computer science

TimeTree

TimeTree is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand TimeTree rather than just read about it. In short: TimeTree is a free public database developed by S. Blair Hedges and Sudhir Kumar, now at Temple University, for presenting times of divergence in the tree of life.

Key takeaways

TimeTree belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect TimeTree to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of TimeTree from memory before moving on to harder problems.

Reference excerpt

TimeTree is a free public database developed by S. Blair Hedges and Sudhir Kumar, now at Temple University, for presenting times of divergence in the tree of life. The basic concept has been to produce and present a community consensus of the timetree of life from published studies, and allow easy access to that information on the web or mobile device. The database permits searching for average node times between two species or higher taxa, viewing a timeline from the perspective of a taxon, which shows all divergences back to the origin of life, and building a timetree of a chosen taxon or user-submitted group of taxa. TimeTree has been used in public education to conceptualize the evolution of life, such as in high school settings. David Attenborough's Emmy Award-winning film and television program Rise of Animals used Hedges and Kumar's circular timetree of life, generated from the TimeTree database, as a framework for the production. The timetree was brought to life using animated computer-generated imagery in scenes every 10 minutes during the 2-hour movie. The original development of TimeTree, by Hedges and Kumar, dates to the late 1990s, with initial support from NASA Astrobiology Institute. Since then, it has been supported by additional grants from NASA, and by NSF and NIH. The current version (v5) was released in 2022 and contains data from 4,075 studies and 137,306 species.

Features

TimeTree users can search for the names of two species, such as cat and dog, to obtain the mean and median time estimates for their divergence, in millions of years. The results also show all individual time estimates, from each study, next to a geologic timescale, indicating geologic periods. Different aspects of the Earth's environment are shown next to the timescale for comparison, including Earth impacts, solar luminosity, carbon dioxide levels, and oxygen levels. Separately, a table lists the time estimates, downloadable as a spreadsheet, from each study along with references and links to the abstracts of the original articles. Users can download the original study data as Newick-formatted timetrees for further research. In the timeline search, users type the name of a taxon, and all divergences back to the origin of life are show with their taxon names, in a vertical ladder-like figure. Timepanels of Earth's environment also are shown next to the geological timescale, as in all three search options. The third search option, timetree search, involves building a timetree by either specifying a taxon (group) name or uploading a list of species or other taxa. After specifying a group name, the user can choose which taxonomic level they prefer to view. For example, with a family group name, either a species-level or genus-level timetree can be selected. Then, the timetree is show and can be output as a Newick file or image for publication. Times on the tree can be explored by clicking on nodes, and obtaining tables of data pertaining to the node. The database also allows search of timetree articles by author name. The entire open-access book Timetree of Life is presented on the site.

References

External links Official website

Illustrations

Worked examples

Example 1 — a first encounter with TimeTree

Start with the simplest possible case. Write down what TimeTree claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to TimeTree before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about TimeTree ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of TimeTree

In research: TimeTree appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses TimeTree in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: TimeTree is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics software, so understanding it makes those chapters shorter.
In everyday life: Look for TimeTree outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study TimeTree in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what TimeTree means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain TimeTree out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is TimeTree in simple terms?

TimeTree is a free public database developed by S. Blair Hedges and Sudhir Kumar, now at Temple University, for presenting times of divergence in the tree of life.

Why does TimeTree matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study TimeTree?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on TimeTree.