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Phylogenomics glossary & taxonomy
Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions?

Mary Chitty MSLS

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:   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  

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.  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

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:

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  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]  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]

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  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 2phylogenetic 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}  

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?

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

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:   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  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] 

systematics: 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.
PhyloCode Glossary,
UCMP Glossary of Natural History Terms: Vol. 1, Phylogenetics terms, Univ. of California, Berkeley [US] Museum of Paleontology, 2001, 40+ terms.

How to look for other unfamiliar  terms

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