The 10kTrees Website is a new web resource for conducting phylogenetic comparative studies of primates, and has now been extended to mammals in general. 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 10,000 phylogenies (with branch lengths) for different mammalian orders (such as primates, odd-toed and even-toed ungulates, carnivorans, cetaceans, or artiodactyles) sampled from a Bayesian tree inference. Moreover, the trees that we provide are updated regularly. For example, for primates, three versions are already available, for example, and Version 3 includes over 300 species and is based on 17 genes. Furthermore, we updated the website and now provide additional tools, such as a taxonomic translation tool and trees with branches that reflect the time since two species last shared a common ancestor (i.e., dated trees). We expect that the website itself will further evolve to provide more tools for mammalian comparative biology in the future (see the News section of the website).

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 documentation.

We are interested in posting additional mammal phylogenies provided by other research groups.

We require a tree block of 10,000 trees sampled from a Bayesian analysis, as might be conducted using the program MrBayes. We also require a 50% majority-rule consensus tree. Contributors should also identify whether and how burn-in was evaluated, and, optionally, provide the necessary files so that others can evaluate whether the chains have reached stationarity (e.g., the corresponding likelihoods and topologies of the trees during the Bayesian tree inference).

Finally, all the details of the analysis necessary for replicating the study must be provided, including methods used to align sequences, the substitution model, details on sources of data and genes used, an availability matrix for the species and the sequences, the raw sequence data, and the final dataset that was used for tree inference. Please see our online content for primates as an example to follow. The files will be made available zipped via the website.

If you have questions regarding these criteria, how to obtain the required files using the program of your choice, please contact us. We will be happy to help and assist you!