This track shows measures of evolutionary conservation
generated using the
phyloP (Phylogenetic P-Values) program from the
Two measurements are provided:
conservation across 28 species, and an alternative measurement
restricted to the placental mammal subset (17 species plus human)
of the multiple alignment.
PhyloP differs from phastCons — which is used to produce the
scores in the main Conservation track — in several key ways. The scores
produced by phyloP reflect individual alignment columns, and do not take into
account conservation at neighboring sites. As a result, the phyloP
conservation plot has a less smooth appearance, with more "texture"
at individual bases, than the phastCons plot. In addition, this property
makes phyloP more appropriate than phastCons for evaluating signatures of
selection at particular bases or classes of bases in the genome (e.g., all
third codon positions). In addition, phyloP requires fewer assumptions than
phastCons, by depending only on a model of neutral evolution, rather than on
models of both neutral evolution and negative selection (conservation).
Finally, rather than representing probabilities of negative selection and
ranging between 0 and 1, the phyloP scores represent -log p-values under a
null hypothesis of neutral evolution, and range from 0 to infinity
(although in practice there is a maximum achievable value for any particular
See the Conservation track description for information about
the multiple alignments used as the basis of these conservation measurements.
Display Conventions and Configuration
The track configuration options allow the user to display either
the vertebrate or placental mammal conservation scores, or both
In full and pack display modes, conservation scores are displayed as a
wiggle track in which the height reflects the size of the score.
The conservation wiggles can be configured in a variety of ways to
highlight different aspects of the displayed information.
For example, the windowing function option controls how
scores are combined across sites, with averaging as the default.
This will have a strong effect on how the plot appears when zoomed out.
Click the Graph configuration help link for an explanation
of the configuration options.
Conservation scoring was performed using the phyloP program
from the PHAST package.
PhyloP is a general method for computing p-values of conservation
by comparing estimated numbers of substitutions along the
branches of a phylogeny with the distribution expected
under neutral evolution (Siepel, Pollard, and Haussler, 2006).
Here it was used to produce separate scores at each
base (--wig-scores option), considering all branches of
the phylogeny rather than a particular subtree or
lineage (i.e., --subtree was not used).
Alignment gaps were treated as missing data.
PhyloP relies on a tree model containing the tree topology,
branch lengths representing evolutionary distance at neutrally
evolving sites, the background distribution of nucleotides, and a substitution
rate matrix. The
vertebrate tree model for this track was
generated using the phyloFit program from the PHAST package
(REV model, EM algorithm, medium precision) using multiple alignments of
4-fold degenerate sites extracted from the 28way alignment
(msa_view). The 4d sites were derived from the
Oct 2005 Gencode Reference Gene set,
which was filtered to select single-coverage long transcripts. A second,
mammalian tree model including only placental mammals was used
to generate the placental mammal conservation scoring.
This track was created using phyloP, phyloFit, and other programs in PHAST by
Adam Siepel's group at Cold Spring Harbor Laboratory (original development
done at the Haussler lab at UCSC).
The phylogenetic tree is based on Murphy et al. (2001) and general
consensus in the vertebrate phylogeny community as of March 2007.
Siepel A, Pollard KS, Haussler D.
New methods for detecting lineage-specific selection.
Proc. 10th Int'l Conf. on Research in Computational Molecular Biology
(RECOMB '06). 2006.
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E,
Ryder OA, Stanhope MJ, de Jong WW, et al.
Resolution of the early placental mammal radiation using Bayesian
phylogenetics. Science. 14 Dec 2001;294(5550):2348-51.