Graph used to visualize evolutionary relationships, including reticulation events
A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly)[1] between nucleotide sequences, genes, chromosomes, genomes, or species.[2] They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent).[3] Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree,[4] the R-package, phangorn,[5][6]
and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.[7]
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, ancestral recombination graphs (ARGs) from binary sequences, median networks from a set of splits, optimal realizations and reticulograms from a distance matrix), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks).
^Huson DH, Scornavacca C (2011). "A survey of combinatorial methods for phylogenetic networks". Genome Biology and Evolution. 3: 23–35. doi:10.1093/gbe/evq077. PMC 3017387. PMID 21081312.
^Huson DH, Rupp R, Scornavacca C (2010). Phylogenetic Networks. Cambridge University Press. Archived from the original on 2014-07-14. Retrieved 2010-03-23.{{cite book}}: CS1 maint: location missing publisher (link)
^Arenas M, Valiente G, Posada D (December 2008). "Characterization of reticulate networks based on the coalescent with recombination". Molecular Biology and Evolution. 25 (12): 2517–20. doi:10.1093/molbev/msn219. PMC 2582979. PMID 18927089.
^Huson DH, Bryant D (February 2006). "Application of phylogenetic networks in evolutionary studies". Molecular Biology and Evolution. 23 (2): 254–67. doi:10.1093/molbev/msj030. PMID 16221896.
^Schliep K, Potts AJ, Morrison DA, Grimm GW (2017). "Intertwining phylogenetic trees and networks". Methods in Ecology and Evolution. 8 (10): 1212–1220. doi:10.1111/2041-210X.12760.
^Schliep KP (2018). "R package: Estimating phylogenetic trees with phangorn" (PDF).
^Cardona G, Rosselló F, Valiente G (December 2008). "Extended Newick: it is time for a standard representation of phylogenetic networks". BMC Bioinformatics. 9: 532. doi:10.1186/1471-2105-9-532. PMC 2621367. PMID 19077301.
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