primary aim of the study was to examine if this gradient could be detected in coral records and, if so, whether the gradient has changed over time with changing land use in the adjacent river catchments. Y/Ca was the trace element ratio which varied spatially across the gradient, with concentrations progressively decreasing away from the river mouths. The Ba/Ca and Y/Ca ratios were the only indicators of change in the gradient through time, increasing shortly after European settlement. The Mn/Ca ratio responded to local disturbance related to the construction of tourism infrastructure. Nitrogen isotope ratios showed no apparent trend over time. This study highlights the importance of site selection when using coral records to record regional environmental signals.