This track shows multiple alignments of 77 vertebrate species: 55 birds, 10 reptiles (alligator, snake, frog) and 12 other species (fish, human, mouse, lamprey) and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 77 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 Assembly name browser or
NCBI sourcealignment type Chicken Gallus gallus Mar. 2018 (GRCg6a/galGal6) Mar. 2018 (GRCg6a/galGal6) reference Adelie penguin Pygoscelis adeliae Jun 2014 (ASM69910v1/pygAde1) Jun 2014 (ASM69910v1/pygAde1) syntenic African clawed frog Xenopus laevis Aug. 2016 (Xenopus_laevis_v2/xenLae2) Aug. 2016 (Xenopus_laevis_v2/xenLae2) net American alligator Alligator mississippiensis Aug. 2012 (allMis0.2/allMis1) Aug. 2012 (allMis0.2/allMis1) reciprocal best American crow Corvus brachyrhynchos Jun 2014 (ASM69197v1/corBra1) Jun 2014 (ASM69197v1/corBra1) syntenic American flamingo Phoenicopterus ruber ruber May 2014 (ASM68726v1/phoRub1) May 2014 (ASM68726v1/phoRub1) reciprocal best Anna's hummingbird Calypte anna Jun 2014 (ASM69908v1/calAnn1) Jun 2014 (ASM69908v1/calAnn1) syntenic Arctic lamprey Lethenteron camtschaticum Sep 2013 (LetJap1.0/letCam1) Sep 2013 (LetJap1.0/letCam1) net Bald eagle Haliaeetus leucocephalus Aug 2014 (Haliaeetus_leucocephalus-4.0/halLeu1) Aug 2014 (Haliaeetus_leucocephalus-4.0/halLeu1) syntenic Bar tailed trogon Apaloderma vittatum 16 Jun 2014 (ASM70340v1/apaVit1) 16 Jun 2014 (ASM70340v1/apaVit1) reciprocal best Barn owl Tyto alba May 2014 (ASM68720v1/tytAlb1) May 2014 (ASM68720v1/tytAlb1) reciprocal best Brown roatelo Mesitornis unicolor Jun 2014 (ASM69576v1/mesUni1) Jun 2014 (ASM69576v1/mesUni1) reciprocal best Budgerigar Melopsittacus undulatus Sep. 2011 (WUSTL v6.3/melUnd1) Sep. 2011 (WUSTL v6.3/melUnd1) syntenic Burmese python Python bivittatus Sep. 2013 (Python_molurus_bivittatus-5.0.2/pytBiv1) Sep. 2013 (Python_molurus_bivittatus-5.0.2/pytBiv1) net Canary Serinus canaria 15 Jan-2014 (SCA1/serCan1) 15 Jan-2014 (SCA1/serCan1) syntenic Chinese alligator Alligator sinensis 29 Aug 2013 (ASM45574v1/allSin1) 29 Aug 2013 (ASM45574v1/allSin1) reciprocal best Chinese softshell turtle Pelodiscus sinensis Oct 2011 (PelSin_1.0/pelSin1) Oct 2011 (PelSin_1.0/pelSin1) reciprocal best Chuck-will's-widow Caprimulgus carolinensis Jun 2014 (ASM70074v1/capCar1) Jun 2014 (ASM70074v1/capCar1) reciprocal best Collared flycatcher Ficedula albicollis Jun 2013 (FicAlb1.5/ficAlb2) Jun 2013 (FicAlb1.5/ficAlb2) syntenic Common cuckoo Cuculus canorus Jun 2014 (ASM70932v1/cucCan1) Jun 2014 (ASM70932v1/cucCan1) reciprocal best Crested ibis Nipponia nippon Jun 2014 (ASM70822v1/nipNip1) Jun 2014 (ASM70822v1/nipNip1) syntenic Crowned crain Balearica pavonina gibbericeps Jun 2014 (ASM70989v1/balPav1) Jun 2014 (ASM70989v1/balPav1) reciprocal best Cuckoo roller Leptosomus discolor May 2014 (ASM69178v1/lepDis1) May 2014 (ASM69178v1/lepDis1) reciprocal best Dalmatian pelican Pelecanus crispus May 2014 (ASM68737v1/pelCri1) May 2014 (ASM68737v1/pelCri1) reciprocal best Downy woodpecker Picoides pubescens Jun 2014 (ASM69900v1/picPub1) Jun 2014 (ASM69900v1/picPub1) reciprocal best Emperor penguin Aptenodytes forsteri 06 Jun 2014 (ASM69914v1/aptFor1) 06 Jun 2014 (ASM69914v1/aptFor1) syntenic Fugu Takifugu rubripes Oct. 2011 (FUGU5/fr3) Oct. 2011 (FUGU5/fr3) net Garter snake Thamnophis sirtalis Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) net Golden eagle Aquila chrysaetos canadensis Oct. 2014 (aquChr-1.0.2/aquChr2) Oct. 2014 (aquChr-1.0.2/aquChr2) syntenic Great cormorant Phalacrocorax carbo Jun 2014 (ASM70892v1/phaCar1) Jun 2014 (ASM70892v1/phaCar1) reciprocal best Green seaturtle Chelonia mydas Mar 2013 (CheMyd_1.0/cheMyd1) Mar 2013 (CheMyd_1.0/cheMyd1) reciprocal best Hoatzin Opisthocomus hoazin May 2014 (ASM69207v1/opiHoa1) May 2014 (ASM69207v1/opiHoa1) reciprocal best Hooded crow Corvus cornix cornix Aug 2014 (Hooded_Crow_genome/corCor1) Aug 2014 (Hooded_Crow_genome/corCor1) syntenic Houbara bustard Chlamydotis undulata macqueenii Jun 2014 (ASM69519v1/chlUnd1) Jun 2014 (ASM69519v1/chlUnd1) reciprocal best Human Homo sapiens Dec. 2013 (GRCh38/hg38) Dec. 2013 (GRCh38/hg38) net Japanese eel Anguilla japonica 18 Mar-2014 (japanese_eel_genome_v1 25_oct_2011_japonica_c401b400k25m200 sspacepremiumk3a02n24 extra.final.scaffolds/angJap1) 18 Mar-2014 (japanese_eel_genome_v1 25_oct_2011_japonica_c401b400k25m200 sspacepremiumk3a02n24 extra.final.scaffolds/angJap1) net Japanese quail Coturnix japonica Mar. 2016 (Coturnix japonica 2.0/cotJap2) Mar. 2016 (Coturnix japonica 2.0/cotJap2) reciprocal best Killdeer Charadrius vociferus Aug 2014 (ASM70802v2/chaVoc2) Aug 2014 (ASM70802v2/chaVoc2) syntenic Lamprey Petromyzon marinus Dec. 2017 (Pmar_germline 1.0/petMar3) Dec. 2017 (Pmar_germline 1.0/petMar3) net Little egret Egretta garzetta May 2014 (ASM68718v1/egrGar1) May 2014 (ASM68718v1/egrGar1) reciprocal best Lizard Anolis carolinensis May 2010 (Broad AnoCar2.0/anoCar2) May 2010 (Broad AnoCar2.0/anoCar2) net Mallard duck Anas platyrhynchos Apr 2013 (BGI_duck_1.0/anaPla1) Apr 2013 (BGI_duck_1.0/anaPla1) reciprocal best Medaka Oryzias latipes Oct. 2005 (NIG/UT MEDAKA1/oryLat2) Oct. 2005 (NIG/UT MEDAKA1/oryLat2) net Medium ground finch Geospiza fortis Apr. 2012 (GeoFor_1.0/geoFor1) Apr. 2012 (GeoFor_1.0/geoFor1) syntenic Mouse Mus musculus Dec. 2011 (GRCm38/mm10) Dec. 2011 (GRCm38/mm10) net Nile tilapia Oreochromis niloticus Nov. 2016 (ASM185804v2/oreNil3) Nov. 2016 (ASM185804v2/oreNil3) net Northern carmine bee-eater Merops nubicus May 2014 (ASM69184v1/merNub1) May 2014 (ASM69184v1/merNub1) reciprocal best Northern fulmar Fulmarus glacialis May 2014 (ASM69083v1/fulGla1) May 2014 (ASM69083v1/fulGla1) reciprocal best Ostrich Struthio camelus australis 06 Jun-2014 (ASM69896v1/strCam1) 06 Jun-2014 (ASM69896v1/strCam1) reciprocal best Painted turtle Chrysemys picta bellii Mar. 2014 (v3.0.3/chrPic2) Mar. 2014 (v3.0.3/chrPic2) syntenic Parrot Amazona vittata Jan. 2013 (AV1/amaVit1) Jan. 2013 (AV1/amaVit1) reciprocal best Peregrine falcon Falco peregrinus Feb 2013 (F_peregrinus_v1.0/falPer1) Feb 2013 (F_peregrinus_v1.0/falPer1) syntenic Red crested turaco Tauraco erythrolophus Jun 2014 (ASM70936v1/tauEry1) Jun 2014 (ASM70936v1/tauEry1) reciprocal best Red-legged seriema Cariama cristata May 2014 (ASM69053v1/carCri1) May 2014 (ASM69053v1/carCri1) reciprocal best Red-throated loon Gavia stellata May 2014 (ASM69087v1/gavSte1) May 2014 (ASM69087v1/gavSte1) reciprocal best Rhinoceros hornbill Buceros rhinoceros silvestris Jun 2014 (ASM71030v1/bucRhi1) Jun 2014 (ASM71030v1/bucRhi1) reciprocal best Rifleman Acanthisitta chloris 27 May 2014 (ASM69581v1/acaChl1) 27 May 2014 (ASM69581v1/acaChl1) reciprocal best Rock pigeon Columba livia Feb 2013 (Cliv_1.0/colLiv1) Feb 2013 (Cliv_1.0/colLiv1) syntenic Saker falcon Falco cherrug Feb 2013 (F_cherrug_v1.0/falChe1) Feb 2013 (F_cherrug_v1.0/falChe1) syntenic Scarlet macaw Ara macao Jun 2013 (SMACv1.1/araMac1) Jun 2013 (SMACv1.1/araMac1) reciprocal best Speckled mousebird Colius striatus May 2014 (ASM69071v1/colStr1) May 2014 (ASM69071v1/colStr1) reciprocal best Spiny softshell turtle Apalone spinifera May 2013 (ASM38561v1/apaSpi1) May 2013 (ASM38561v1/apaSpi1) reciprocal best Stickleback Gasterosteus aculeatus Feb. 2006 (Broad/gasAcu1) Feb. 2006 (Broad/gasAcu1) net Sunbittern Eurypyga helias May 2014 (ASM69077v1/eurHel1) May 2014 (ASM69077v1/eurHel1) reciprocal best Tetraodon Tetraodon nigroviridis Mar. 2007 (Genoscope 8.0/tetNig2) Mar. 2007 (Genoscope 8.0/tetNig2) net Tibetan frog Nanorana parkeri Mar. 2015 (BGI_ZX_2015/nanPar1) Mar. 2015 (BGI_ZX_2015/nanPar1) net Tibetan ground jay Pseudopodoces humilis Jan 2013 (PseHum1.0/pseHum1) Jan 2013 (PseHum1.0/pseHum1) syntenic Turkey Meleagris gallopavo Nov. 2014 (Turkey_5.0/melGal5) Nov. 2014 (Turkey_5.0/melGal5) reciprocal best White throated tinamou Tinamus guttatus Aug 2014 (ASM70537v2/tinGut2) Aug 2014 (ASM70537v2/tinGut2) reciprocal best White-tailed eagle Haliaeetus albicilla May 2014 (ASM69140v1/halAlb1) May 2014 (ASM69140v1/halAlb1) reciprocal best White-tailed tropicbird Phaethon lepturus May 2014 (ASM68728v1/phaLep1) May 2014 (ASM68728v1/phaLep1) reciprocal best White-throated sparrow Zonotrichia albicollis Apr 2013 (ASM38545v1/zonAlb1) Apr 2013 (ASM38545v1/zonAlb1) syntenic X. tropicalis Xenopus tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) net Yellow-throated sandgrouse Pterocles gutturalis Jun 2014 (ASM69924v1/pteGut1) Jun 2014 (ASM69924v1/pteGut1) reciprocal best Zebra finch Taeniopygia guttata Feb. 2013 (WashU taeGut324/taeGut2) Feb. 2013 (WashU taeGut324/taeGut2) syntenic Zebra mbuna Maylandia zebra Mar 2012 (MetZeb1.1/mayZeb1) Mar 2012 (MetZeb1.1/mayZeb1) net Zebrafish Danio rerio May 2017 (GRCz11/danRer11) May 2017 (GRCz11/danRer11) net
Table 1. Genome assemblies included in the 77-way Conservation track.
The track configuration options allow the user to display the three different sets of alignments: all, birds, reptiles 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 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 NCBI RefSeq Genes Chicken, Japanese quail, Turkey, Medium ground finch, Zebra finch, Budgerigar, American alligator Ensembl Genes v92 Mallard duck, Chinese softshell turtle Xeno RefGene Golden eagle, Painted turtle no annotations all others
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. Please note the specific parametersfor the alignments. 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 for each species, see the description pages for the Chain and Net tracks.
An additional filtering step was introduced in the generation of the 77-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: some of the pairwise alignments were filtered based on synteny; and others were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). Note the indication in the table above for this filtering option.
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 77-way alignment (msa_view). The 4d sites were derived from the NCBI 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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