Neighbor-net

NeighborNet[1] is an algorithm for constructing phylogenetic networks which is loosely based on the neighbor joining algorithm. Like neighbor joining, the method takes a distance matrix as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a hierarchy, and are represented using a type of phylogenetic network called a splits graph. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering.[2][3] The method is implemented in the SplitsTree and R/Phangorn[4][5] packages.

An example of a neighbor-net phylogenetic network generated by SplitsTree v4.6.

Examples of the application of Neighbor-net can be found in virology,[6] horticulture,[7] dinosaur genetics,[8] comparative linguistics, and archaeology.[9]

References
  1. Bryant D, Moulton V (February 2004). "Neighbor-net: an agglomerative method for the construction of phylogenetic networks". Molecular Biology and Evolution. 21 (2): 255–65. doi:10.1093/molbev/msh018. PMID 14660700.
  2. Bryant D, Moulton V, Spillner A (June 2007). "Consistency of the neighbor-net algorithm". Algorithms for Molecular Biology. 2: 8. doi:10.1186/1748-7188-2-8. PMC 1948893. PMID 17597551.
  3. Levy D, Pachter L (August 2011). "The neighbor-net algorithm". Advances in Applied Mathematics. 47 (2): 240–58. doi:10.1016/j.aam.2010.09.002.
  4. Schliep KP (February 2011). "phangorn: phylogenetic analysis in R". Bioinformatics. 27 (4): 592–3. doi:10.1093/bioinformatics/btq706. PMC 3035803. PMID 21169378.
  5. Schliep K, Potts AA, 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.
  6. Schmidt-Chanasit J, Bialonski A, Heinemann P, Ulrich RG, Günther S, Rabenau HF, Doerr HW (March 2009). "A 10-year molecular survey of herpes simplex virus type 1 in Germany demonstrates a stable and high prevalence of genotypes A and B". Journal of Clinical Virology. 44 (3): 235–7. doi:10.1016/j.jcv.2008.12.016. PMID 19186100.
  7. Kilian B, Ozkan H, Deusch O, Effgen S, Brandolini A, Kohl J, et al. (January 2007). "Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes". Molecular Biology and Evolution. 24 (1): 217–27. doi:10.1093/molbev/msl151. PMID 17053048.
  8. Buckley M, Walker A, Ho SY, Yang Y, Smith C, Ashton P, et al. (January 2008). "Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"". Science. 319 (5859): 33, author reply 33. Bibcode:2008Sci...319...33B. doi:10.1126/science.1147046. PMC 2694913. PMID 18174420.
  9. Shennan S (200). Pattern and process in cultural evolution. University of California Press.
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