jhpoelen edited this page Oct 24, 2014 · 33 revisions

Traitathon wiki

How-to materials

Instructions for installing the aRbor package in R.

Videos describing Arbor Web Interface:

Test cases

We have a number of test cases where we built workflows both in R and Arbor to analyze trait evolution.

Anolis

Anolis lizards are the butterflies of the herp world. They flap their ridiculous dewlaps for reasons that remain mysterious.

Brown anole

In addition to their colorful dewlaps, anoles have Ecomorphs, which are habitat specialists types found in anoles like "trunk-crown," "crown-giant", and "twig." These ecomorphs have evolved repeatedly on islands in the Greater Antilles.

For Anolis, we envision the scenario where a researcher wants to reconstruct the historical patterns of ecomorph evolution in a phylogenetic context. The researcher might come to us with a list of anole species classified by ecomorph. They want to know if each of these ecomorphs have evolved more than once on the phylogenetic tree. We can address this question with two steps: (1) obtain a tree of anoles from open tree, and (2) use ancestral state reconstruction, which calculates relative likelihoods for each ecomorph on every node in the tree given some model of evolution.

Our work on anoles can be seen here.

Heliconia

Heliconia are striking plants that are found in the Neotropics and Pacific Islands. They look bad-ass:

heliconia

As a part of the Arbor project, we have put together a massive database of trait data for Heliconia species. We envision the scenario where a researcher might be interested in processing this database in a phylogenetic context using data from opentree.

You can see a summary of our Heliconia workflows here.

Pocket Gophers and Their Parasitic Chewing Lice

Gophers are, disgustingly, covered in lice. This is how they feel.

gopher

For this test case, we focus on relating two phylogenies to one another, as one might do to study, for example, cospeciation of gophers and their horrible lice. You can see the results here.

Solanaceae

If you're like me, you have encountered Solanaeae many times in your life. For example, when you eat a BLT, or that time your neighbor tried to poison you with mandrake brownies and you thought that you were papa smurf for three days.

a flower

In this test case, we show an example of a dataset with binary data across hundreds of species. You can see our Solanaceae results here.

Tree of sex

The "tree of sex" sounds like a part of Burning Man you might want to avoid, but it's actually a great database of sexual systems across the tree of life.

tree of sex

Here are some walkthrough examples of how to touch these data yourself. Walkthroughs

Lifemapper

Lifemapper is a project to create distribution maps for species in the tree of life.

lifemapper

There is an example workflow for Lifemapper in Arbor described in this video, and more connections that we built between Lifemapper, Arbor, and other services here.

EOL

You probably already know that Encyclopedia of life is awesome, but you might not know about EOL traitbank. It includes 7.5 million records so far of a wide range of species.

fish

An example R script and aRbor workflow are described here.

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