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OneZoom: a fractal explorer for the tree of life.

Rosindell J, Harmon LJ - PLoS Biol. (2012)

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom. james@rosindell.org

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Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently (for example, see http://www.opentree.wikispaces.com)... Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps... Recent methods of phylogenetic tree visualization attempt to buy extra space in the paper paradigm—for example, by using walls consisting of multiple displays (see Figure 7a in )... This approach is costly and does not give tree visualization capabilities to the masses, which is what is really needed... Furthermore, expensive display technology does not really solve the problem—according to our estimates, even the most advanced technology, such as NASA's “Hyperwall2” of 128 LCD displays, would not be large enough to clearly display 5,000 tip trees using conventional techniques... Other currently available methods make exploration of phylogenetic trees interactive, enabling the user to expand or magnify parts of the tree that may be too small to see in detail at the scale of the screen... Hyperbolic tree browsers, are a good example of this and they can display large trees, but users do not find them intuitive and we don't see the inclusion of rich metadata as being realistically achievable... Fractals are objects that look similar at different scales and have a dimension that is not a whole number; they often appear in the natural world ,... For example, an effective lung requires a large surface area to be packed into a small a volume—its surface is therefore so convoluted and labyrinthine that at some scales it can be regarded mathematically as having a dimension greater than two (a surface) but less than three (a solid object)... Data is always displayed in both intuitive and raw formats... For example, in the “natural” view of the tree of life (see Figure 3), the balance at each node (indicative of the ratio of species richness in each descendent branch) can be taken in at a glance from the thickness and angles of the branches, but the raw numbers can also be found by zooming in on the nodes... The phylogenetic tree is also the most logical structure within which to explore the breadth of biodiversity on Earth, and so OneZoom could potentially be used to browse existing ecological databases of species such as the Encyclopedia of Life (http://eol.org/)... The logical way to do this is to build around the tree of life visualized using OneZoom; we may yet see the Google Maps equivalent for all life on earth.

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A mammal tree using data from [8] incorporating IUCN Red List metadata and common names [13].
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pbio-1001406-g004: A mammal tree using data from [8] incorporating IUCN Red List metadata and common names [13].

Mentions: There is no theoretical limit to the amount of metadata that can be put on a leaf or branch of the tree because these data can be displayed at any size and zoomed in on. Allowing branches to have a thickness assists the concept of scale when zooming and allows data such as graphs, maps, paragraphs of text, and images to be embedded inside branches and leaves. There are many further possibilities for using the colors and shapes of branches and leaves to reflect different metadata (Figure 4).


OneZoom: a fractal explorer for the tree of life.

Rosindell J, Harmon LJ - PLoS Biol. (2012)

A mammal tree using data from [8] incorporating IUCN Red List metadata and common names [13].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472976&req=5

pbio-1001406-g004: A mammal tree using data from [8] incorporating IUCN Red List metadata and common names [13].
Mentions: There is no theoretical limit to the amount of metadata that can be put on a leaf or branch of the tree because these data can be displayed at any size and zoomed in on. Allowing branches to have a thickness assists the concept of scale when zooming and allows data such as graphs, maps, paragraphs of text, and images to be embedded inside branches and leaves. There are many further possibilities for using the colors and shapes of branches and leaves to reflect different metadata (Figure 4).

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom. james@rosindell.org

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently (for example, see http://www.opentree.wikispaces.com)... Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps... Recent methods of phylogenetic tree visualization attempt to buy extra space in the paper paradigm—for example, by using walls consisting of multiple displays (see Figure 7a in )... This approach is costly and does not give tree visualization capabilities to the masses, which is what is really needed... Furthermore, expensive display technology does not really solve the problem—according to our estimates, even the most advanced technology, such as NASA's “Hyperwall2” of 128 LCD displays, would not be large enough to clearly display 5,000 tip trees using conventional techniques... Other currently available methods make exploration of phylogenetic trees interactive, enabling the user to expand or magnify parts of the tree that may be too small to see in detail at the scale of the screen... Hyperbolic tree browsers, are a good example of this and they can display large trees, but users do not find them intuitive and we don't see the inclusion of rich metadata as being realistically achievable... Fractals are objects that look similar at different scales and have a dimension that is not a whole number; they often appear in the natural world ,... For example, an effective lung requires a large surface area to be packed into a small a volume—its surface is therefore so convoluted and labyrinthine that at some scales it can be regarded mathematically as having a dimension greater than two (a surface) but less than three (a solid object)... Data is always displayed in both intuitive and raw formats... For example, in the “natural” view of the tree of life (see Figure 3), the balance at each node (indicative of the ratio of species richness in each descendent branch) can be taken in at a glance from the thickness and angles of the branches, but the raw numbers can also be found by zooming in on the nodes... The phylogenetic tree is also the most logical structure within which to explore the breadth of biodiversity on Earth, and so OneZoom could potentially be used to browse existing ecological databases of species such as the Encyclopedia of Life (http://eol.org/)... The logical way to do this is to build around the tree of life visualized using OneZoom; we may yet see the Google Maps equivalent for all life on earth.

Show MeSH