eCite Digital Repository

PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences

Citation

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 Statement

Copyright 2013 The Authors. Methods in Ecology and Evolution Copyright 2013 British Ecological Society

DOI: doi:10.1111/2041-210X.12117

Abstract

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.

Item Details

Item Type:Refereed Article
Keywords:bioinformatics, phylogenetics, reconstruction, software
Research Division:Biological Sciences
Research Group:Evolutionary Biology
Research Field:Phylogeny and Comparative Analysis
Objective Division:Environment
Objective Group:Flora, Fauna and Biodiversity
Objective Field:Antarctic and Sub-Antarctic Flora, Fauna and Biodiversity
Author:Hartmann, K (Dr Klaas Hartmann)
ID Code:89633
Year Published:2013
Web of Science® Times Cited:20
Deposited By:Sustainable Marine Research Collaboration
Deposited On:2014-03-11
Last Modified:2017-11-01
Downloads:0

Repository Staff Only: item control page