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href="/wiki/Genomics" title="Genomics">genomics</a>.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> The term has been used in multiple ways to refer to analysis that involves <a href="/wiki/Genome" title="Genome">genome</a> data and evolutionary reconstructions.<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> It is a group of techniques within the larger fields of <a href="/wiki/Phylogenetics" title="Phylogenetics">phylogenetics</a> and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> 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: </p> <ul><li>Prediction of gene function</li> <li>Establishment and clarification of evolutionary relationships</li> <li>Gene family evolution</li> <li>Prediction and retracing <a href="/wiki/Lateral_gene_transfer" class="mw-redirect" title="Lateral gene transfer">lateral gene transfer</a>.</li></ul> <p>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. <a href="/wiki/Bayesian_inference" title="Bayesian inference">Bayesian inference</a> or <a href="/wiki/Maximum_likelihood_estimation" title="Maximum likelihood estimation">maximum likelihood estimation</a>). <sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Prediction_of_gene_function">Prediction of gene function</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=1" title="Edit section: Prediction of gene function"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>When <a href="/wiki/Jonathan_Eisen" title="Jonathan Eisen">Jonathan Eisen</a> originally coined <i>phylogenomics</i>, 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".<sup id="cite_ref-Eisen_5-0" class="reference"><a href="#cite_note-Eisen-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> Gene predictions based on sequence similarity alone had been used to predict that <i><a href="/wiki/Helicobacter_pylori" title="Helicobacter pylori">Helicobacter pylori</a></i> can repair mismatched <a href="/wiki/DNA" title="DNA">DNA</a>.<sup id="cite_ref-Tomb_6-0" class="reference"><a href="#cite_note-Tomb-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> 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 <i>H. pylori</i> 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 <i>H. pylori</i> was not in the same subfamily as those known to be involved in mismatch repair.<sup id="cite_ref-Eisen_5-1" class="reference"><a href="#cite_note-Eisen-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> For reviews of this aspect of phylogenomics see Brown D, Sjölander K. Functional classification using phylogenomic inference.<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Prediction_and_retracing_lateral_gene_transfer">Prediction and retracing lateral gene transfer</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=2" title="Edit section: Prediction and retracing lateral gene transfer"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>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 <a href="/wiki/Taxonomy_(biology)" title="Taxonomy (biology)">taxonomy</a> 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.<sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Gene_family_evolution">Gene family evolution</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=3" title="Edit section: Gene family evolution"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The comparison of complete gene sets for a group of organisms allows the identification of events in gene evolution such as <a href="/wiki/Gene_duplication" title="Gene duplication">gene duplication</a> or <a href="/wiki/Gene_deletion" class="mw-redirect" title="Gene deletion">gene deletion</a>. 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 <a href="/wiki/Reductive_evolution" title="Reductive evolution">reductive evolution</a>, such as in intracellular parasites or symbionts. <a href="/wiki/Whole_genome_duplication" class="mw-redirect" title="Whole genome duplication">Whole genome duplication</a> 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. </p> <div class="mw-heading mw-heading2"><h2 id="Establishment_of_evolutionary_relationships">Establishment of evolutionary relationships</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=4" title="Edit section: Establishment of evolutionary relationships"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>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 <a href="/wiki/Lateral_gene_transfer" class="mw-redirect" title="Lateral gene transfer">lateral gene transfer</a>, <a href="/wiki/Convergent_evolution" title="Convergent evolution">convergence</a>, 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.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> Through <b>phylogenomics</b>, 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 <a href="/wiki/Species" title="Species">species</a> of photosynthetic organisms. These included <a href="/wiki/Plants" class="mw-redirect" title="Plants">plants</a>, <a href="/wiki/Alveolates" class="mw-redirect" title="Alveolates">alveolates</a>, <a href="/wiki/Rhizaria" title="Rhizaria">rhizarians</a>, <a href="/wiki/Haptophytes" class="mw-redirect" title="Haptophytes">haptophytes</a> and <a href="/wiki/Cryptomonads" class="mw-redirect" title="Cryptomonads">cryptomonads</a>.<sup id="cite_ref-14" class="reference"><a href="#cite_note-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> This has been referred to as the <a href="/wiki/Plants%2BHC%2BSAR_megagroup" class="mw-redirect" title="Plants+HC+SAR megagroup">Plants+HC+SAR megagroup</a>. Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately.<sup id="cite_ref-Dos_Reis2012_15-0" class="reference"><a href="#cite_note-Dos_Reis2012-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Databases">Databases</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=5" title="Edit section: Databases"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ol><li><a href="/wiki/PhylomeDB" title="PhylomeDB">PhylomeDB</a></li></ol> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=6" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><i><a href="/wiki/Archaeopteryx_(evolutionary_tree_visualization_and_analysis)" class="mw-redirect" title="Archaeopteryx (evolutionary tree visualization and analysis)">Archaeopteryx</a></i> (phylogenomics software)</li> <li><a href="/wiki/Microbial_phylogenetics" title="Microbial phylogenetics">Microbial phylogenetics</a></li> <li><a href="/wiki/Phylogenetics" title="Phylogenetics">Phylogenetics</a></li> <li><a href="/wiki/Sequence_alignment" title="Sequence alignment">Sequence alignment</a></li> <li><a href="/wiki/Supertree" title="Supertree">Supertree</a></li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Phylogenomics&action=edit&section=7" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output 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navbar-mini"><ul><li class="nv-view"><a href="/wiki/Template:Phylogenetics" title="Template:Phylogenetics"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Phylogenetics" title="Template talk:Phylogenetics"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Phylogenetics" title="Special:EditPage/Template:Phylogenetics"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Phylogenetics" style="font-size:114%;margin:0 4em"><a href="/wiki/Phylogenetics" title="Phylogenetics">Phylogenetics</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%">Relevant fields</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Computational_phylogenetics" title="Computational phylogenetics">Computational phylogenetics</a></li> <li><a href="/wiki/Molecular_phylogenetics" title="Molecular phylogenetics">Molecular phylogenetics</a></li> <li><a href="/wiki/Cladistics" title="Cladistics">Cladistics</a></li> <li><a href="/wiki/Taxonomy_(biology)" title="Taxonomy (biology)">Taxonomy</a></li> <li><a href="/wiki/Evolutionary_taxonomy" title="Evolutionary taxonomy">Evolutionary taxonomy</a></li> <li><a href="/wiki/Systematics" title="Systematics">Systematics</a></li></ul> </div></td><td class="noviewer navbox-image" rowspan="7" style="width:1px;padding:0 0 0 2px"><div><ul role="navigation" aria-label="Portals" class="noprint portalbox portalborder portalright"> <li class="portalbox-entry"><span class="portalbox-image"><span class="noviewer" typeof="mw:File"><a href="/wiki/File:Tree_of_life.svg" class="mw-file-description"><img alt="icon" src="//upload.wikimedia.org/wikipedia/commons/thumb/0/09/Tree_of_life.svg/32px-Tree_of_life.svg.png" decoding="async" width="32" height="27" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/09/Tree_of_life.svg/48px-Tree_of_life.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/09/Tree_of_life.svg/64px-Tree_of_life.svg.png 2x" data-file-width="915" data-file-height="760" /></a></span></span><span class="portalbox-link"><a href="/wiki/Portal:Evolutionary_biology" title="Portal:Evolutionary biology">Evolutionary biology portal</a></span></li></ul></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Basic concepts</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Phylogenesis" title="Phylogenesis">Phylogenesis</a> <ul><li><a href="/wiki/Cladogenesis" title="Cladogenesis">Cladogenesis</a></li></ul></li> <li><a href="/wiki/Phylogenetic_tree" title="Phylogenetic tree">Phylogenetic tree</a> <ul><li><a href="/wiki/Cladogram" title="Cladogram">Cladogram</a></li></ul></li> <li><a href="/wiki/Phylogenetic_network" title="Phylogenetic network">Phylogenetic network</a></li> <li><a href="/wiki/Long_branch_attraction" title="Long branch attraction">Long branch attraction</a></li> <li><a href="/wiki/Clade" title="Clade">Clade</a> vs <a href="/wiki/Evolutionary_grade" title="Evolutionary grade">Grade</a></li> <li><a href="/wiki/Lineage_(evolution)" title="Lineage (evolution)">Lineage</a> <ul><li><a href="/wiki/Ghost_lineage" title="Ghost lineage">Ghost lineage</a></li></ul></li> <li><a href="/wiki/Ghost_population" title="Ghost population">Ghost population</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Inference methods</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Maximum_parsimony_(phylogenetics)" title="Maximum parsimony (phylogenetics)">Maximum parsimony</a></li> <li><a href="/wiki/Phylogenetic_reconciliation" title="Phylogenetic reconciliation">Phylogenetic reconciliation</a></li> <li>Probabilistic methods <ul><li><a href="/wiki/Maximum_likelihood" class="mw-redirect" title="Maximum likelihood">Maximum likelihood</a></li> <li><a href="/wiki/Bayesian_inference_in_phylogeny" title="Bayesian inference in phylogeny">Bayesian inference</a></li></ul></li> <li><a href="/wiki/Distance_matrices_in_phylogeny" title="Distance matrices in phylogeny">Distance-matrix methods</a> <ul><li><a href="/wiki/Neighbor-joining" class="mw-redirect" title="Neighbor-joining">Neighbor-joining</a></li> <li><a href="/wiki/UPGMA" title="UPGMA">UPGMA</a></li> <li><a href="/wiki/Least_squares_inference_in_phylogeny" title="Least squares inference in phylogeny">Least squares</a></li></ul></li> <li><a href="/wiki/Three-taxon_analysis" title="Three-taxon analysis">Three-taxon analysis</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Current topics</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><i><a href="/wiki/PhyloCode" title="PhyloCode">PhyloCode</a></i></li> <li><a href="/wiki/DNA_barcoding" title="DNA barcoding">DNA barcoding</a></li> <li><a href="/wiki/Molecular_phylogenetics" title="Molecular phylogenetics">Molecular phylogenetics</a></li> <li><a href="/wiki/Phylogenetic_comparative_methods" title="Phylogenetic comparative methods">Phylogenetic comparative methods</a></li> <li><a href="/wiki/Phylogenetic_niche_conservatism" title="Phylogenetic niche conservatism">Phylogenetic niche conservatism</a></li> <li><a href="/wiki/Phylogenetic_signal" title="Phylogenetic signal">Phylogenetic signal</a></li> <li><a href="/wiki/List_of_phylogenetics_software" title="List of phylogenetics software">Phylogenetics software</a></li> <li><a class="mw-selflink selflink">Phylogenomics</a></li> <li><a href="/wiki/Phylogeography" title="Phylogeography">Phylogeography</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Group traits</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Primitive_(phylogenetics)" title="Primitive (phylogenetics)">Primitive</a> <ul><li><a href="/wiki/Plesiomorphy" class="mw-redirect" title="Plesiomorphy">Plesiomorphy</a></li> <li><a href="/wiki/Symplesiomorphy" class="mw-redirect" title="Symplesiomorphy">Symplesiomorphy</a></li></ul></li> <li>Derived <ul><li><a href="/wiki/Synapomorphy" class="mw-redirect" title="Synapomorphy">Apomorphy</a></li> <li><a href="/wiki/Synapomorphy" class="mw-redirect" title="Synapomorphy">Synapomorphy</a></li> <li><a href="/wiki/Autapomorphy" title="Autapomorphy">Autapomorphy</a></li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Group types</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Monophyly" title="Monophyly">Monophyly</a></li> <li><a href="/wiki/Paraphyly" title="Paraphyly">Paraphyly</a></li> <li><a href="/wiki/Polyphyly" title="Polyphyly">Polyphyly</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Nomenclature</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Phylogenetic_nomenclature" title="Phylogenetic nomenclature">Phylogenetic nomenclature</a></li> <li><a href="/wiki/Crown_group" title="Crown group">Crown group</a></li> <li><a href="/wiki/Sister_group" title="Sister group">Sister group</a></li> <li><a href="/wiki/Basal_(phylogenetics)" title="Basal (phylogenetics)">Basal</a></li> <li><a href="/wiki/Supertree" title="Supertree">Supertree</a></li></ul> </div></td></tr><tr><td class="navbox-abovebelow" colspan="3"><div> <ul><li><span class="noviewer" typeof="mw:File"><span 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