Indigenous communities share how to live with wildlife
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Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems
Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts’ distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiation degrading their virions. To better understand these complex links of phages to their hosts and the environment, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (EP) and nutrient-poor Tropical Western Atlantic (WA) provinces. We could thus compare patterns of phage and prokaryotic communities at both global scales (between oceans) and local-scales (between habitats within an ocean). Although both phage and prokaryotic communities differed sharply between the oceans, phage community composition did not significantly differ between mangroves and reefs of the WA, while prokaryotic communities were distinct. These results suggest phages are more shaped by dispersal processes than local conditions regardless of spatial scale, while prokaryotes tend to be shaped by local conditions at smaller spatial scales. Collectively, we provide a framework for addressing the co-variability between phages and prokaryotes in marine systems and identifying factors that drive consistent versus disparate trends in community shifts, essential to informing models of biogeochemical cycles that include these interactions.
A genetic perspective on the recent demographic history of Ireland and Britain
While subtle yet discrete clusters of genetic identity across Ireland and Britain have been identified, their recent demographic history is unclear. Using genotype data from 6574 individuals with associated regional Irish or British ancestry, we identified genetic communities by applying Leiden community detection. Using haplotype segments segregated by length as proxy for time, we inferred regional Irish and British demographic histories. Using a subset of Irish participants, we provide genealogical context by estimating the enrichment/depletion of surnames within the Irish genetic communities. Through patterns of haplotype sharing, we find evidence of recent population bottlenecks in Orcadian, Manx and Welsh genetic communities. We observed temporal changes in genetic affinities within and between genetic communities in Ireland and Britain. Structure in Ireland is subtler compared to neighbouring British communities, with the Irish groups sharing relatively more short haplotype segments. In addition, we detected varying degrees of genetic isolation in peripheral Irish and British genetic communities across different time periods. Further, we observe a stable migration corridor between north-east Ireland and south-west Scotland while there is a recent migration barrier between south-east and west Ireland. Genealogical analysis of surnames in Ireland reflects history—Anglo-Norman surnames are enriched in the Wexford community while Scottish and Gallowglass surnames were enriched in the Ulster community. Using these new insights into the regional demographic history of Ireland and Britain across different time periods, we hope to understand the driving forces of rare allele frequencies and disease risk association within these populations.
Ubiquitous, B12-dependent virioplankton utilizing ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean
Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B12-dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling–downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral–host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.
Regional autozygosity association with albumin-to-creatinine ratio reveals a novel FTO region in an Indigenous Australian population
The genetic distinctiveness of Indigenous Australian populations is well established, yet the Tiwi population remains underrepresented in genetic research. Due to their prolonged geographic isolation, these populations are prone to increased runs of homozygosity (ROH). We investigated the genetic diversity of the Tiwi population, isolated from mainland Australia for decades, based on ROH and their associations with clinical traits. We analyzed 455 whole genome sequences to identify population structure via PCA and performed a comparison with UK Biobank, Melanesian, and Polynesian cohorts. ROH assessment and genome-wide and regional measures of homozygosity were used to explore associations between clinical traits and autozygosity. Our analysis revealed distinct genetic characteristics of the Tiwi population that aligned closely with those of the Melanesian cohort. Tiwi individuals exhibited an increased burden of ROH, particularly in LINC0109, FMLN1, and RPL17P45 genes on chromosomes 2, 17, and 18, respectively, indicating prolonged isolation and genetic drift. A positive correlation was observed between genomic FROH and albumin-to-creatinine ratio (ACR) levels, suggesting a potential link between autozygosity and renal health markers. Furthermore, regional autozygosity association analysis revealed an association between elevated ACR and a region in FTO, implicating its role in obesity, kidney disease, and cardiovascular conditions. Importantly, we found that this association is strong under the recessive model. This research lays a robust foundation for further exploration of ROH mapping and its implications for disease susceptibility within Indigenous communities worldwide.
Environmental public health research at the U.S. Environmental Protection Agency: A blueprint for exposure science in a connected world
Exposure science plays an essential role in the U.S. Environmental Protection Agency’s (U.S. EPA) mission to protect human health and the environment. The U.S. EPA’s Center for Public Health and Environmental Assessment (CPHEA) within the Office of Research and Development (ORD) provides the exposure science needed to characterize the multifaceted relationships between people and their surroundings in support of national, regional, local and individual-level actions. Furthermore, exposure science research must position its enterprise to tackle the most pressing public health challenges in an ever-changing environment. These challenges include understanding and confronting complex human disease etiologies, disparities in the social environment, and system-level changes in the physical environment. Solutions will sustainably balance and optimize the health of people, animals, and ecosystems. Our objectives for this paper are to review the role of CPHEA exposure science research in various recent decision-making contexts, to present current challenges facing U.S. EPA and the larger exposure science field, and to provide illustrative case examples where CPHEA exposure science is demonstrating the latest methodologies at the intersection of these two motivations. This blueprint provides a foundation for applying exposomic tools and approaches to holistically understand real-world exposures so optimal environmental public health protective actions can be realized within the broader context of a One Health framework.
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