PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences
Thomas, GH and Hartmann, K and Jetz, W and Joy, JB and Mimoto, A and Mooers, AO, PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences, Methods in Ecology and Evolution, 4, (11) pp. 1011-1017. ISSN 2041-210X (2013) [Refereed Article]
Copyright 2013 The Authors. Methods in Ecology and Evolution Copyright 2013 British Ecological Society
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 theirmost exclusive clade, essentially
grafting them onto existing and static topologies as polytomies.
2. We describe an R package, PASTIS, that enables a two-stage Bayesian method usingMrBayes 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 inMrBayes 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 ofmissing taxa in the posterior distribution.
3. 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.