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In theory, the Tree of Life represents all living organisms, along with their parents, grandparents, and so on, all the way up to a single common ancestor.
Each name labels a node, and represents a biological taxon, such as a species or genus. The top node is the root, and those at the bottom are leaves.
The metaphor doesn't always fit. For example, many bacteria can transfer DNA to each other without creating children. But the concept is still helpful for visualisation.
Determining the structure of the tree is an ongoing area of work, but much of it has been traced out using genetic information, statistical analysis, and human inference.
(More info can be found in the tutorial)
Visualising the Tree
Tilo displays the Tree of Life by representing nodes with tiles, and placing tiles within other tiles to show structure.
Within a tile's header:
- The color denotes the number of child tiles. White means zero, green means 1+, orange means 10+, and red means 100+.
- An asterisk indicates uncertain placement. (In the Open Tree of Life, a node can have supporting or conflicting hypothesized trees. The asterisk means no supporting trees, or at least one conflicting tree.)
There are many other methods of visualisation. Examples include iTOL and OneZoom
Settings
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Sweep leaves left
If disabled, an expanded tile's children are simply laid out left to right, top to bottom. This can leave a lot of empty space when large children are near small ones. Moving the unexpanded children (the 'leaves') to the left helps avoid this.
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Sweep into parent
Allows leaves being swept left to be moved beyond the tile's rectangle, into empty space in the parent.
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Trees to use
These are simplified versions of the tree from the Open Tree of Life. (In the original, some nodes have over 10k children, which can be quite slow to render)
- Complex: The least simplified. In short, only keeps nodes with an image or description, with a soft limit of 600 children. (Has about 450k nodes)
- Visual: Only keeps nodes with images, with a soft limit of 300 children. (About 140k)
- Minimal: Created using a rough list of 'well known' taxons, and adding a few more at random. (About 3k)
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Auto-hide ancestors
Normally, if there isn't enough space to expand a tile, an ancestor is hidden, and expansion is tried again. Disabling this can make tile movements more predictable.
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Slider resets
{{touchDevice ? 'Tapping' : 'Clicking'}} on a slider's label resets it to the default value.
Keyboard Shortcuts
- Ctrl-F opens the search bar
- Ctrl-Shift-F toggles the search animation
- Esc closes an open pane, and cancels an active search or auto mode
Unusual Node Names
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Disambiguation Nodes
These have names like 'Iris [2]'. When multiple nodes are found to have the same name, numbers are added to disambiguate.
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Compound Nodes
These are only present in the Complex tree, and have names like '[Homo Sapiens + Homo Heidelbergensis]'. They provide structure for other nodes, and are named after two prominent descendants.
- The tree structure was obtained from the Open Tree of Life, in synthesis release version 13.4, accessed 23/04/2022. The data is licensed under CC0.
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The images and alternative-names data was partly obtained from the
Encyclopedia of Life.
Name data was obtained from
here,
and image metadata from
here,
accessed 24/04/2022.
For the source of a specific tile's image, look in it's info pane. -
The short descriptions, along with most of the remaining images and name data,
were obtained from Wikipedia.
Descriptions were extracted from the Wikipedia dump for 01/05/22, and also obtained from the DBpedia knowledge base for 01/03/22. The page content is available under CC BY-SA 3.0. Images were downloaded during June 2022.
How accurate is the information?
This is hard to answer precisely. The datasets are from large projects with many contributors, trying to track a constantly changing field of knowledge. And the process of merging them was inherently imprecise. Significant effort has been expended to minimise errors, but, inevitably, there are always more of them.
Here's a list of the most common kinds. If you find any major errors, feel free to let me know at terry06890@gmail.com.
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Errors in node linkage
The datasets don't share the same set of node identifiers. So, in order to link nodes from one dataset with another, their plain names were used. This doesn't work when names are ambiguous. For example, 'Proboscidea' might denote a taxon for elephants, but also plants. Most of these were manually corrected, but there are almost certainly more.
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Errors within the datasets
Some issues are internal to the datasets themselves. For example, an image from EOL might display a plant that is in the wrong taxon. Some of these can be quite difficult to recognise, or may require specialised knowledge.
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Errors in descriptions
The short descriptions were extracted using imprecise heuristics. There are many cases of leftover wikitext markup, or cut-off sentences.
Where are the dogs?
Generally, the nodes in the tree don't go below the species level. And dog breeds aren't considered separate species, but as variant descendants of Canis familiaris.
Why is there no tile for the dinosaurs?
Some names don't correspond to a single node, but to multiple nodes from different ancestors. Many dinosaurs are under Sauria, but share that parent with non-dinosaurs, such as turtles.
Shouldn't there be more bacteria?
Many of the bacteria don't have images, and were excluded from the default Visual tree.
Why do some grasses share the same description?
Nodes are largely matched with descriptions using Wikipedia page names. And, if two names redirect to a page that provides a generic description, they will both get the same description. Unfortunately, this can result in two species of grass being described like a third closely-related species.
Why did searching for 'goat' send me to the moths?
When you search for a name, then press enter, the first result is used. Currently, search suggestions are not ordered by well-known the taxons are, so the first result might mean 'Goat Moth' instead of 'Domestic Goat'.
Why do a lot of fish have their heads clipped out?
Cropping images into squares was done semi-automatically, and sometimes this doesn't work well, especially for animals with long bodies. It's not always straightforward to figure out which end is the head, and should be kept in frame.
Why do some snail images just look like documents?
Not all organisms are easy to get live images of. Some of them only have small parts shown, or are in a preserved form, with nearby documentation appearing more prominent.
I'm an arachnophobe. How do I avoid spider images?
Spiders are placed under Araneae, so don't go there. You might want to avoid Chelicerata in general, as it contains pseudo-spiders like harvestmen and tickspiders. Actually, maybe avoid the arthropods altogether, as they include spider crabs. Come to think of it, some of the bird images show them eating spiders, so maybe that won't work either ...
Other Credits
- The UI was largely coded in Typescript, and built using the Vue framework.
- Tree data was processed using Python, and stored using Sqlite
- Styling was enhanced using Tailwind
- The font is called Ubuntu Font
- Icons were obtained from Feathericons and Ionicons
- Images were cropped using Smartcrop