This track shows multiple alignments of 20 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all twenty species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.
PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).
Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.
Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.
See also: lastz parameters and other details and chain minimum score and gap parameters used in these alignments.
Missing sequence in the assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below).
Downloads for data in this track are available:
Organism Species Release date UCSC version alignment type Human Homo sapiens Dec. 2013 GRCh38/hg38 reference species Chimp Pan troglodytes Feb. 2011 GSAC 2.1.4/panTro4 Syntenic net Bonobo Pan paniscus May. 2012 Max-Planck/panPan1 Reciprocal best net Gorilla Gorilla gorilla gorilla May. 2011 WTSI gorGor3.1/gorGor3 Reciprocal best net Orangutan Pongo pygmaeus abelii Jul. 2007 WUGSC 2.0.2/ponAbe2* Syntenic net Gibbon Nomascus leucogenys Oct. 2012 GGSC Nleu3.0/nomLeu3 Syntenic net Proboscis monkey Nasalis larvatus Nov. 2014 PMFGC Charlie1.0/nasLar1 Reciprocal best net Golden snub-nosed monkey Rhinopithecus roxellana Oct. 2014 Rrox_v1/rhiRox1 Reciprocal best net Green monkey Chlorocebus sabaeus Mar. 2014 VGC Chlorocebus_sabeus 1.1/chlSab2 Syntenic net Crab-eating macaque Macaca fascicularis Jun. 2013 WashU 5.0/macFas5 Syntenic net Rhesus Macaca mulatta Oct. 2010 BGI CR 1.0/rheMac3 Syntenic net Baboon Papio anubis Mar. 2012 Baylor Panu_2.0/papAnu2 Syntenic net Squirrel monkey Saimiri boliviensis Oct. 2011 Broad/saiBol1 Reciprocal best net Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3 Syntenic net Tarsier Tarsius syrichta Sep. 2013 WashU 2.0.1/tarSyr2 Syntenic net Mouse lemur Microcebus murinus Jul. 2007 Broad/micMur1 Reciprocal best net Bushbaby Otolemur garnettii Mar. 2011 Broad/otoGar3 Reciprocal best net Tree shrew Tupaia belangeri Dec. 2006 Broad/tupBel1 Reciprocal best net Dog Canis lupis familiaris Sep. 2011 Broad/canFam3 Syntenic net Mouse Mus musculus Dec. 2011 GRChm38/mm10 Syntenic net
Table 1. Genome assemblies included in the 20-way Conservation track.
The track configuration options allow the user to display the three different sets of scores, all, birds or vertebrate, individually or all simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the value of the score. The conservation wiggles can 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.
Pairwise alignments of each species to the $organism genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.
Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the the conservation score display.
To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.
The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:
Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:
When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the $organism sequence at those alignment positions relative to the longest non-$organism sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".
Codon translation 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:
Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2).
Table 2. Gene tracks used for codon translation.
Gene Track Species Known Genes human, mouse Ensembl Genes v78 baboon, bushbaby, chimp, dog, gorilla, marmoset, mouse lemur, orangutan, tree shrew RefSeq crab-eating macaque, rhesus no annotation bonobo, green monkey, gibbon, proboscis monkey, golden snub-nosed monkey, squirrel monkey, tarsier
Pairwise alignments with the $organism genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.
An additional filtering step was introduced in the generation of the 20-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies.
Table 3. Type of Net alignment
type of net alignment Species Syntenic Net baboon, chimp, dog, gibbon, green monkey, crab-eating macaque, marmoset, mouse, orangutan, rhesus Reciprocal best Net bushbaby, bonobo, gorilla, golden snub-nosed monkey, mouse lemur, proboscis monkey, squirrel monkey, tarsier, tree shrew
The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.
Both phastCons and phyloP are phylogenetic methods that rely 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 all species 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 20-way alignment (msa_view). The 4d sites were derived from the Xeno RefSeq gene set, filtered to select single-coverage long transcripts.
This same tree model was used in the phyloP calculations, however their background frequencies were modified to maintain reversibility. The resulting tree model for all species.
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. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, 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).
The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.
The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.cshl.edu/phast/). 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., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).
The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".
This track was created using the following programs:
The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007.
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