Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

Kim, Namshin; Lee, Chris

doi:10.1186/1471-2105-8-213

Cited by 9 publications

(2 citation statements)

References 21 publications

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“…Computational inference of species trees from gene trees 31 can now employ a rapidly growing array of methods 32 . When applied to multigene studies, the challenge of visualizing many gene trees 11,17 may be best guided by the image of a “cloudigram” 29 rather than simple lineal trees and, apart from networks and ordination 14 , visualizations such as rotatable three-dimensional trees 33 and tanglegrams 34 become relevant.…”

Section: Visualizing Infraspecific Relationshipsmentioning

confidence: 99%

Integrated species–phenon trees: visualizing infraspecific diversity within lineages

Zehady

Fordham

Ogg

2019

Sci Rep

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The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species–phenon tree merges ancestor–descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into “species boxes” and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent–child hierarchy in the integrated tree has been the progressive population of a species–phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others’ important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.

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Section: Visualizing Infraspecific Relationshipsmentioning

confidence: 99%

Integrated species–phenon trees: visualizing infraspecific diversity within lineages

Zehady

Fordham

Ogg

2019

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Here a different set of evolutionary events is considered including cospeciation events, duplications, extinctions and host switches. Few tools are currently available to visualize reconciliations: Tarzan/CoRe-PA (Merkle et al, 2005), Jane (Conow et al, 2010) and PrIMETV (Sennblad et al, 2007) packages use a two dimensional Euclidean slanted layout for the representation of reconciliations; the 3DPE editor (Kim et al, 2007) uses a 2.5D representation of a slanted layout, crossing species (X) vs. evolutionary distance (Y) vs. paralogs (Z). In spite of these powerful tools for illustrating how a "guest" tree (e.g.…”

Section: Introductionmentioning

confidence: 99%