This track shows the multiple alignments of 26 Drosophila
species and measurements of evolutionary conservation using two
from the PHAST package. The pairwise sequence alignments
were generated using LAST. The
multiple sequence alignments were generated using the tools
developed by UCSC and the Miller lab at the Penn
State University Center for Comparative Genomics and Bioinformatics.
Conserved elements identified by phastCons are also displayed in
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
Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as
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).
Genome assemblies included in the 26-way Drosophila Conservation track
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 value of the
score. The conservation wiggles can be configured in a variety of ways to
highlight different aspects of the displayed information. (See the "Configuring
graph-based tracks" page for details.)
Pairwise alignments of each species to the D. melanogaster 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. The "+" and "-" buttons allow
you to select or unselect multiple species at once. 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 following display conventions are used to depict the different types of gaps
in the alignment:
- Single line: No bases in the aligned species. Possibly due to a
lineage-specific insertion between the aligned blocks in the D. melanogaster genome
or a lineage-specific deletion between the aligned blocks in the aligning
- 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
- 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.
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
- 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 D. melanogaster genome that aligns to a paralogous copy somewhere
else in the aligned species, or other similar occurrence.
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 D. melanogaster sequence at those
alignment positions relative to the longest non-D. melanogaster 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
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
- 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.
Pairwise alignments with the D. melanogaster genome were generated for
each species using LAST 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
The resulting best-in-genome pairwise alignments were progressively
aligned using ROAST,
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. 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 tree model was produced using
4-fold degenerate sites extracted from the 26-way alignments. The 4-fold
degenerate sites were derived from the D. melanogaster gene annotations
produced by FlyBase, filtered to select
single-coverage long transcripts.
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 following parameters were used in the phastCons analysis:
expected-length=10, target-coverage=0.1, rho=0.1.
The phyloP program supports several different methods for computing
p-values of conservation or acceleration, for individual nucleotides
or larger elements. 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 (
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:
Alignment tools: LAST by Szymon M. Kiełbasa, Raymond
Wan, Kengo Sato, Paul Horton and Martin C. Frith;
ROAST by Minmei Hou.
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.
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.
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.
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.
A space-time process model for the evolution of DNA
Genetics. 1995 Feb;139(2):993-1005.
PMID: 7713447; PMC: PMC1206396
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
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
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
Whole genome alignment:
Kiełbasa SM1, Wan R, Sato K, Horton P, Frith MC.
Adaptive seeds tame genomic
sequence comparison. Genome Res. 2011 Mar;21(3):487-93.
PMID: 21209072; PMC: