This track shows basewise measurements of evolutionary conservation/acceleration in particular clades of interest, relative to the levels of conservation/acceleration displayed elsewhere in the phylogeny. These scores were produced by the phyloP program from the PHAST package , using the same species set, multiz alignment, and neutral model of evolution that were used for the main conservation track (see description page for "Vertebrate Multiz Alignment & Conservation (44 Species)" track for details). The individual scores represent -log p-values for a slow-down or speed-up in the estimated evolutionary rate for the clade of interest, relative to the estimated rate outside that clade, under a null hypothesis of neutral evolution (see Methods).
As with the phyloP scores for the main conservation track, positive values indicate a decrease in rate (conservation) and negative values indicate an increase in rate (acceleration). In this case, however, the score measures a change in evolutionary rate in a clade of interest, possibly indicating clade-specific selection rather than the absolute rate across the phylogeny. Note that this track does not attempt to distinguish between negative and positive directional selection. For example, a clade-specific increase in rate could be due to clade-specific positive selection or relaxation of constraint. Similarly, a clade-specific decrease in rate could be due to gain of negative selection or loss of positive selection.
The scores were produced by running phyloP with the options --method
LRT --mode CONACC --wig-scores, and by indicating the clade of interest
with the --subtree option (see PHAST docs
Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS,
Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares
M, Vanderhaeghen P, and Haussler D. An RNA gene expressed during
cortical development evolved rapidly in humans.
Siepel A, Pollard KS, Haussler D. New methods for detecting
lineage-specific selection.