CASTER: Direct species tree inference from whole-genome alignments

Genomes contain mosaics of discordant evolutionary histories, challenging
the accurate inference of the tree of life. While genome-wide data are
routinely used for discordance-aware phylogenomic analyses, due to
modeling and scalability limitations, the current practice leaves out
large chunks of the genomes. As more high-quality genomes become
available, we urgently need discordance-aware methods to infer the tree
directly from a multiple genome alignment. Here, we introduce CASTER, a
site-based method that eliminates the need to predefine recombination-free
loci. CASTER is statistically consistent under incomplete lineage sorting
and is scalable to hundreds of mammalian whole genomes. We show both in
simulations and on real data that CASTER is scalable and accurate and that
its per-site scores can reveal interesting patterns of evolution across
the genome.