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A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network Science
No full textReconstructing and visualizing phylogenetic relationships among living organisms is a fundamental challenge because not all organisms share the same genes. As a result, the first phylogenetic visualizations employed a single gene, e.g., rRNA genes, sufficiently conserved to be present in all organisms but divergent enough to provide discrimination between groups. As more genome data became available, researchers began concatenating different combinations of genes or proteins to construct phylogenetic trees believed to be more robust because they incorporated more information. However, the genes or proteins chosen were based on ad hoc approaches. The large number of complete genome sequences available today allows the use of whole genomes to analyze relationships among organisms rather than using an ad hoc set of genes. We present a systematic approach for constructing a phylogenetic tree based on simultaneously clustering the complete proteomes of 360 bacterial species. From the homologous clusters, we identify 49 protein sequences shared by 99% of the organisms to build a tree. Of the 49 sequences, 47 have homologous sequences in both archaea and eukarya. The clusters are also used to create a network from which bacterial species with horizontally-transferred genes from other phyla are identified.Published copyKhaledian, E., K.A. Brayton, and S. L. Broschat. (2020). A systematic approach to bacterial phylogeny using order-level sampling with identification of HGT using network science. Microorganisms, Vol. 8, No. 2, 312. doi:10.3390/microorganisms8020312. PMCID: PMC7074868
Building a tradition of adaptive rangeland management : Brenda and Tony Richards
No full textTony and Brenda Richards run a family cow-calf operation in Murphy, Idaho. Their cattle graze a combination of private and public rangelands. The Richards actively work with agencies and other entities that have rule-making authority around grazing management on public lands. Though engagement is not a quick solution, the Richards highlight their experience with the 2015 Soda Fire, where this involvement with other entities benefitted their operation. The Richards are hopeful that by engaging in this way they can help change public lands management so that it provides them with the flexibility they need to have a resilient operation, necessary to address both current and future challenges that arise as the climate, their community, and society's needs and values change. This case study is part of the Rancher-to-Rancher Case Study project, which explores innovative approaches regional ranchers are using that increase their resilience in the face of a changing climate