Apply for Tree-for-all: a hackathon to access OpenTree resources
Full call for participation and link to application: http://bit.ly/1ioPPMc
A global “tree of life” will transform biological research in a broad range of disciplines from ecology to bioengineering. To help facilitate that transformation, the OpenTree <http://opentreeoflife.org> project  now provides online access to >4000 published phylogenies, and a newly generated tree covering more than 2.5 million species.
The next step is to build tools to enable the community to use these resources. To meet this aim, OpenTree <http://www.opentreeoflife.org/>, Arbor <http://www.arborworkflows.com/>  and NESCent’s HIP<http://www.evoio.org/wiki/HIP> working groups  are staging a week-long hackathon September 15 to 19 at U. Michigan, Ann Arbor. Participants in this “Tree-for-all” will work in small teams to develop tools that use OpenTree’s web services to extract, annotate, or add data in ways useful to the community. Teams also may focus on testing, expanding and documenting the web services.
If you can imagine using these resources, and you have the skills to work collaboratively to turn those ideas into products (as a coder, or working side-by-side with coders), we invite you to apply for the hackathon. The full call for participation (http://bit.ly/1ioPPMc) provides instructions for how to apply, and how to share your ideas with potential teammates (strongly encouraged prior to applying). Applications are due July 8th. Travel support is provided. Women and underrepresented minorities are especially encouraged to apply.
If you have questions, contact Karen Cranston (email@example.com, @kcranstn, OpenTree), Arlin Stoltzfus (firstname.lastname@example.org, HIP), Julie Allen (email@example.com, HIP), or Luke Harmon (firstname.lastname@example.org, Arbor).
 http://www.evoio.org/wiki/HIP (Hackathons, Interoperability, Phylogenies)
The Crandall lab explores solutions to incomplete phylogenies
The Crandall Lab is in charge of uploading and curating animal studies for the AVAToL-Open Tree project. Chris Owen, postdoctoral researcher, has been leading this portion of the project for the animals beginning in March 2013. To date, the Crandall Lab has contributed over 400 studies and sent requests for over 100 studies for authors to contribute their phylogenies to the Open Tree project.
Similar to the Solitis Lab group, the Crandall Lab success rate for obtaining published phylogenies directly from authors has been rather low. As a result, many animal lineages are currently represented in the Open Tree as taxonomic graphs. One example of a poorly sampled group is the decapods (crabs, crayfish, lobsters, prawns, and shrimp). Dr. Keith Crandall has studied decapods most of his career and his phylogenies generate a well-sampled backbone, but each higher taxon is represented by few species. Many researchers want to use the tree for some downstream analysis that benefits from sampling all species; therefore, at this stage of the project one must ask, “How can I obtain a phylogeny of all species for my favorite group, if the only thing available in Open Tree is a well-resolved backbone, while lower taxonomic ranks are represented primarily by unresolved taxonomic graphs?”.
Recently, a paper was published in the journal Nature that may present a workaround for people who wish to obtain a mostly bifurcating comprehensive phylogeny, although only a bifurcating backbone is available on OpenTree. The published study by Jetz et al. (2013) aimed to use a phylogeny of birds to explore changes in speciation and extinction rate through time, while also mapping all bird diversity, to gain insight into bird evolution. In order to explore these characteristics of bird evolution, the authors first needed a phylogeny of birds that included all species. However, no such phylogeny has ever been published and the most comprehensive bird phylogenies available at the time of the study did not contain all species for each crown clade. Their solution to generating a phylogeny of all birds began first by assigning each avian genus to a crown clade represented in the backbone phylogenies. Next, sequence data for a set of loci for each species in a crown clade was downloaded from public databases and the phylogeny was estimated using Bayesian inference. Since the crown clades of the backbone tree contain taxa also in the newly estimated crown phylogenies, the newly estimated crown phylogenies were sub-sampled with the backbone phylogenies to generate a pseudo-posterior distribution of complete avian phylogenies, which was used to depict the avian phylogeny with all species for downstream analyses.
As the organismal labs continue to track down studies and wait for requested published phylogenies, a method such as this may be a temporary solution to obtain mostly bifurcating phylogenies for lineages not well-represented by source trees. Furthermore, variations of this theme could also be used. For example, one could estimate a single tree for each crown clade and merge each tree with the Open Tree phylogeny that has a well-resolved backbone that has unresolved recent clades, using Open Tree Software, and ultimately create a synthetic tree for your favorite group.
These are a couple of potential methods to generate comprehensive phylogenies using the Open Tree for poorly resolved lineages represented only by taxonomy and we look forward to new ideas other researchers offer once the tree becomes public.
Keith Crandall is a professor and director at the George Washington University Institute of Computational Biology.
Chris Owen is a post-doctoral researcher for the AVAToL grant at George Washington University.
Online publication to follow the three AVAToL projects
PLOS Currents: Tree of Life
Peer-reviewed articles about the Open Tree of Life as well as two related projects, Arbor and Phenomics, will be available on PLOS Currents: Tree of Life. The online publication allows the researchers to document their progress in developing software and other tools.
The three research endeavors were developed during an Ideas Lab last year as part of the National Science Foundation’s (NSF) Assembling, Visualizing, and Analyzing the Tree of Life (AVAToL) program. The Open Tree of Life project strives to produce the first draft of a comprehensive tree of life and provides tools for community enhancement and annotation. The Arbor project is developing comparative methods with utility across large sections and the entire tree of life. Finally, the Phenomics project is developing approaches for exploring and documenting phenotypic diversity across the tree of life.
“It’s meant to be a quick outlet for solid phylogenetic studies”
PLOS Currents websites encourage researchers to share their findings with a minimal delay to their peers. The Tree of Life section is focused on rapid publication of phylogenetic and systematic studies with novel data and/or analyses. According to Keith Crandall, one of the three editors of the journal and an investigator of the Open Tree of Life, “it’s meant to be a quick outlet for solid phylogenetic studies to get them and their data into the public domain.” (more…)
Presentation slides from Evolution 2013 available
Open Tree of Life at meetings
The Open Tree of Life project is one of the many phylogeny projects that are featured during the Evolution 2013 meeting that currently takes place in Snowbird (UT). The presentation slides from Karen Cranston, the principal investigator of Open Tree of Life, are available online (LINK). Presentation slides from other investigators are added here in the upcoming days.
Evolution 2013 is the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). The conference meets jointly with the iEvoBio conference. Open Tree of Life is represented at both events. About 1400 participants are expected to share their research in evolution, systematics, biodiversity, software, and mathematics.
Free webinar: Putting all species in a graph database
Biology + Technology = OTOL
One of the developers of the Open Tree of Life demonstrates Thursday, during a free webinar, how graph databases are used to construct a tree of life. The lecture is organized by Neo Technology, which is the maker of Neo4j, an open-source database that is used for OTOL.
Stephen Smith, an ecology and evolutionary biology professor at the University of Michigan, is going to explain how Neo4j and other digital technologies are assisting in constructing the tree of life. Starting at 10:00 PDT (19:00 CEST), he will also discuss other aspects of the interface of biology with next generation technologies.
“Our project is building the tools with which scientists in the community can continually improve the tree of life as we gather new information. Neo4j allows us to not only store trees in their native graph form, but also allows us to map trees to the same structure, the graph. So in fact, we are facilitating the construction of the graph of life,” says Smith.
Neo4j approached the Open Tree of Life team to present a webinar because it is a project that utilizes the Neo4j graph database to represent the interconnectedness of biological data. The company considers the project a great example of how a graph database can better model the natural world.
The online lecture is intended for a broad audience including beginner computer programmers, advanced hackers, data scientists, natural scientists, and anyone interested in the cross-section of science and technology, especially data modeling. Over 150 people have already registered online.
The registration form: LINK
Update: The video from this webinar is available on vimeo: http://vimeo.com/67870035
Interview with Open Tree of Life investigator
Crandall featured on PeerJ blog
Open Tree of Life investigator Keith Crandall is featured on the blog of PeerJ, which is a peer-reviewed, open access journal on the Internet. Crandall is an Academic Editor for PeerJ and is the director of the Computational Biology Institute at George Washington University. He was the editor for the “living fossil” manuscript that got much news media attention last week. Here’s the link to the interview.
Building an API for the Open Tree of Life database
Do you want an app for this?
The developers of the Open Tree of Life would like to know from the phylogenetic community what kind of information they want to extract from its database when the first draft is released later this year. With those preferences, it is possible to develop an API that gives scientists the opportunity to build their own websites or software packages that use the data.
An API (application programming interface) is a digital tool that allows one website or software program to “talk” to another website to dig up certain pieces of data. For instance, a lot of people use Tweetdeck to navigate the ongoing bombardment of messages in the Twittersphere. In that case, Tweetdeck is connecting to Twitter, through its API, to receive and order the messages according to the preferences of the user.
In case of the Open Tree of Life, an API gives researchers advanced access to the data of about two million species, the phylogenies that have been created to illustrate possible relationships between them, and the underlying data and methods of synthesis. “For example, it will be possible to select smaller trees for specific species or find out how many studies there are for a particular node within the database,” says Karen Cranston, the lead investigator of the project. (more…)
“We need a sense of ownership of phylogenetic trees”
Where are the fungi datasets?
A couple thousand fungi phylogeny studies have been published in the past twelve years. Clark University postdoc researcher Romina Gazis has gone through all of them. Now she is working on a bigger challenge: finding all the trees and datasets that were the foundation of those studies.
Ideally, all scientists who publish a phylogenetic tree would also deposit the datasets they used to create such trees at a publicly available online database. That allow other researchers to synthesize data from different sources to advance the knowledge about relationships between certain species and their evolutionary history.
Unfortunately, most of those datasets are not publicly available. Gazis only found datasets for about a quarter of the two-thousand fungi articles she surveyed. “Around 600 studies had tree files available, but not necessarily complete,” she concluded. “Some scientists deposited one but not all the trees.” (more…)
Tree of Life: Are big changes looming on the horizon?
All species like some gadgets
While movie hero James Bond gets his spy gadgets from his loyal developer Q, almost every other species on Earth has to put a little more effort in armoring themselves. But that does not mean they cannot rely on some good ol’ friends to do so. In fact, the acquisition of genes from two or more species through lateral gene transfer can lead to innovations that at times can be painful—sometimes even deadly—to others.
One of those evolutionary novelties is noticeable for certain types of jellyfish that developed the ability to sting after their ancestors acquired a gene from a bacterium and incorporated that material in their own DNA. This gene transmission helped jellyfish to create an innovative defense tool to fend off other species that could endanger them. The result is quite frightening: more humans get killed by jellyfish than sharks. (more…)
Connecting millions of pieces
Creating the entire tree of life is like completing a jigsaw puzzle with more than two million pieces. And to make it even harder; the illustration of how the solved puzzle would look like is missing.
No one knows precisely how all pieces are related.
This disparity is unmistakably demonstrated by disagreements between evolutionary biologists about how certain species and branches are linked together. Throughout the years they have created a large variety of trees with specific groups of species that contradict each other. For example, one researcher maintains that species A is the closest living relative of species B, but another scientist thinks that species C is actually most closely related to B. (more…)
Is it a plant? Or is it a monkey?
It should not be hard to recognize the differences between furry night monkeys and the bright yellow flowers of golden peas. But they have something peculiar in common that leads to some confusion once in while: their name. Both genera are officially known as Aotus.
There are about two million known species on the planet, so it should not come to a surprise that scientists accidentally have given certain species, or groups of species, similar names. For instance, Proboscidea is considered an order of elephants, but it is also the name for the genus of devil’s claws. Other examples include Myrmecia pyriformis (insect and green algae), Ficus elegans (mollusc and plant), Ormosia nobilis (insect and plant), and Trigonidium grande (orchid and katydid).
Wanted: All your favorite trees
With eleven investigators, the Open Tree of Life project is already a large-scale research endeavor. But that does not mean that they can add all 1.9 million known species to a database by themselves. In fact, they are looking for help.
A lot of help.
The main goal of the project is to merge all existing phylogenetic trees in one overarching tree of life. In the past few months, the researchers have been working on software applications to make it possible to store all known species and, more important, to specify how they are all linked to each other in evolutionary terms.