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Advancements in Genome Analysis: CASTER Method Developed at UC San Diego

A team of researchers at the University of California San Diego has introduced a groundbreaking technique for comparative genomic analysis that enhances our understanding of the evolutionary relationships among different species over extensive geological periods.

This innovative method, named CASTER, represents a significant advancement in the field, offering insights into the way evolution has influenced contemporary genomes and the broader organization of the tree of life. Details of this methodology were published on January 23, 2025, in the journal Science.

As the volume of sequenced genomes continues to grow exponentially, including those from both living and extinct species, CASTER provides a more scalable solution for full genome comparisons. It enables biologists to conduct phylogenomic analyses more effectively, delivering outputs that are not only interpretable but also enhance understanding of species relationships and the intricate tapestry of evolutionary histories embedded within genomes.

“Many studies since the early 2000s have claimed to conduct ‘genome-wide’ phylogeny reconstruction, but they primarily relied on subsampling methods that examined only small regions of full genomes,” explained Siavash Mirarab, an electrical engineering professor at UC San Diego and corresponding author of the study. “Until now, analyzing all genomic positions with sophisticated models seemed impractical. What excites me is our ability to now execute comprehensive genome-wide analyses utilizing every base pair across species with commonly accessible computational resources.”

Chao Zhang, the first author of the paper and a former PhD student in the Bioinformatics and Systems Biology program at UC San Diego, emphasized the interdisciplinary effort that led to this achievement. “Reaching this pivotal point involved collaboration across multiple fields, including statistics, computer science, and biology,” Zhang noted. He is currently a faculty member at the University of Copenhagen.

The CASTER method stands to transform how scientists approach genomic analysis, potentially leading to new insights into evolutionary biology and enhancing our comprehension of the genetic diversity present among living organisms today.

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