Phylogenomics offers the potential to fully resolve the Tree of Life, but 
increasing genomic coverage also reveals conflicting evolutionary histories 
among genes, demanding new analytical strategies for elucidating a single 
history of life. Here, we outline a phylogenomic approach using a novel class of 
phylogenetic markers derived from ultraconserved elements and flanking DNA. 
Using species-tree analysis that accounts for discord among hundreds of 
independent loci, we show that this class of marker is useful for recovering 
deep-level phylogeny in placental mammals. In broad outline, our phylogeny 
agrees with recent phylogenomic studies of mammals, including several formerly 
controversial relationships. Our results also inform two outstanding questions 
in placental mammal phylogeny involving rapid speciation, where species-tree 
methods are particularly needed. Contrary to most phylogenomic studies, our 
study supports a first-diverging placental mammal lineage that includes 
elephants and tenrecs (Afrotheria). The level of conflict among gene histories 
is consistent with this basal divergence occurring in or near a phylogenetic 
"anomaly zone" where a failure to account for coalescent stochasticity will 
mislead phylogenetic inference. Addressing a long-standing phylogenetic mystery, 
we find some support from a high genomic coverage data set for a traditional 
placement of bats (Chiroptera) sister to a clade containing Perissodactyla, 
Cetartiodactyla, and Carnivora, and not nested within the latter clade, as has 
been suggested recently, although other results were conflicting. One of the 
most remarkable findings of our study is that ultraconserved elements and their 
flanking DNA are a rich source of phylogenetic information with strong potential 
for application across Amniotes.