We have conducted a comprehensive search for conserved elements in vertebrate 
genomes, using genome-wide multiple alignments of five vertebrate species 
(human, mouse, rat, chicken, and Fugu rubripes). Parallel searches have been 
performed with multiple alignments of four insect species (three species of 
Drosophila and Anopheles gambiae), two species of Caenorhabditis, and seven 
species of Saccharomyces. Conserved elements were identified with a computer 
program called phastCons, which is based on a two-state phylogenetic hidden 
Markov model (phylo-HMM). PhastCons works by fitting a phylo-HMM to the data by 
maximum likelihood, subject to constraints designed to calibrate the model 
across species groups, and then predicting conserved elements based on this 
model. The predicted elements cover roughly 3%-8% of the human genome (depending 
on the details of the calibration procedure) and substantially higher fractions 
of the more compact Drosophila melanogaster (37%-53%), Caenorhabditis elegans 
(18%-37%), and Saccharaomyces cerevisiae (47%-68%) genomes. From yeasts to 
vertebrates, in order of increasing genome size and general biological 
complexity, increasing fractions of conserved bases are found to lie outside of 
the exons of known protein-coding genes. In all groups, the most highly 
conserved elements (HCEs), by log-odds score, are hundreds or thousands of bases 
long. These elements share certain properties with ultraconserved elements, but 
they tend to be longer and less perfectly conserved, and they overlap genes of 
somewhat different functional categories. In vertebrates, HCEs are associated 
with the 3' UTRs of regulatory genes, stable gene deserts, and megabase-sized 
regions rich in moderately conserved noncoding sequences. Noncoding HCEs also 
show strong statistical evidence of an enrichment for RNA secondary structure.