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
For more information, see the 10kTrees documentation.