## Description

This track shows a measure of evolutionary conservation in $organism, Tetraodon, Fugu, mouse and human based on a phylogenetic hidden Markov model, phastCons (Siepel et al., 2005). Multiz alignments of the following assemblies were used to generate this annotation:

- $organism ($date, $db)
- Tetraodon (Feb. 2004, tetNig1)
- Fugu (Aug. 2002, fr1)
- human (Feb. 2006, hg18)
- mouse (Aug. 2005, mm7)

## Display Conventions and Configuration

In dense display mode, conservation scores are shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. In squish, pack, and full display modes, the phastCons scores are represented by a "wiggle" track (histogram) in which the bar or point height reflects the size of the score. In full and pack modes, the track also displays pairwise alignments of each species to the $organism genome using a density gradient (pack mode) or wiggle track (full mode) to indicate the level of conservation. The checkboxes in the track configuration section allow the exclusion of species from the pairwise display; however, this does not remove them from the conservation score display. To view detailed information about the alignments at a specific position, zoom in the display to 30,000 or fewer bases, then click on the alignment.

This track may be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Gaps between pairwise alignment blocks are annotated as follows:

- Single line: no bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the $organism genome or a lineage-specific deletion between the aligned blocks in the aligning species.
- Double line: aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
- Yellowish-white coloring: aligning species has Ns in the gap region. Reflects uncertaintly in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are annotated as follows:

- Vertical blue bar: represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
- Green square brackets: enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the $organism genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

When zoomed-in to the base-display level, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the zebrafish sequence at those alignment positions relative to the longest non-zebrafish sequence. If there is sufficient space in the display, the size of the gap is shown; if not, and if the gap size is a multiple of 3, a "*" is displayed, otherwise "+" is shown.

Codon translation annotation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

- No codon translation: the gene annotation is not used; the bases are displayed without translation.
- Use default species reading frames for translation: the annotations from the genome displayed in the "Default species for translation" pull-down menu are used to translate all the aligned species present in the alignment.
- Use reading frames for species if available, otherwise no translation: codon translation is done only on those species that are annotated as being coding over the aligned region.
- Use reading frames for species if available, otherwise use default species: codon translation is done on those species that are annotated as being coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

## Methods

Best-in-genome blastz pairwise alignments were multiply aligned using multiz, beginning with $organism-human alignments and subsequently adding in mouse. This was added to an alignment of $organism-Tetraodon aligned to Fugu. The resulting multiple alignments were then assigned conservation scores by phastCons.

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (2005).

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

## Credits

This track was created using the following programs:

- Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
- Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
- Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by Adam Siepel while at UCSC, now at Cornell University
- MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; genePredToMafFrames by Mark Diekhans, UCSC
- Tree image generator: phyloGif by Galt Barber, UCSC
- Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community.

## References

### Phylo-HMMs and phastCons

Felsenstein J and Churchill GA (1996). A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol 13:93-104.

Siepel A and Haussler D (2005). Phylogenetic hidden Markov models. In R. Nielsen, ed., Statistical Methods in Molecular Evolution, pp. 325-351, Springer, New York.

Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).

Yang Z (1995). A space-time process model for the evolution of DNA sequences. Genetics, 139:993-1005.

### Chain/Net

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).

### Multiz

Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4), 708-15 (2004).

### Blastz

Chiaromonte, F., Yap, V.B., Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).

### Phylogenetic Tree

Murphy, W.J., et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294(5550), 2348-51 (2001).