Conservation Track Settings
 
Vertebrate Multiz Alignment & Conservation (60 Species)   (All Comparative Genomics tracks)

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Multiz Alignments ▾       Basewise Conservation (phyloP) ▾       Element Conservation (phastCons) ▾       Conserved Elements ▾      
 
Multiz Alignments Configuration

Species selection:  + - default

  Glires  + -

rat
kangaroo rat
naked mole-rat
guinea pig
squirrel
rabbit
pika

  Euarchontoglires  + -

human
chimp
gorilla
orangutan
gibbon
rhesus
baboon
marmoset
squirrel monkey
tarsier
mouse lemur
bushbaby
tree shrew

  Placental Mammal  + -

pig
alpaca
dolphin
sheep
cow
cat
dog
panda
horse
microbat
megabat
hedgehog
shrew
elephant
rock hyrax
tenrec
manatee
armadillo
sloth

  Vertebrate  + -

opossum
tasmanian devil
wallaby
platypus
turkey
chicken
zebra finch
budgerigar
lizard
painted turtle
x. tropicalis
coelacanth
tetraodon
fugu
nile tilapia
stickleback
medaka
atlantic cod
zebrafish
lamprey

Multiple alignment base-level:
Display bases identical to reference as dots
Display chains between alignments

Codon Translation:
Default species to establish reading frame:
No codon translation
Use default species reading frames for translation
Use reading frames for species if available, otherwise no translation
Use reading frames for species if available, otherwise use default species
Select subtracks by clade:
  Clade Euarchontoglires  Placental  All species 
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 Euarch Cons  Euarchontoglires Basewise Conservation by PhyloP   Schema 
 
full
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 Placental Cons  Placental Mammal Basewise Conservation by PhyloP   Schema 
 
full
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 60 Vert. Cons  60 vertebrates Basewise Conservation by PhyloP   Schema 
 
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 Euarch Cons  Euarchontoglires Conservation by PhastCons   Schema 
 
hide
 Configure
 Placental Cons  Placental Mammal Conservation by PhastCons   Schema 
 
hide
 Configure
 60 Vert. Cons  60 vertebrates conservation by PhastCons   Schema 
 
hide
 Configure
 Euarch El  Euarchontoglires Conserved Elements   Schema 
 
hide
 Configure
 Placental El  Placental Mammal Conserved Elements   Schema 
 
hide
 Configure
 60 Vert. El  60 vertebrates Conserved Elements   Schema 
 
pack
 Multiz Align  Multiz Alignments of 60 Vertebrates   Schema 
    

Downloads for data in this track are available:

Description

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
OrganismSpeciesRelease dateUCSC versionAlignment type
MouseMus musculusDec. 2011GRCm38/mm10reference species
Guinea pigCavia porcellusFeb. 2008Broad/cavPor3Syntenic net
Kangaroo ratDipodomys ordiiJul. 2008Broad/dipOrd1Reciprocal best net
Naked mole-ratHeterocephalus glaberJan. 2012Broad HetGla_female_1.0/hetGla2Syntenic net
PikaOchotona princepsJul. 2008Broad/ochPri2Reciprocal best net
RabbitOryctolagus cuniculusApr. 2009Broad/oryCun2Syntenic net
RatRattus norvegicusMar. 2012RGSC 5.0/rn5Syntenic net
SquirrelSpermophilus tridecemlineatusNov. 2011Broad/speTri2Syntenic net
Euarchontoglires subset - the Glires set above, plus:
OrganismSpeciesRelease dateUCSC versionAlignment type
BaboonPapio hamadryasNov. 2008Baylor 1.0/papHam1Reciprocal best net
BushbabyOtolemur garnettiiMar. 2011Broad/otoGar3Syntenic net
ChimpPan troglodytesFeb. 2011WUGSC Pan_troglodytes-2.1.4/panTro4Syntenic net
RhesusMacaca mulattaOct. 2010BGI CR_1.0/rheMac3Syntenic net
GibbonNomascus leucogenysJun. 2011GGSC Nleu1.1/nomLeu2Syntenic net
GorillaGorilla gorilla gorillaMay 2011WTSI/gorGor3Syntenic net
HumanHomo sapiensFeb. 2009GRCh37/hg19Syntenic net
MarmosetCallithrix jacchusMar. 2009WUGSC 3.2/calJac3Syntenic net
Mouse lemurMicrocebus murinusJun. 2003Broad/micMur1Reciprocal best net
OrangutanPongo pygmaeus abeliiJul. 2007WUGSC 2.0.2/ponAbe2Syntenic net
Squirrel monkeySaimiri boliviensisOct. 2011Broad/saiBol1Syntenic net
TarsierTarsius syrichtaAug. 2008Broad/tarSyr1Reciprocal best net
Tree shrewTupaia belangeriDec. 2006Broad/tupBel1Reciprocal best net
Placental mammal subset - the Glires and Euarchontoglires sets above, plus:
OrganismSpeciesRelease dateUCSC versionAlignment type
AlpacaVicugna pacosJul. 2008Broad/vicPac1Reciprocal best net
ArmadilloDasypus novemcinctusDec. 2011Baylor/dasNov3Reciprocal best net
CatFelis catusSep. 2011ICGSC Felis_catus 6.2/felCat5Reciprocal best net
CowBos taurusOct. 2011Baylor Btau_4.6.1/bosTau7Syntenic net
DogCanis lupus familiarisSep. 2011Broad/canFam3Syntenic net
DolphinTursiops truncatusOct. 2011Baylor Ttru_1.4/turTru2Reciprocal best net
ElephantLoxodonta africanaJul. 2009Broad/loxAfr3Syntenic net
HedgehogErinaceus europaeusJun. 2006Broad/eriEur1Reciprocal best net
HorseEquus caballusSep. 2007EquCab3.0/equCab3Syntenic net
ManateeTrichechus manatus latirostrisOct. 2011Broad v1.0/triMan1Syntenic net
MegabatPteropus vampyrusJul. 2008Broad/pteVam1Reciprocal best net
MicrobatMyotis lucifugusJul. 2010Broad/myoLuc2Reciprocal best net
PandaAiluropoda melanoleucaDec. 2009BGI-Shenzhen 1.0/ailMel1Syntenic net
PigSus scrofaAug. 2011SGSC Sscrofa10.2/susScr3Syntenic net
Rock hyraxProcavia capensisJul. 2008Broad/proCap1Reciprocal best net
SheepOvis ariesFeb. 2010ISGC Ovis_aries_1.0/oviAri1Reciprocal best net
ShrewSorex araneusJun. 2006Broad/sorAra1Reciprocal best net
SlothCholoepus hoffmanniJul. 2008Broad/choHof1Reciprocal best net
TenrecEchinops telfairiJul. 2005Broad/echTel1Reciprocal best net
All species (vertebrate) - the three sets above, plus:
OrganismSpeciesRelease dateUCSC versionAlignment type
Atlantic codGadus morhuaMay. 2010Genofisk GadMor_May2010/gadMor1Net
BudgerigarMelopsittacus undulatusSep. 2011WUGSC v6.3/melUnd1Net
ChickenGallus gallusNov. 2011ICGSC Gallus_gallus-4.0/galGal4Net
CoelacanthLatimeria chalumnaeAug. 2011Broad/latCha1Net
FuguTakifugu rubripesOct. 2011FUGU5/fr3Net
LampreyPetromyzon marinusMar. 2007WUGSC 3.0/petMar1Net
LizardAnolis carolinensisMay 2010Broad/anoCar2Net
MedakaOryzias latipesOct. 2005NIG/UT MEDAKA1/oryLat2Net
Nile tilapiaOreochromis niloticusJan. 2011Broad/oreNil2Net
OpossumMonodelphis domesticaOct. 2006Broad/monDom5Net
Painted turtleChrysemys picta belliiDec. 2011IPTGSC v3.0.1/chrPic1Net
PlatypusOrnithorhynchus anatinusMar. 2007WUGSC 5.0.1/ornAna1Net
SticklebackGasterosteus aculeatusFeb. 2006Broad/gasAcu1Net
Tasmanian devilSarcophilus harrisiiFeb. 2011WTSI Devil_ref v7.0/sarHar1Net
TetraodonTetraodon nigroviridisMar. 2007Genoscope 8.0/tetNig2Net
TurkeyMeleagris gallopavoDec. 2009TGC Turkey_2.01/melGal1Net
WallabyMacropus eugeniiSep. 2009TWGS Meug_1.1/macEug2Reciprocal best net
X. tropicalisXenopus tropicalisNov. 2009JGI 4.2/xenTro3Net
Zebra finchTaeniopygia guttataJul. 2008WUGSC 3.2.4/taeGut1Net
ZebrafishDanio rerioJul. 2010WTSI Zv9/danRer7Net

Table 1. Genome assemblies included in the 60-way Conservation track.

Display Conventions and Configuration

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 mouse 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.

Gap Annotation

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:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the mouse 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.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown 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 mouse genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

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 mouse sequence at those alignment positions relative to the longest non-mouse 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:

  • 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 to establish reading frame 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 performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation:

Gene TrackSpecies
UCSC Geneshuman
RefSeq Geneschicken, cow, mouse, pig, rat, rhesus, frog (x. tropicalis), zebrafish
Ensembl Genes v65fugu
Ensembl Genes v75alpaca, chimp, elephant, 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 RefSeqarmadillo, baboon, bushbaby, cat, coelacanth, dog, gibbon, lamprey, manatee, naked mole-rat, painted turtle, sheep, squirrel monkey, tasmanian devil, wallaby
Genscan Genesatlantic cod, budgerigar, dolphin, nile tilapia, squirrel
Table 2. Gene tracks used for codon translation.

Methods

Pairwise alignments with the mouse genome were generated for each species using lastz 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.

Phylogenetic Tree Model

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 modified to maintain reversibility. The resulting tree models: all species, Glires, Euarchontoglires and placental mammal.

PhastCons Conservation

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.

PhyloP Conservation

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).

Conserved Elements

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".

Credits

This track was created using the following programs:

  • Alignment tools: lastz (formerly 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, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
  • Tree image generator: phyloPng 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. Thanks to Giacomo Bernardi for help with the fish relationships.

References

Phylo-HMMs, phastCons, and phyloP:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

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. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

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. PMID: 14500911; PMC: PMC208784

Multiz:

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. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

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. PMID: 12529312; PMC: PMC430961

Phylogenetic Tree:

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. PMID: 11743200