Stochastic character mapping: Characters are evolved up a tree according to a model of evolution and subject to matching the observed tip states

Citations(s) (based on web hits only through time [why]):

Reference(s):

Rasmus Nielsen 2002 "Mapping Mutations on Phylogenies" Systematic Biology 51(5): 729 - 739

Criteria ? :

• Bayesian

Questions ? addressed by the method:

• Reconstruct state everywhere on tree (At every point along every branch (i.e., not just at nodes), reconstruct the optimal state, perhaps with uncertainty). Topic area: Reconstruct ancestor(s)
• Reconstruct state at all internal nodes (Reconstruct the optimal state, perhaps with uncertainty, of a particular character at all internal nodes on the tree (note that for likelihood, this category includes methods creating marginal and/or joint estimates)). Topic area: Reconstruct ancestor(s)
• Reconstruct state at one node (Reconstruct the optimal state, perhaps with uncertainty, of a particular character at one node (such as the root node)). Topic area: Reconstruct ancestor(s)
• Correlate states of two characters, same character type (Correlate the state of a single character of one type with the state of a single character of the same type). Topic area: Correlate character states

Character combinations ? addressed by the method:

• DNA strict-None-None
• RNA strict-None-None
• AA strict-None-None
• Binary-None-None
• Multistate unordered-None-None
• DNA strict-DNA strict-None
• DNA strict-RNA strict-None
• DNA strict-AA strict-None
• DNA strict-Binary-None
• DNA strict-Multistate unordered-None
• RNA strict-DNA strict-None
• RNA strict-RNA strict-None
• RNA strict-AA strict-None
• RNA strict-Binary-None
• RNA strict-Multistate unordered-None
• AA strict-DNA strict-None
• AA strict-RNA strict-None
• AA strict-AA strict-None
• AA strict-Binary-None
• AA strict-Multistate unordered-None
• Binary-Binary-None
• Binary-Multistate unordered-None
• Multistate unordered-DNA strict-None
• Multistate unordered-RNA strict-None
• Multistate unordered-AA strict-None
• Multistate unordered-Binary-None
• Multistate unordered-Multistate unordered-None

Software ? implementing the method:

• SIMMAP (SIMMAP is a post tree analysis software package for stochastically mapping characters (mutations) on phylogenies. It uses an \"indirect\" approach as first developed by Nielsen (2002). The name SIMMAP is an acronym for StochastIc Mutational MApping on Phylogenies. SIMMAP has been developed to implement stochastic character mapping that is useful to molecular evolutionists, systematists, and bioinformaticians. Stochastic mutational mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities are accommodated by using Markov chain Monte Carlo (MCMC) samples from their respective posterior distributions. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. )