Phylogenomics, the estimation of species phylogenies from genome-scale datasets, is a common step in many biological studies. This estimation is complicated by the fact that genes can evolve under processes, including incomplete lineage sorting (ILS), gene duplication and loss (GDL) and horizontal gene transfer (HGT), that make their trees conflict with the species history. I will survey recent progress on some statistical questions that arise in this context. Specifically, the identifiability of standard probabilistic models of phylogenomic data will be discussed, as well as the large-sample properties of computationally efficient methods for species tree estimation.