Electrical engineers have created an improved method for comparing entire genomes, which allows for the exploration of relationships among various species over extensive geological periods. This innovative technique is anticipated to lead to significant insights into how evolution has influenced today’s genomes and the structure of the tree of life.
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 new method, known as CASTER, is positioned to reveal new findings about how evolution has affected current genomes and the arrangement of life’s tree. Described in a paper published in Science on January 23, 2025, CASTER represents a significant advancement in how comparative genomics is approached.
CASTER promises to provide biologists with a much more efficient way to compare complete genomes, especially important given the rapid increase in sequenced genomes from both living and extinct species. This wealth of genomic data is now accessible for phylogenomic studies. CASTER generates results that are interpretable and will aid biologists in understanding not only the relationships among species but also the complex evolutionary histories reflected in the genome.
“Since the early 2000s, numerous studies have asserted ‘genome-wide’ phylogeny reconstruction, but these have relied on sampling small parts of genomes, encompassing only a minor portion of the whole genome in any given research. Conducting analyses on all genomic positions using advanced models seemed unattainable,” said Siavash Mirarab, an electrical engineering professor at UC San Diego and the lead author of the new paper in Science. “What excites me is that we can now execute genuinely genome-wide analyses utilizing every base pair aligned across species with readily available computational resources.”
“Reaching this achievement necessitated collaborative efforts from various fields, including statistics, computer science, and biology,” stated Chao Zhang, the primary author of the recent Science paper. Zhang completed his PhD at UC San Diego in the Bioinformatics and Systems Biology program and is currently a faculty member at the University of Copenhagen.
