Genomics, Proteomics, Bioinformatics

Analyzing Microbial Evolution Through Gene And Genome Phylogenies

By Keith Cowing
Status Report
January 9, 2024
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Analyzing Microbial Evolution Through Gene And Genome Phylogenies
A screenshot of the interactive tool. A scatterplot showing the relationships between a collection of trees can be shown alongside a selected individual gene tree (or collection of individual gene trees) . Additional gene-level variables such as functional annotation can also be visualized. —

Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole.

However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary histories.

To address this challenge, we propose to treat estimated gene-level phylogenies as data objects, and present an interactive method for the analysis of a collection of gene phylogenies.

We use a local linear approximation of phylogenetic tree space to visualize estimated gene trees as points in low-dimensional Euclidean space, and address important practical limitations of existing related approaches, allowing an intuitive visualization of complex data objects.

We demonstrate the utility of our proposed approach through microbial data analyses, including by identifying outlying gene histories in strains of Prevotella, and by contrasting Streptococcus phylogenies estimated using different gene sets.

Our method is available as an open-source R package, and assists with estimating, visualizing and interacting with a collection of bacterial gene phylogenies. dimension reduction, microbiome, non-Euclidean, statistical genetics, visualization

Sarah Teichman, Michael D. Lee, Amy D. Willis


Explorers Club Fellow, ex-NASA Space Station Payload manager/space biologist, Away Teams, Journalist, Lapsed climber, Synaesthete, Na’Vi-Jedi-Freman-Buddhist-mix, ASL, Devon Island and Everest Base Camp veteran, (he/him) 🖖🏻