This National Science Foundation (NSF) Directorate for Mathematical and Physical Sciences Project Grant of $295,263 aims to improve the estimation of species trees from genomic datasets. The award, under the Mathematical and Physical Sciences program (CFDA 47.049), will fund the development of innovative mathematical, statistical, and computational techniques to analyze phylogenomic data without relying on gene tree estimation. This approach is intended to produce more reliable species tree estimates in the presence of confounding evolutionary processes, enhancing the precision of biological discoveries based on species trees. The 3-year project will be conducted by the University of Wisconsin - Madison, advancing research utilizing phylogenies and providing interdisciplinary research training for graduate and undergraduate students.