Assembling, Visualizing, and Analyzing the Tree of Life

Posts tagged “species

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

PLOSPeer-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.


Building an API for the Open Tree of Life database

Do you want an app for this?

Screen Shot 2012-08-29 at 9.22.20 PMThe 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…)


Connecting millions of data points in a graph database

Creating ‘Facebook’ for species

Neo4j screenshotThe Open Tree of Life database is not just a list with about two million species. Information is added about their special characteristics and possible relationships with others as well. “It may become tens or hundreds of million pieces of data when we are all done.”

Stephen Smith, an evolutionary biology professor at the University of Michigan, is working together with the other researchers of the Open Tree of Life project to develop the programs and tools that will be used to construct the full tree of life. Scientists from all over the world can then synthesize all the information in the database.

“We are currently building the back-end of the Open Tree of Life. We need to create software that allows us to put all our information in a graph network, so that we can easily retrieve the information that researchers are specifically looking for.” (more…)


Tree of Life: Are big changes looming on the horizon?

All species like some gadgets

Photo by PublicDomainPictures (Creative Commons Deed CC0)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…)


You don’t want to build a new tree from scratch?

‘Let the computer do the work’

Creating a phylogenetic tree is no easy task. It usually involves a complex synthesis of multiple datasets, but it leads to much satisfaction when all work is done—until new data come in.

Then, the process typically starts all over again: building a new tree from scratch.

Mark Holder, a professor of statistical phylogenetics at Kansas University and one of the investigators of the Open Tree of Life project, maintains that there is a real need for scientists to have access to digital tools that save them from doing quite a few labor-intensive procedures.

“In the past, researchers combined information from different trees and then analyzed the data. But they never made good computer systems that allowed for continuous updating. They would not be able to see how an entire tree would look like when they added more data or another individual tree. In that case, they had to start over.”

(more…)


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