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Phylogenomics is the intersection of the fields of
evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
and genomics. The term has been used in multiple ways to refer to analysis that involves
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
data and evolutionary reconstructions. It is a group of techniques within the larger fields of
phylogenetics In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics: * Prediction of gene function * Establishment and clarification of evolutionary relationships * Gene family evolution * Prediction and retracing lateral gene transfer. The ultimate goal of phylogenomics is to reconstruct the evolutionary history of species through their genomes. This history is usually inferred from a series of genomes by using a genome evolution model and standard statistical inference methods (e.g. Bayesian inference or
maximum likelihood estimation In statistics, maximum likelihood estimation (MLE) is a method of estimating the parameters of an assumed probability distribution, given some observed data. This is achieved by maximizing a likelihood function so that, under the assumed stati ...
).


Prediction of gene function

When
Jonathan Eisen Jonathan Andrew Eisen (born August 31, 1968) is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the ac ...
originally coined ''phylogenomics'', it applied to prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. When several genes with similar sequences but differing functions are involved, this method alone is ineffective in determining function. A specific example is presented in the paper "Gastronomic Delights: A movable feast". Gene predictions based on sequence similarity alone had been used to predict that ''Helicobacter pylori'' can repair mismatched DNA. This prediction was based on the fact that this organism has a gene for which the sequence is highly similar to genes from other species in the "MutS" gene family which included many known to be involved in mismatch repair. However, Eisen noted that ''H. pylori'' lacks other genes thought to be essential for this function (specifically, members of the MutL family). Eisen suggested a solution to this apparent discrepancy – phylogenetic trees of genes in the MutS family revealed that the gene found in ''H. pylori'' was not in the same subfamily as those known to be involved in mismatch repair. Furthermore, he suggested that this "phylogenomic" approach could be used as a general method for prediction functions of genes. This approach was formally described in 1998. For reviews of this aspect of phylogenomics see Brown D, Sjölander K. Functional classification using phylogenomic inference.


Prediction and retracing lateral gene transfer

Traditional phylogenetic techniques have difficulty establishing differences between genes that are similar because of lateral gene transfer and those that are similar because the organisms shared an ancestor. By comparing large numbers of genes or entire genomes among many species, it is possible to identify transferred genes, since these sequences behave differently from what is expected given the
taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
of the organism. Using these methods, researchers were able to identify over 2,000 metabolic enzymes obtained by various eukaryotic parasites from lateral gene transfer.


Gene family evolution

The comparison of complete gene sets for a group of organisms allows the identification of events in gene evolution such as gene duplication or gene deletion. Often, such events are evolutionarily relevant. For example, multiple duplications of genes encoding degradative enzymes of certain families is a common adaptation in microbes to new nutrient sources. On the contrary, loss of genes is important in reductive evolution, such as in intracellular parasites or symbionts.
Whole genome duplication Paleopolyploidy is the result of genome duplications which occurred at least several million years ago (MYA). Such an event could either double the genome of a single species (autopolyploidy) or combine those of two species (allopolyploidy). Bec ...
events, which potentially duplicate all the genes in a genome at once, are drastic evolutionary events with great relevance in the evolution of many clades, and whose signal can be traced with phylogenomic methods.


Establishment of evolutionary relationships

Traditional single-gene studies are effective in establishing phylogenetic trees among closely related organisms, but have drawbacks when comparing more distantly related organisms or microorganisms. This is because of lateral gene transfer,
convergence Convergence may refer to: Arts and media Literature *''Convergence'' (book series), edited by Ruth Nanda Anshen *Convergence (comics), "Convergence" (comics), two separate story lines published by DC Comics: **A four-part crossover storyline that ...
, and varying rates of evolution for different genes. By using entire genomes in these comparisons, the anomalies created from these factors are overwhelmed by the pattern of evolution indicated by the majority of the data. Through phylogenomics, it has been discovered that most of the photosynthetic eukaryotes are linked and possibly share a single ancestor. Researchers compared 135 genes from 65 different
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
of photosynthetic organisms. These included
plants Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclude ...
,
alveolates The alveolates (meaning "pitted like a honeycomb") are a group of protists, considered a major clade and superphylum within Eukarya. They are currently grouped with the stramenopiles and Rhizaria among the protists with tubulocristate mitochond ...
, rhizarians, haptophytes and
cryptomonads The cryptomonads (or cryptophytes) are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anteri ...
. This has been referred to as the
Plants+HC+SAR megagroup Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclude ...
. Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately. However, in practice this is not always the case. Due to insufficient data, multiple trees can sometimes be supported by the same data when analyzed using different methods.


Databases

# PhylomeDB


See also

* '' Archaeopteryx'' * Microbial phylogenetics *
Phylogenetics In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
* Sequence alignment * Supertree


References

{{Phylogenetics Genomics Phylogenetics