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Phylogenomics
glossary & taxonomy
Evolving Terminologies for Emerging Technologies Comments? Questions?
Revisions?
Mary Chitty
MSLS mchitty@healthtech.com
Last revised
September 12, 2019
Phylogenomics is a sub-category
of Functional
genomics Related glossaries include Biology Expression
gene & protein
automated phylogenomics:
Zmasek C.M. and Eddy S.R. (2002) RIO:
> Bioinformatics, 3:14. paper available at: http://www.biomedcentral.com/1471-2105/3/14/
Zmasek C.M. and Eddy S.R. (2001) A simple algorithm to
infer gene duplication and speciation events on a gene tree. Bioinformatics, 17,
821-828
cenancestor:
The most recent common ancestor of the taxa under
consideration. Walter Fitch “Homology a personal view on some
of the problem” Trends in Genetics 16 (5): 227-231 May 2000
Related terms: homology,
phylogenomics
clade:
One of the two kinds of
biological entities whose names are governed by this code; a group of species
comprising a common ancestor and all of its descendants. PhyloCode Glossary,
Ohio Univ. US, 2000 http://www.ohiou.edu/phylocode/glossary.html
A monophyletic taxon; a group of organisms which includes
the most recent common ancestor of all of its members and all of the descendants
of that most recent common ancestor. From the Greek word "klados",
meaning branch or twig. [UCMP]
Compare species.
cladistics: (1) The Journal of the Willi Hennig Society. (2) The scientific discipline of classifying organisms according to the doctrine of Willi Hennig's 1966 book. (3) The belief that the organisation of taxa into groups can only be done by the identification of synapomorphies for that group.
[Molecular Systematics
evolutionary genetics: Evolutionary study of genes has been
purely theoretical, but it can provide useful information for guiding gene
mapping. People are now finding, for example, that a lot of things are not
true associations; instead, they are an artifact of association. You can make
such mistakes when you are looking at two individuals who share a common
ancestry. Understanding the phylogeny helps us, for example, understand
horizontal gene transfer between microorganisms. For humans or other sexually
reproducing organisms, the use of phylogenetic information improves resolution
for making associations by helping to avoid type I errors - that is, finding an
association that is actually merely due to sharing a recent common ancestor, or,
in other words, being closely related.
evolutionary genomics:
The field of plant molecular systematics
and phylogeny - using genes to inform taxonomic relationships and evolutionary
history ... [aimed at improving our] understanding of how eukaryotic genomes
evolve and interact. BA Palevitz, "Evolutionary Genomics: A conversation
with pioneer Jeffrey Palmer" The Scientist 14(16): 12, August 21, 2000
Looking at how genes have been
preserved through evolution, or how genes or their functions have diverged.
evolutionary homology:
The methods currently available [1994] for
interpreting DNA and protein sequences largely utilize evolutionary homology.
The consensus sequence method looks for highly conserved amino acids or
bases in specific locations. The weight matrix or profile methods perform the
same task quantitatively. Sequence alignments even attempt to
recapitulate evolution by specifically postulating substitution, insertion and
deletion events that occurred during the evolutionary process. Using these
evolutionary based methods, much hypothetical information can be gained from the
study of a single gene and protein molecule. However, these evolutionary
methods do not give much insight into the flow of genetic information from genes
to structure and to phenotype. [Douglas L. Brutlag "Understanding the human
genome" in Leder, P., Clayton, D. A. and Rubenstein, E. (Ed.), Scientific
American: Introduction to Molecular Medicine (pp. 153-168). New York NY:
Scientific American Inc. 1994. http://cmgm.stanford.edu/~brutlag/Abstracts/brutlag94.html Broader term: Functional
genomics homology; Related term
evolutionary genomics
genome prospecting:
the
use of comparative analyses of mammalian genomes to follow the course of
evolutionary history from hypothetical rat-sized primordial mammals to humans.
Comparison of genes and gene orders is invaluable in identifying animal models
for human diseases, in understanding our animal neighbors, and in appreciating
our own genetic heritage. Comparative genomics illuminates not only the path of
evolution through epochs but also the path of cultural evolution through human
history. Questions thought to be the domain of historians and anthropologists
are now approachable with genomics. Science15
October 1999:
Vol.
286
no 5439 page 443
INTRODUCTION
TO SPECIAL ISSUE Genome Prospecting Barbara
R. Jasny, Pamela
J. Hines http://www.sciencemag.org/content/286/5439/443.full
homology: Functional genomics
Narrower terms: evolutionary
homology, positional homology; Proteomics regulatory
homology; Sequencing
sequence
homology; Structural
genomics structural homology Related terms: Functional genomics
orthology, paralogy, similarity; Structural
genomics homology modeling
horizontal gene transfer: See xenology; Related term:
-Omes & -omics microbiome
lateral genomics:
It is possible that a single universal phylogenetic
tree is not the best way to depict relationships between all living
and extinct species. Instead a web- or not - like pattern, reflecting the
importance of horizontal or lateral gene transfer between lineages of organisms,
might provide a more appropriate visual metaphor. W. Ford Doolittle
“Lateral genomics” Trends Millennial Issue (TCB 9(12) TIBS 24 (12) TIG
15 (12): M5-8 December 1999
molecular
phylogenetics:
http://en.wikipedia.org/wiki/Molecular_phylogenetics
molecular taxonomy:
Relatively new;
measure molecular similarity between organisms - related to how close they are
related to each other (members of the same species are identical, progressively
more distantly related organisms are more and more different at the molecular
level). Gordon Curry, Molecular Taxonomy Slide 2 Taxonomy - identifying and
classifying organisms , Paleobiology, Earth Sciences Dept., Univ. of Glasgow,
Scotland http://www.earthsci.gla.ac.uk/staff/gbc/teaching/Palaeo_Level_3_files/frame.htm
See also Cancer
genomics
monophyletic:
A group consisting of an ancestor and all
of its descendants; usually used for groups the members of which are more
closely related to each other than to any non- members in terms of common
ancestry. [PhyloCode] http://www.ohiou.edu/phylocode/glossary.html
Related terms
clade, species.
ortholog
(orthologue), orthologous:
Functional genomics Narrower term: super- orthologs
paralog
(paralogue), paralogous:
Functional genomics Narrower term: ultra-paralogs
phylogenetic:
Of or pertaining to the history of ancestry and descent.
[PhyloCode Glossary, Ohio Univ. US, 2000] http://www.ohiou.edu/phylocode/glossary.html
phylogenetic footprinting: is
a technique used to identify transcription
factor binding
sites (TFBS) within a non-coding region of DNA of interest by comparing it
to the orthologous sequence in
different species.
When this technique is used with a large number of closely related
species, this is called phylogenetic
shadowing.[1]
Wikipedia
https://en.wikipedia.org/wiki/Phylogenetic_footprinting
accessed 2018 Jan 26
phylogenetic profiles:
Proteins having the same pattern of presence
or absence in surveyed genomes ... if there are n fully sequenced genes, there are up to 2n phylogenetic profiles. Currently
there are about 30 fully sequenced genomes in the public domain, meaning
there are 230 (~10 9 ) possible phylogenetic profiles.
This number far exceeds the number of protein
families, so that a protein’s
phylogenetic profile is a nearly unique characterization of its pattern
of distribution among genomes. Hence any two proteins having identical
or similar phylogenetic profiles are likely to be engaged in a common pathway
or complex. [David Eisenberg et al "Protein function in the post- genomic
era" Nature 405: 823- 826, 15 June 2000]
Looks
at the correlation of protein inheritance across different species. Each
protein is given a phylogenetic profile denoting the presence or absence
of that protein in various genomes. The result is that function can be
assigned to uncharacterized proteins if they have a phylogenetic profile
similar to the model profile. [S Spengler “Bioinformatics in the Information
Age” Science 287 (5456: 1221-1223, 18 Feb. 2000, citing M. Pellegrini et
al. “Assigning protein functions by comparative genome analysis: protein
phylogenetic profiles” PNAS 1999 Apr 13, 96(8):4285-8.]
Related terms: phylogenetics, phylogenetic tree, phylogenomics
phylogenetic shadowing:
See under phylogenetic footprinting
phylogenetic taxonomy: A system of naming only monophyletic groups of organisms. The hierarchical structure of the names
devised by such a system, in principle, accurately reflects the evolutionary relationships of all the named groups of organisms.
[Glossary, Natural History Museum, London, UK} http://www.nhm.ac.uk/hosted_sites/pe/2000_1/retinal/gloss.htm
phylogenetic tree:
A diagram showing evolutionary lineages of
organisms. [Edinburgh]
In practice, phylogenetic trees are unreliable. Errors in
trees will produce spurious inferred duplications. This is obviously problematic
if duplications are to be used as indicators of potential functional changes. [Christian M. Zmasek,
Sean R. Eddy, RIO: Analyzing
proteomes by automated phylogenomics using resampled inference of orthologs, BMC
Bioinformatics. 2002; 3 (1): 14,
2002]
A graphical depiction of homology.
phylogenomics:
Functional prediction via phylogenetic analysis
... When analyzing protein sequences using sequence similarity
searches, orthologous sequences (diverged by speciation) are more
reliable predictors of a new protein's function than
paralogous
sequences (diverged by gene duplication), because duplication enables
functional diversification. The utility of phylogenetic information in
high- throughput genome annotation ("phylogenomics", [1]) is
widely recognized, but existing approaches are either manual or indirect
(e.g. not based on phylogenetic trees). Here we present a procedure for
automated phylogenomics using explicit phylogenetic inference.
Christian M. Zmasek, Sean A. Eddy, Washington Univ. School of
Medicine; "RIO: Analyzing proteomes by automated phylogenomics using
resampled inference of orthologs" Intelligent Systems in Molecular
Biology " July 21- 25, 2001, Copenhagen, Denmark poster abstracts] There are many ways in which evolutionary information can
be used to improve functional predictions.
Related terms: evolutionary genomics, lateral genomics, clades, cladistics, phylogenetic
profiles, phylogenetic tree, phylome, subtree- neighbors, super-orthologs, ultra-paralogs
phyloinformatics:
What is phyloinformatics?
https://www.slideshare.net/rdmpage/phyloinformatics-introduction
phylome:
The complete set of phylogenetic trees derived from the proteome of an organism.
[T Sicheritz- Ponten, SG Andersson, "A phylogenomic approach to microbial
evolution" Nucleic Acids Research 15; 29(2): 545- 552 Jan. 2001
positional homology:
Sequence alignment for
phylogenetic analysis has a particular purpose
it
is the assignment of positional homology. Each column in a
multiple sequence alignment is assumed to include amino acids or
nucleotides that have a common evolutionary history, and each column
is treated separately in the phylogenetic analysis. Therefore, regions
in which the assignment of positional homology is ambiguous should be
excluded (Gatesy et al. 1993).
The exclusion of certain alignment positions (also known as masking)
helps to give phylogenetic methods much of their discriminatory
power. Phylogenetic trees generated without masking (as is done in
many sequence analysis software packages) are less likely to
accurately reflect the evolution of the genes than trees with
masking. Jonathan A. Eisen, Phylogenomics: Improving Functional
Predictions for Uncharacterized Genes by Evolutionary Analysis, Genome
Research 8 (3): 163-167, March 1998
http://www.genome.org/cgi/content/full/8/3/163
punctuated equilibrium: A model of evolution in which change occurs in relatively rapid bursts, followed by longer periods of stasis.
[UCMP]
rooted gene trees: The concept of speciation and
duplication is only meaningful on rooted gene trees, but the neighbor joining
algorithm infers unrooted trees. We use a simple parsimony criterion for
rooting. Gene trees are rooted on each branch, resulting in 2N-3
differently rooted trees for a gene tree of N sequences. For each of
these, the number of inferred duplications is determined. [Christian M. Zmasek,
Sean R. Eddy, RIO:
>
Bioinformatics, 3:14. paper available at: http://www.biomedcentral.com/1471-2105/3/14/
Zmasek C.M. and Eddy S.R. (2001) A simple algorithm to infer gene duplication
and speciation events on a gene tree. Bioinformatics, 17, 821-828
species:
One of the two kinds of biological entities
whose names will eventually be governed by this code; a segment of a population-
level lineage that is separate from other such lineage segments as
indicated by one or more of various possible criteria (e.g., distinguishability,
reproductive isolation, monophyly, etc.). PhyloCode Glossary, Ohio
Univ. US http://www.ohiou.edu/phylocode/glossary.html
Compare
clade.
subtree: See clade; Narrower term:
subtree-
neighbors
super-orthologs: Given a rooted gene tree
with duplication or speciation assigned to each of its internal nodes, two
sequences are super-orthologous if and only if each internal node on their
connecting path represents a speciation event. [Christian M. Zmasek,
Sean R. Eddy, RIO:
Analyzing
proteomes by automated phylogenomics using resampled inference of orthologs, BMC
Bioinformatics. 2002; 3 (1): 14,
2002]
s ystematics: See under molecular phylogenetics
taxonomy:
Study of the
characterization, classification, and naming of organisms according to standard
rules. Most modern taxonomies are phylogenetic (or natural); they attempt to
group organisms according to evolutionary descent. [NABIR] This is
different from the taxonomies in Ontologies
& Taxonomies
Phylogenomics resources
Molecular systematics] and evolution, The Natural History Museum, London and Instituto Oswaldo Cruz, FIOCRUZ Rio de Janeiro, Brazil, 100 + terms.
http://www.dbbm.fiocruz.br/james/glossary.html
PhyloCode Glossary,
https://www.ohio.edu/phylocode/glossary.html
UCMP Glossary of Natural History Terms: Vol. 1, Phylogenetics terms, Univ.
of California, Berkeley [US] Museum of Paleontology, 2001, 40+ terms. http://www.ucmp.berkeley.edu/glossary/gloss1phylo.html
How
to look for other unfamiliar terms
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