This track shows multiple alignments of 10 nematode species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (nematode) and one subset (caenorhabditis). 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, and both were run with the same parameters for each species set (nematode and caenorhabditis). Thus, in regions in which only caenorhabditis appear in the alignment, the two sets of scores will be the same, but in regions in which additional species are available, the nematode scores may differ from the caenorhabditis scores. The alternative plots help to identify sequences that are under different evolutionary pressures in caenorhabditis and non-caenorhabditis.
The species aligned for this track include 10 nematode genome sequences. Compared to the previous 6-nematode alignment (ce9), this track includes 4 new nematode genomes and 2 nematode genomes with updated sequence assemblies (Table 1). The four new species are the assemblies: H. contortus (haeCon1) at an unknown coverage, M. Hapla (melHap1) at 10.4X coverage, M. incognita (melInc1) at 5X coverage, and B. Malayi (bruMal1) at 9X coverage, The C. Japonica (22X, caeJap3) and P. pacificus (8.92X, priPac2) assemblies have been updated from those used in the previous 6-species nematode alignment.
Downloads for data in this track are available:
Organism Species Release date UCSC/WormBase
versionalignment type C. elegans Caenorhabditis elegans Jan. 2010 ce9/WS210 reference species C. briggsae Caenorhabditis briggsae Jan. 2007 cb3/WS210 MAF Net C. remanei Caenorhabditis remanei May 2007 caeRem3/WS210 MAF Net C. brenneri Caenorhabditis brenneri Feb. 2008 caePb2/WS210 MAF Net C. japonica Caenorhabditis japonica Sep. 2010 caeJap3/WUGSC 7.0.1 MAF Net H. contortus Haemonchus contortus Dec. 2009 haeCon1/WS210 MAF Net P. pacificus Pristionchus pacificus Dec. 2008 priPac2/WUGSC 5.0.1 MAF Net M. hapla Meloidogyne hapla Sep. 2008 melHap1/WS210 MAF Net M. incognita Meloidogyne incognita Feb. 2008 melInc1/WS210 MAF Net B. malayi Brugia malayi Sep. 2007 bruMal1/WS210 MAF Net
Table 1. Genome assemblies included in the 10-way Conservation track.
The track configuration options allow the user to display either the nematode or caenorhabditisconservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) 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. 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). By default, the following 4 species are included in the pairwise display: C. briggsae, C. remanei, C. brenneri, and C. japonica. 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). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.
Table 2. Gene tracks used for codon translation.
Gene Track Species WS210 Worm Base Genes (Sanger Genes) C. elegans WS210 coding gene annotations C. remanei WS210 coding gene annotations C. briggsae WS210 coding gene annotations C. brenneri WS210 coding gene annotations C. japonica WS210 coding gene annotations H. contortus WS210 coding gene annotations P. pacificus WS210 coding gene annotations M. hapla C. elegans WS210 mapped genes M. incognita WS210 coding gene annotations B. malayi
Pairwise alignments with the C. elegans 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.
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 nematode 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 10-way alignment (msa_view). The 4d sites were derived from the WormBase/Sanger gene set of C. elegans, filtered to select single-coverage long transcripts. The caenorhabditis tree model was simple extracted from the nematode model with tree_doctor (PHAST).
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 were tuned to produce approximately 70% conserved elements in the C. elegans WormBase/Sanger gene coding regions. This parameter set (expected-length=15, target-coverage=0.55, rho=0.3) was then used to generate the nematode and caenorhabditis conservation scoring.
The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.bscb.cornell.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 --most-conserved (aka --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 Kiontke et al. (2007).
Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Res. 2009 Oct 26. [Epub ahead of print]
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50.
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15.
Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002;:115-26.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.
Karin Kiontke, Antoine Barri~Ore, Irina Kolotuev, Benjamin Podbilewicz, Ralf Sommer, David H.A. Fitch and Marie-Anne F~Nlix Trends, Stasis, and Drift in the Evolution of Nematode Vulva Development. Current Biology. Volume 17, Issue 22, 1925-1937, 20 November 2007