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. 2017 May 1;12(5):e0175895.
doi: 10.1371/journal.pone.0175895. eCollection 2017.

Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape

Jamie Waese  1 , Nicholas J Provart  1   2 , David S Guttman  1   2
Affiliations

Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape

Jamie Waese et al. PLoS One. .

Abstract

Phylogenetic trees are the de facto standard for visualizing evolutionary relationships, but large trees can be difficult to interpret because they require a high cognitive load to identify relationships between multiple operational taxonomic units (OTUs). We present a new tool for displaying phylogenetic relationships as a topographic map in which OTUs autonomously attract or repel one another based on their individual branch lengths and distance to a common ancestor. This data visualization paradigm makes it possible to preattentively identify the nature of the relationship between items without having to trace a complex network of branches back to the root. This tool was developed for exploring phylogenetic data, but the technique could be extended for visualizing other hierarchical structures as well.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1
a) Max Fürbringer’s “Phylogenetic Tree of Birds”. b) A horizontal projection from the middle section of the tree. These figures, reproduced from https://en.wikipedia.org/wiki/Max_F%C3%BCrbringer, were originally published in 1888 and are in the public domain. c) A topographic map of Hawaii island, retrieved from https://en.wikipedia.org/wiki/Hawaii_(island)#/media/File:Hawaii_Island_topographic_map-en.svg. Reprinted with permission as per http://creativecommons.org/licenses/by-sa/3.0/.
Fig 2
Fig 2
a) Phylogenetic tree with 16 OTUs. b) Topo-phylogeny chart based on the same structure. The equivalent branches are highlighted red in both figures.
Fig 3
Fig 3
a) Nodes consist of stacks of interleaved SVG circle elements. b) Vector images can be scaled to any resolution. c) Links can be drawn above the nodes to help indicate the hierarchical structure.
Fig 4
Fig 4
a) Phylogenetic tree with 96 OTUs. b) Topo-phylogeny chart based on the same structure. The same OTU is highlighted red in both figures. c) Topo-phylogeny chart based on Hug et al.’s Tree of Life (2016) with 3740 OTUs.
See this image and copyright information in PMC

References

    1. Carrizo SF. Phylogenetic Trees: An Information Visualisation Perspective. In: Proceedings of the Second Conference on Asia-Pacific Bioinformatics—Volume 29 [Internet]. Darlinghurst, Australia, Australia: Australian Computer Society, Inc.; 2004 [cited 2014 Oct 27]. p. 315–320. (APBC ‘04). Available from: http://dl.acm.org/citation.cfm?id=976520.976563
    1. Zhang J, Mamlouk AM, Martinetz T, Chang S, Wang J, Hilgenfeld R. PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome. BMC Bioinformatics. 2011. June 20;12(1):248. - PMC - PubMed
    1. Munzner T, Guimbretière F, Tasiran S, Zhang L, Zhou Y. TreeJuxtaposer: Scalable Tree Comparison Using Focus+Context with Guaranteed Visibility. In: ACM SIGGRAPH 2003 Papers [Internet]. New York, NY, USA: ACM; 2003 [cited 2014 Oct 29]. p. 453–462. (SIGGRAPH ‘03).
    1. Rost U, Bornberg-Bauer E. TreeWiz: interactive exploration of huge trees. Bioinformatics. 2002. January 1;18(1):109–14. - PubMed
    1. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics. 2007;8:460 doi: 10.1186/1471-2105-8-460 - DOI - PMC - PubMed

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