Although massively parallel sequencing has facilitated large-scale DNA 
sequencing, comparisons among distantly related species rely upon small portions 
of the genome that are easily aligned. Methods are needed to efficiently obtain 
comparable DNA fragments prior to massively parallel sequencing, particularly 
for biologists working with non-model organisms. We introduce a new class of 
molecular marker, anchored by ultraconserved genomic elements (UCEs), that 
universally enable target enrichment and sequencing of thousands of orthologous 
loci across species separated by hundreds of millions of years of evolution. Our 
analyses here focus on use of UCE markers in Amniota because UCEs and 
phylogenetic relationships are well-known in some amniotes. We perform an in 
silico experiment to demonstrate that sequence flanking 2030 UCEs contains 
information sufficient to enable unambiguous recovery of the established primate 
phylogeny. We extend this experiment by performing an in vitro enrichment of 
2386 UCE-anchored loci from nine, non-model avian species. We then use 
alignments of 854 of these loci to unambiguously recover the established 
evolutionary relationships within and among three ancient bird lineages. Because 
many organismal lineages have UCEs, this type of genetic marker and the 
analytical framework we outline can be applied across the tree of life, 
potentially reshaping our understanding of phylogeny at many taxonomic levels.