Downloads for data in this track are available:
This track shows multiple alignments of 60 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (vertebrate) and three subsets (Glires, Euarchontoglires and placental mammal). 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 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 (Glires, Euarchontoglires, placental mammals, and vertebrates). Thus, in regions in which only Glires appear in the alignment, all four sets of scores will be the same, but in regions in which additional species are available, the Euarchontoglires, placental mammal, and/or vertebrate scores may differ from the Glires scores. The alternative plots help to identify sequences that are under different evolutionary pressures in, for example, Glires and non-Glires, or placentals and non-placentals.
UCSC has repeatmasked and aligned the low-coverage genome assemblies, and provides the sequence for download; genome browsers are under construction and will be released over time. Missing sequence in the low-coverage assemblies is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level (see Gap Annotation, below).
Glires subset Organism Species Release date UCSC version Alignment type Mouse Mus musculus Dec. 2011 GRCm38/mm10 reference species Guinea pig Cavia porcellus Feb. 2008 Broad/cavPor3 Syntenic net Kangaroo rat Dipodomys ordii Jul. 2008 Broad/dipOrd1 Reciprocal best net Naked mole-rat Heterocephalus glaber Jan. 2012 Broad HetGla_female_1.0/hetGla2 Syntenic net Pika Ochotona princeps Jul. 2008 Broad/ochPri2 Reciprocal best net Rabbit Oryctolagus cuniculus Apr. 2009 Broad/oryCun2 Syntenic net Rat Rattus norvegicus Mar. 2012 RGSC 5.0/rn5 Syntenic net Squirrel Spermophilus tridecemlineatus Nov. 2011 Broad/speTri2 Syntenic net Euarchontoglires subset - the Glires set above, plus: Organism Species Release date UCSC version Alignment type Baboon Papio hamadryas Nov. 2008 Baylor 1.0/papHam1 Reciprocal best net Bushbaby Otolemur garnettii Mar. 2011 Broad/otoGar3 Syntenic net Chimp Pan troglodytes Feb. 2011 WUGSC Pan_troglodytes-2.1.4/panTro4 Syntenic net Rhesus Macaca mulatta Oct. 2010 BGI CR_1.0/rheMac3 Syntenic net Gibbon Nomascus leucogenys Jun. 2011 GGSC Nleu1.1/nomLeu2 Syntenic net Gorilla Gorilla gorilla gorilla May 2011 WTSI/gorGor3 Syntenic net Human Homo sapiens Feb. 2009 GRCh37/hg19 Syntenic net Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3 Syntenic net Mouse lemur Microcebus murinus Jun. 2003 Broad/micMur1 Reciprocal best net Orangutan Pongo pygmaeus abelii Jul. 2007 WUGSC 2.0.2/ponAbe2 Syntenic net Squirrel monkey Saimiri boliviensis Oct. 2011 Broad/saiBol1 Syntenic net Tarsier Tarsius syrichta Aug. 2008 Broad/tarSyr1 Reciprocal best net Tree shrew Tupaia belangeri Dec. 2006 Broad/tupBel1 Reciprocal best net Placental mammal subset - the Glires and Euarchontoglires sets above, plus: Organism Species Release date UCSC version Alignment type Alpaca Vicugna pacos Jul. 2008 Broad/vicPac1 Reciprocal best net Armadillo Dasypus novemcinctus Dec. 2011 Baylor/dasNov3 Reciprocal best net Cat Felis catus Sep. 2011 ICGSC Felis_catus 6.2/felCat5 Reciprocal best net Cow Bos taurus Oct. 2011 Baylor Btau_4.6.1/bosTau7 Syntenic net Dog Canis lupus familiaris Sep. 2011 Broad/canFam3 Syntenic net Dolphin Tursiops truncatus Oct. 2011 Baylor Ttru_1.4/turTru2 Reciprocal best net Elephant Loxodonta africana Jul. 2009 Broad/loxAfr3 Syntenic net Hedgehog Erinaceus europaeus Jun. 2006 Broad/eriEur1 Reciprocal best net Horse Equus caballus Sep. 2007 Broad/equCab2 Syntenic net Manatee Trichechus manatus latirostris Oct. 2011 Broad v1.0/triMan1 Syntenic net Megabat Pteropus vampyrus Jul. 2008 Broad/pteVam1 Reciprocal best net Microbat Myotis lucifugus Jul. 2010 Broad/myoLuc2 Reciprocal best net Panda Ailuropoda melanoleuca Dec. 2009 BGI-Shenzhen 1.0/ailMel1 Syntenic net Pig Sus scrofa Aug. 2011 SGSC Sscrofa10.2/susScr3 Syntenic net Rock hyrax Procavia capensis Jul. 2008 Broad/proCap1 Reciprocal best net Sheep Ovis aries Feb. 2010 ISGC Ovis_aries_1.0/oviAri1 Reciprocal best net Shrew Sorex araneus Jun. 2006 Broad/sorAra1 Reciprocal best net Sloth Choloepus hoffmanni Jul. 2008 Broad/choHof1 Reciprocal best net Tenrec Echinops telfairi Jul. 2005 Broad/echTel1 Reciprocal best net All species (vertebrate) - the three sets above, plus: Organism Species Release date UCSC version Alignment type Atlantic cod Gadus morhua May. 2010 Genofisk GadMor_May2010/gadMor1 Net Budgerigar Melopsittacus undulatus Sep. 2011 WUGSC v6.3/melUnd1 Net Chicken Gallus gallus Nov. 2011 ICGSC Gallus_gallus-4.0/galGal4 Net Coelacanth Latimeria chalumnae Aug. 2011 Broad/latCha1 Net Fugu Takifugu rubripes Oct. 2011 FUGU5/fr3 Net Lamprey Petromyzon marinus Mar. 2007 WUGSC 3.0/petMar1 Net Lizard Anolis carolinensis May 2010 Broad/anoCar2 Net Medaka Oryzias latipes Oct. 2005 NIG/UT MEDAKA1/oryLat2 Net Nile tilapia Oreochromis niloticus Jan. 2011 Broad/oreNil2 Net Opossum Monodelphis domestica Oct. 2006 Broad/monDom5 Net Painted turtle Chrysemys picta bellii Dec. 2011 IPTGSC v3.0.1/chrPic1 Net Platypus Ornithorhynchus anatinus Mar. 2007 WUGSC 5.0.1/ornAna1 Net Stickleback Gasterosteus aculeatus Feb. 2006 Broad/gasAcu1 Net Tasmanian devil Sarcophilus harrisii Feb. 2011 WTSI Devil_ref v7.0/sarHar1 Net Tetraodon Tetraodon nigroviridis Mar. 2007 Genoscope 8.0/tetNig2 Net Turkey Meleagris gallopavo Dec. 2009 TGC Turkey_2.01/melGal1 Net Wallaby Macropus eugenii Sep. 2009 TWGS Meug_1.1/macEug2 Reciprocal best net X. tropicalis Xenopus tropicalis Nov. 2009 JGI 4.2/xenTro3 Net Zebra finch Taeniopygia guttata Jul. 2008 WUGSC 3.2.4/taeGut1 Net Zebrafish Danio rerio Jul. 2010 WTSI Zv9/danRer7 Net
Table 1. Genome assemblies included in the 60-way Conservation track.
The track configuration options allow the user to display any of the subset conservation scores, or all 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. 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:
Table 2. Gene tracks used for codon translation.
Gene Track Species UCSC Genes human, mouse RefSeq Genes chicken, cow, pig, rat, rhesus, frog (x. tropicalis), zebrafish Ensembl Genes v68 alpaca, chimp, elephant, fugu, gorilla, guinea pig, hedgehog, horse, kangaroo rat, lizard, marmoset, medaka, megabat, microbat, mouse lemur, opossum, orangutan, panda, pika, platypus, rabbit, rock hyrax, shrew, sloth, stickleback, tarsier, tenrec, tetraodon, tree shrew, turkey, zebra finch Other RefSeq armadillo, baboon, bushbaby, cat, coelacanth, dog, gibbon, lamprey, manatee, naked mole-rat, painted turtle, sheep, squirrel monkey, tasmanian devil, wallaby Genscan Genes atlantic cod, budgerigar, dolphin, nile tilapia, squirrel
Pairwise alignments with the $organism genome were generated for each species using blastz from repeat-masked genomic sequence. Lineage-specific repeats were removed prior to alignment, then reinserted. 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 60-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: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best").
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 60-way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts. The Glires, Euarchontoglires and placental mammal subset tree models were extracted from the all species model.
These same tree models were used in the phyloP calculations; however, their background frequencies were modfied to maintain reversibility. The resulting tree models: all species, Glires, Euarchontoglires and placental mammal.
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.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 --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.
Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
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.
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51.