New Tool Enables Phylogenomic Analyses of Entire Genomes

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• Daniel Kane- [email protected]

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Researchers led by electrical engineers at the University of California San Diego have developed a better way to perform the comparative analysis of entire genomes. This approach can be used to study relationships between different species across geological time scales.

This work is poised to unlock discoveries regarding how evolution has shaped present-day genomes and also how the tree of life is organized. The new method, named CASTER, is described in a paper published in Scienceon 23 January 2025.

CASTER offers biologists a far more scalable approach than state-of-the-art for comparing full genomes. This is especially relevant given the exploding number of sequenced genomes of both living and also extinct species. All these genomes are available for comparative study through phylogenomic analyses. CASTER provides interpretable outputs that will help biologists understand not only the species relationships but also the mosaic of evolutionary histories across the genome.

"Since the early 2000s, countless studies have claimed 'genome-wide' phylogeny reconstruction; however, these have been all based on subsampling regions scattered across the genomes, totalling only a small fraction of each full genome that is part of any given study. Analyzing all genomic positions while using complex models had seemed out of reach," said Siavash Mirarab, an electrical engineering professor at the UC San Diego Jacobs School of Engineering and the corresponding author of the new paper in Science "What excites me is that we can now perform truly genome-wide analyses using every base pair aligned across species with widely available computational resources."

"Arriving at this milestone required combined efforts from many disciplines, including statistics, computer science, and biology," said Chao Zhang, the first author on the new Sciencepaper. Zhang completed his PhD at UC San Diego in the Bioinformatics and Systems Biology program. He is now on the faculty of the University of Copenhagen.

Paper

"CASTER: Direct species tree inference from whole-genome alignments," published on 23 January, 2025 in the journal Science

Paper authors

Chao Zhang^1,2,3, Rasmus Nielsen^2,3, Siavash Mirarab^1,*

¹University of California San Diego

²University of Copenhagen

³University of California Berkeley

Corresponding author

Siavash Mirarab is a professor in the Department of Electrical and Computer Engineering at the UC San Diego Jacobs School of Engineering.

Funding

This works is supported by National Institutes of Health grant R35GM142725; National Science Foundation grants #1845967, #2138259, #2138286, #2138307, #2137603, and #2138296; Villum Foundation grant #40582. This work used Expanse at SDSC through allocation ASC150046 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by National Science Foundation grants. The authors declare no conflicts of interest.

Technical Summary

A technical summary of the paper is available upon request.