Noncoding markers have a particular appeal as tools for phylogenomic analysis 
because, at least in vertebrates, they appear less subject to strong variation 
in GC content among lineages. Thus far, ultraconserved elements (UCEs) and 
introns have been the most widely used noncoding markers. Here we analyze and 
study the evolutionary properties of a new type of noncoding marker, conserved 
nonexonic elements (CNEEs), which consists of noncoding elements that are 
estimated to evolve slower than the neutral rate across a set of species. 
Although they often include UCEs, CNEEs are distinct from UCEs because they are 
not ultraconserved, and, most importantly, the core region alone is analyzed, 
rather than both the core and its flanking regions. Using a data set of 16 birds 
plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that 
although CNEEs were less variable than bioinformatically derived UCEs or introns 
and in some cases exhibited a slower approach to branch resolution as determined 
by phylogenomic subsampling, the quality of CNEE alignments was superior to 
those of the other markers, with fewer gaps and missing species. Phylogenetic 
resolution using coalescent approaches was comparable among the three marker 
types, with most nodes being fully and congruently resolved. Comparison of 
phylogenetic results across the three marker types indicated that one branch, 
the sister group to the passerine + falcon clade, was resolved differently and 
with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. 
Overall, CNEEs appear to be promising as phylogenomic markers, yielding 
phylogenetic resolution as high as for UCEs and introns but with fewer gaps, 
less ambiguity in alignments and with patterns of nucleotide substitution more 
consistent with the assumptions of commonly used methods of phylogenetic 
analysis.