The 10kTrees Project


Arnold, C., Matthews, L. J., Nunn, C. L. 2010.
The 10kTrees Website: A New Online Resource for Primate Phylogeny. Evolutionary Anthropology 19:114-118. [PDF]

Project Description:

The 10kTrees Website is a new web resource for conducting phylogenetic comparative studies of primates. The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits and cognitive abilities. Using new phylogeny-based methods, it is now possible to incorporate evolutionary history directly into comparative research.

The true phylogeny of a group of organisms is never known with certainty, and phylogenetic relationships should be continually reassessed as new data become available. This last fact recommends against the continued use of older phylogenies, as better data are now available. Furthermore, when conducting a comparative test, different trees can produce different results during comparative analysis, which argues against conditioning comparative tests on a single hypothesis of evolutionary relationships when that hypothesis is legitimately uncertain. A major development in recent phylogenetics research involves the use of statistical methods that control for phylogenetic uncertainty through application of Bayesian phylogenetics. We follow these recommendations by providing a set of trees that are sampled in proportion to their posterior probabilities using Markov chain Monte Carlo (MCMC). This allows researchers to run analyses on an entire set of trees rather than using a single tree; thus, results are then no longer conditioned on a single tree being correct.

Using the 10kTrees Website, users can download up to at least 10,000 primate phylogenies (with branch lengths) sampled from a Bayesian tree inference. Moreover, we designed the website so that it can be easily updated as new versions of the phylogeny become available. For example, Version 3 of the dataset is already available, which includes over 300 species and additional genes as compared to Version 1 and Version 2. We also expect that the website itself will evolve to provide more tools for primate comparative biology.

What do you do once you have your trees? A number of programs are well suited to analyzing a set of trees in a comparative context. BayesTraits provides a way to investigate correlated evolution and reconstruct ancestral states, and it does so very readily across multiple trees, including through Bayesian approaches. In addition, the PDAP module of Mesquite can be used to calculate independent contrasts and reconstruct ancestral states on a tree-by-tree basis. Mesquite can be used to view the trees, as can the program FigTree. We also formatted the output files so that they can be read by the APE package of R, which opens up a wide array of analysis options.

For more information, see the 10kTrees Website.