These authors contributed equally.
PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences
Article first published online: 6 NOV 2013
© 2013 The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 11, pages 1011–1017, November 2013
How to Cite
Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., Mooers, A. O. (2013), PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4: 1011–1017. doi: 10.1111/2041-210X.12117
Tweetable abstract: PASTIS for R integrates taxa lacking genetic data into MrBayes version 3.2 input using topology constraints.
- Issue published online: 6 NOV 2013
- Article first published online: 6 NOV 2013
- Accepted manuscript online: 24 SEP 2013 10:46AM EST
- Manuscript Accepted: 17 SEP 2013
- Manuscript Received: 26 JUL 2013
- NSF. Grant Numbers: DBI 0960550, DEB 1026764
- Natural Environment Research Council. Grant Number: NE/G012938/1
- Yale Institute for Biospheric Sciences
- Phylogenetic trees that include all member lineages are necessary for many questions in macroevolution, biogeography and conservation. Currently, producing such trees when genetic data or phenotypic characters for some tips are missing generally involves assigning missing species to the root of their most exclusive clade, essentially grafting them onto existing and static topologies as polytomies.
- We describe an R package, ‘PASTIS’, that enables a two-stage Bayesian method using MrBayes version 3.2 (or higher) to incorporate lineages lacking genetic data at the tree inference stage. The inputs include a consensus topology, a set of taxonomic statements (e.g. placing species in genera and aligning some genera with each other or placing subspecies within species) and user-defined priors on edge lengths and topologies. PASTIS produces input files for execution in MrBayes that will produce a posterior distribution of complete ultrametric trees that captures uncertainty under a homogeneous birth-death prior model of diversification and placement constraints. If the age distribution of a focal node is known (e.g. from fossils), the ultrametric tree distribution can be converted to a set of dated trees. We also provide functions to visualize the placement of missing taxa in the posterior distribution.
- The PASTIS approach is not limited to the level of species and could equally be applied to higher or lower levels of organization (e.g. accounting for all recognized subspecies or populations within a species) given an appropriate choice of priors on branching times.