A new method tackles evolutionary chaos in genomes to build accurate species trees.
The Problem: Genomes Are Evolutionary Mosaics
Genomes aren’t tidy family albums—they’re patchworks of conflicting histories. Recombination, hybridization, and incomplete lineage sorting scramble evolutionary signals, making it hard to reconstruct the true “tree of life.” Current methods sidestep this by analyzing small, pre-selected “recombination-free” regions, ignoring vast swaths of genomic data.
Enter CASTER—a groundbreaking tool that sidesteps these limits. Developed by Zhang, Nielsen, and Mirarab (Science, 2025), CASTER directly infers species trees from entire genome alignments, no shortcuts needed.
What Makes CASTER Unique?
- No More Locus Hunting: Unlike traditional methods, CASTER doesn’t require predefined regions. It analyzes every site in a genome alignment.
- Scalability Meets Precision: Built for big data, CASTER handles hundreds of mammalian genomes at once.
- Discordance Decoder: Its per-site scores reveal why parts of the genome disagree—biological processes (e.g., recombination) or technical artifacts.
How It Works
- Site-Based Modeling: CASTER treats each genomic position as a clue, weighing its evolutionary signal against noise.
- Simulation-Proof: Tests with simulated genomes (including recombination) show CASTER outperforms older methods in accuracy.
- Real-World Ready: Applied to biological datasets, it pinpoints hotspots of discordance, helping distinguish true evolutionary drama from sequencing errors.
Why This Matters
- Full Genome Power: Finally use 100% of genome data, not just curated fragments.
- Evolutionary Insights: Uncover hidden stories—like ancient hybridization or gene flow—that fragmented methods miss.
- Future-Proofing: As high-quality genomes flood in (Earth BioGenome Project, etc.), CASTER scales to meet the data deluge.
The Catch
While revolutionary, CASTER isn’t magic:
- Computational Muscle: Whole-genome analysis demands serious hardware.
- Interpretation Required: Users must still distinguish biological signals from artifacts using CASTER’s scores.
The Future of Phylogenomics
CASTER marks a paradigm shift. By embracing genomic chaos instead of avoiding it, we’re one step closer to unraveling life’s true history—no shortcuts, no blind spots.
“This isn’t just a new tool; it’s a new way to think about evolution,” says lead author Chao Zhang.
Read the full study: Science (2025), DOI: Science
Code Availability: Check the authors’ GitHub repositories for updates.
For phylogenomics nerds and genomics newcomers alike, CASTER is a game-changer. The tree of life just got a whole lot clearer—and messier. 🌳🧬
