Description
This track shows multiple alignments of 470 mammal
assemblies and measurements of evolutionary conservation
from the Michael Hiller Lab. There is some duplication of different assemblies for the
same species, hence there are 431 distinct species in this collection.
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.
The base-wise conservation scores are computed using two methods
phastCons and phyloP from the
PHAST package,
for all species.
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).
Assemblies
The genome assemblies are from a variety of sources. Some are equivalent
to UCSC genome browser assemblies, some are from NCBI Genbank assemblies,
and some are from the DNA Zoo.
When available in the UCSC browser system, links are provided in the table
below. Otherwise, links are provided to source locations for the assemblies.
Table 1. Genome assemblies included in the 470-way Conservation track.
Data Access
Downloads for data in this track are available:
Display Conventions and Configuration
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 human 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. Missing sequence in any
assembly is highlighted in the track display by regions of yellow when zoomed
out and by Ns when displayed at base level. 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 human 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 human 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 human sequence at those
alignment positions relative to the longest non-human 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 Track | Species |
| RefSeq Genes | aardvark, American pika, Amur tiger, Angolan colobus, big brown bat, black flying fox, black snub-nosed monkey, Bolivian squirrel monkey, Brandt's bat, Cape elephant shrew, Cape golden mole, cattle, chimpanzee, Chinese tree shrew, Coquerel's sifaka, degu, dog, domestic cat, domestic guinea pig, drill, European shrew, Florida manatee, golden hamster, gray mouse lemur, green monkey, Hawaiian monk seal, horse, house mouse, house mouse, human, killer whale, lesser Egyptian jerboa, little brown bat, long-tailed chinchilla, Ma's night monkey, minke whale, naked mole-rat, nine-banded armadillo, Northern sea otter, Norway rat, Ord's kangaroo rat, Pacific walrus, Panamanian white-faced capuchin, Philippine tarsier, pig, pig-tailed macaque, polar bear, prairie vole, Przewalski's horse, pygmy chimpanzee, rabbit, Rhesus monkey, small Madagascar hedgehog, small-eared galago, sooty mangabey, southern white rhinoceros, star-nosed mole, Sumatran orangutan, thirteen-lined ground squirrel, Upper Galilee mountains blind mole rat, Vespertilio Davidii, Weddell seal, western European hedgehog, western lowland gorilla, Yangtze River dolphin |
| Ensembl Genes | Bos bison bison, Brazilian guinea pig, dog, gray short-tailed opossum, northern tree shrew |
| Xeno RefGene | alpaca, black lemur, Chinese pangolin, common bottlenose dolphin, proboscis monkey, Sclater's lemur, Southern sea otter, tammar wallaby |
| no annotation | African buffalo, African grass rat, African hunting dog, African hunting dog, African savanna elephant, African woodland thicket rat, Agile Gracile Mouse Opossum, Allen's swamp monkey, Alpine ibex, Alpine marmot, alpine musk deer, American beaver, American black bear, American black bear, American mink, Amur leopard cat, antarctic fur seal, Antarctic minke whale, Antillean ghost-faced bat, aoudad, Arabian camel, Arctic fox, Arctic ground squirrel, argali, Asian black bear, Asian palm civet, Asiatic elephant, Asiatic mouflon, Asiatic tapir, Asiatic tapir, ass, Australian echidna, aye-aye, babakoto, Bactrian camel, banded mongoose, Bank vole, bearded seal, beluga whale, bighorn sheep, bighorn sheep, black muntjac, black rat, black rhinoceros, black-footed cat, black-handed spider monkey, Blue whale, Bohar reedbuck, Bolivian squirrel monkey, Bolivian titi, Bonin flying fox, boutu, bowhead whale, Brazilian free-tailed bat, Brazilian porcupine, Brazilian tapir, brindled gnu, brown lemur, brush rabbit, bush duiker, bushbuck, Cacomistle, cactus mouse, California big-eared bat, California sea lion, Canada lynx, Cantor's roundleaf bat, Cape rock hyrax, capybara, Central European red deer, Chacoan peccary, cheetah, Chinese forest musk deer, Chinese hamster, Chinese pangolin, Chinese rufous horseshoe bat, Chinese water deer, chiru, Clouded leopard, Cobus hunteri, common bottlenose dolphin, common bottlenose dolphin, common brushtail, common pipistrelle, common pipistrelle, common vampire bat, Common vole, common wombat, coppery ringtail possum, Coquerel's mouse lemur, crab-eating macaque, crested porcupine, Cuvier's beaked whale, Damara mole-rat, dassie-rat, Daurian ground squirrel, De Brazza's monkey, desert woodrat, dingo, domestic ferret, domestic yak, donkey, dugong, dwarf mongoose, eastern gray kangaroo, eastern mole, Eastern roe deer, Egyptian rousette, Egyptian spiny mouse, Equus burchelli boehmi, ermine, Eurasian elk, Eurasian red squirrel, Eurasian river otter, Eurasian water vole, European polecat, European rabbit, European woodmouse, evening bat, Fat dormouse, fat sand rat, Fin whale, fossa, franciscana, Francois's langur, Gambian giant pouched rat, gaur, gayal, gelada, gemsbok, gerenuk, giant anteater, giant otter, giant otter, giant panda, giraffe, giraffe, goat, Gobi jerboa, golden ringtail possum, golden snub-nosed monkey, golden spiny mouse, gracile shrew mole, Grant's gazelle, gray seal, gray squirrel, great gerbil, great roundleaf bat, greater bamboo lemur, greater bulldog bat, Greater cane rat, greater horseshoe bat, greater Indian rhinoceros, greater kudu, greater mouse-eared bat, grey whale, grizzly bear, ground cuscus, guanaco, Gunnison's prairie dog, Hanuman langur, harbor porpoise, harbor porpoise, harbor seal, Harvey's duiker, hazel dormouse, Hesperomys crinitus, Himalayan marmot, hippopotamus, hippopotamus, Hispaniolan solenodon, hispid cotton rat, hoary bamboo rat, hoary bat, Hoffmann's two-fingered sloth, Hog deer, hog-nosed bat, Honduran yellow-shouldered bat, humpback whale, Iberian mole, impala, Indian false vampire, Indian flying fox, Indo-pacific bottlenose dolphin, Indo-pacific bottlenose dolphin, Indo-pacific humpbacked dolphin, Indus River dolphin, jaguar, jaguar, jaguarundi, Jamaican fruit-eating bat, Jamaican fruit-eating bat, Japanese macaque, Java mouse-deer, kinkajou, Kirk's dik-dik, klipspringer, koala, Kuhl's pipistrelle, Lama pacos huacaya, large flying fox, Leadbeater's possum, lechwe, leopard, Leschenault's rousette, lesser dawn bat, Lesser dwarf lemur, lesser kudu, Lesser long-nosed bat, lesser mouse-deer, lesser panda, lesser short-nosed fruit bat, lion, little brown bat, llama, llama, long-finned pilot whale, long-tongued fruit bat, Madagascan rousette, Malagasy flying fox, Malagasy straw-colored fruit bat, Malayan pangolin, Malayan pangolin, mandrill, mantled howler monkey, Masai giraffe, Maxwell's duiker, meadow jumping mouse, meerkat, meerkat, melon-headed whale, Miniopterus schreibersii natalensis, Mona monkey, Mongolian gerbil, mongoose lemur, Montane guinea pig, mountain beaver, mountain goat, Mountain hare, mouse lemur, mule deer, muntjak, Murina feae, muskrat, narwhal, Nilgiri tahr, North American badger, North American opossum, North American porcupine, North Atlantic right whale, North Pacific right whale, Northern American river otter, Northern elephant seal, northern fur seal, Northern giant mouse lemur, northern gundi, Northern long-eared myotis, Northern mole vole, northern rock mouse, Northern rufous mouse lemur, northern white rhinoceros, northern white-cheeked gibbon, Norway rat, nutria, okapi, oldfield mouse, olive baboon, pacarana, Pacific pocket mouse, Pacific white-sided dolphin, pale spear-nosed bat, Pallas's mastiff bat, pallid bat, Parnell's mustached bat, Patagonian cavy, Pere David's deer, Peromyscus californicus subsp. insignis, platypus, porcupine caribou, prairie deer mouse, pronghorn, Przewalski's gazelle, puma, punctate agouti, pygmy Bryde's whale, pygmy marmoset, pygmy sperm whale, rabbit, raccoon, ratel, red bat, red fox, red guenon, red kangaroo, Red shanked douc langur, reed vole, Reeves' muntjac, reindeer, Ring-tailed lemur, roan antelope, root vole, royal antelope, Ryukyu mouse, sable, sable antelope, saiga antelope, Schizostoma hirsutum, Schreibers' long-fingered bat, scimitar-horned oryx, Sclater's lemur, Seba's short-tailed bat, sheep, short-tailed field vole, shrew mouse, Siberian ibex, Siberian musk deer, silvery gibbon, slow loris, snow sheep, snowshoe hare, social tuco-tuco, South African ground squirrel, Southern elephant seal, southern grasshopper mouse, southern multimammate mouse, southern tamandua, Southern three-banded armadillo, southern two-toed sloth, southern two-toed sloth, Sowerby's beaked whale, Spanish lynx, sperm whale, sperm whale, spotted hyena, springbok, springhare, steenbok, Steller sea lion, Steller's sea cow, Stephens's kangaroo rat, steppe mouse, straw-colored fruit bat, stripe-headed round-eared bat, striped hyena, Sumatran rhinoceros, Sunda flying lemur, suni, tailed tailless bat, Talazac's shrew tenrec, tamarin, tammar wallaby, Tasmanian devil, Tasmanian wolf, Thomson's gazelle, topi, Transcaucasian mole vole, Tree pangolin, Tree pangolin, tufted capuchin, Ugandan red Colobus, Vancouver Island marmot, vaquita, Vicugna mensalis, walrus, water buffalo, waterbuck, western gray kangaroo, Western ringtail oppossum, western spotted skunk, western wild mouse, white-faced saki, white-footed mouse, white-fronted capuchin, white-lipped deer, White-nosed coati, white-tailed deer, white-tailed deer, white-tailed deer, white-tufted-ear marmoset, Wild Bactrian camel, wild goat, wild yak, wolverine, woodchuck, woodchuck, woodland dormouse, Yangtze finless porpoise, Yarkand deer, yellow-bellied marmot, yellow-footed antechinus, yellow-spotted hyrax, zebu cattle,
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Table 2. Gene tracks used for codon translation.
Methods
Pairwise alignments with the human 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.
Phylogenetic Tree Model
The 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 470-way alignment
(msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene
set, filtered to select single-coverage long transcripts.
This same tree model was used in the phyloP calculations; however, the
background frequencies were modified to maintain reversibility.
The resulting tree model:
all species.
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).
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
References
Harris RS.
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis. Pennsylvania State University, USA. 2007.
PhyloP:
Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow
A.
Distribution and intensity of constraint in mammalian genomic sequence.
Genome Res. 2005 Jul;15(7):901-13.
PMID: 15965027;
PMC: PMC1172034;
DOI: 10.1101/gr.3577405
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, Haussler D.
Phylogenetic Hidden Markov Models.
In: Nielsen R, editor. Statistical Methods in Molecular Evolution.
New York: Springer; 2005. pp. 325-351.
DOI: 10.1007/0-387-27733-1_12
Siepel A, Pollard KS, and Haussler D. New methods for detecting
lineage-specific selection. In Proceedings of the 10th International
Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205.
DOI: 10.1007/11732990_17
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