A team of researchers led by engineers at the University of California San Diego has developed a novel approach for analyzing entire genomes. The method, called CASTER, offers a scalable way to study evolutionary relationships across species, with potential applications for exploring both living and extinct organisms. The findings were published in Science on January 23, 2025.
Overcoming Limitations in Genome-Wide Analyses
Phylogenomic studies have long faced challenges in analyzing whole genomes comprehensively.
“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, totaling 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 UC San Diego and the senior author of the study. “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.”
How CASTER Works
CASTER is designed to enable large-scale comparisons of full genomes by using computationally efficient algorithms and models. The approach integrates advances in statistics, computer science, and biology to align and analyze genomic data across species. It produces interpretable outputs that help researchers better understand species relationships and identify evolutionary patterns across genomic regions.
Unlike previous methods that required subsampling and focused on limited genomic regions, CASTER aligns entire genomes and uses computational resources that are readily accessible. This scalability is particularly important given the exponential growth in the number of sequenced genomes, including those of extinct species obtained from ancient DNA.
Applications in Evolutionary Research
The increasing availability of sequenced genomes has created opportunities to explore questions about how evolution has shaped present-day genomes and the organization of the Tree of Life. CASTER’s ability to analyze all positions in a genome enables researchers to uncover previously hidden patterns of evolution and detect the mosaic nature of evolutionary histories across different regions of the genome.
Publication Details
Chao Zhang et al., CASTER: Direct species tree inference from whole-genome alignments. Science 0, eadk9688 DOI:10.1126/science.adk9688
Overcoming Limitations in Genome-Wide Analyses
Phylogenomic studies have long faced challenges in analyzing whole genomes comprehensively.
“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, totaling 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 UC San Diego and the senior author of the study. “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.”
How CASTER Works
CASTER is designed to enable large-scale comparisons of full genomes by using computationally efficient algorithms and models. The approach integrates advances in statistics, computer science, and biology to align and analyze genomic data across species. It produces interpretable outputs that help researchers better understand species relationships and identify evolutionary patterns across genomic regions.
Unlike previous methods that required subsampling and focused on limited genomic regions, CASTER aligns entire genomes and uses computational resources that are readily accessible. This scalability is particularly important given the exponential growth in the number of sequenced genomes, including those of extinct species obtained from ancient DNA.
Applications in Evolutionary Research
The increasing availability of sequenced genomes has created opportunities to explore questions about how evolution has shaped present-day genomes and the organization of the Tree of Life. CASTER’s ability to analyze all positions in a genome enables researchers to uncover previously hidden patterns of evolution and detect the mosaic nature of evolutionary histories across different regions of the genome.
Publication Details
Chao Zhang et al., CASTER: Direct species tree inference from whole-genome alignments. Science 0, eadk9688 DOI:10.1126/science.adk9688