SIMMAP: Stochastic character mapping of discrete traits on phylogenies

By Jonathan P. Bollback. BMC Bioinformatics, 2006

885 citations recorded by the source corpus.

BackgroundCharacter mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny.ResultsSIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution.ConclusionStochastic character 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 is accommodated by using MCMC samples from their respective posterior distributions.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/5fcbd7a46a173843ab85487617548e1efbddad77

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. J. Clavel
2. G. Merceron
3. G. Escarguel
4. Liam J. Revell
5. Richard G. FitzJohn
6. Pamela S. Soltis
7. D. Soltis
8. Joseph F. Ryan

In Molecular Biology

1. Pamela S. Soltis
2. D. Soltis
3. Michael J. Moore
4. J. Clavel
5. Richard G. FitzJohn
6. G. Escarguel
7. G. Merceron
8. M. Westerman

In Paleontology

1. D. Soltis
2. J. Clavel
3. Liam J. Revell
4. G. Merceron
5. G. Escarguel
6. Richard G. FitzJohn
7. Wayne P. Maddison
8. M. Westerman

Citations in the corpus

• mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, methodology): “…missing values and various parameter-izations; it allows the user to handle trees in the SIMMAP -like format (Huelsenbeck, Nielsen & Bollback 2003; Bollback 2006) which provide a flexible way to map evolutionary hypothesis on a phylogeny thanks to existing functions from the phytools package…”
• Two new graphical methods for mapping trait evolution on phylogenies (2013, methodology): “Stochastic character mapping can be conducted in R using the phytools function make.simmap (Revell 2012); or with the stand-alone Mac OS program SIMMAP (Bollback 2006).”
• Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits (2018, positive): “We applied stochastic character mapping [53, 54, 55] to reconstruct ancestral character states for selected traits on our topology (Fig.”
• Mesquite: a modular system for evolutionary analysis. Version 2.6 (2009, background): “While there are many interesting calculations that can be derived from these realizations, as done by the program SIMMAP (Bollback, 2006), none of them is yet done by Mesquite.”
• A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes : Marsupialia) based on nuclear DNA sequences (2008, methodology): “3.2 (Bollback 2006) was used to estimate ancestral states for the four grades of dental organisation defined by Sanson (1989): (1) potoroid and basal macropodoid grade; (2) browser grade; (3) intermediate browser/grazer grade; and (4) grazer grade.”
• Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales (2009, methodology): “The ancestral state at different nodes was assessed using a hierarchical Bayesian ancestral state reconstruction method implemented in the ‘‘posterior ancestral states’’ function of SIMMAP (Bollback 2006).”
• Diversitree: comparative phylogenetic analyses of diversification in R (2012, background): “Ancestral state reconstruction (Schluter et al. 1997) and stochastic character mapping (Bollback 2006) are implemented for discrete characters.”
• phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) (2023, methodology): “4.1 Stochastic character mapping Perhaps the most important and widely-used discrete character analysis of phytools is a popular technique referred to as “stochastic character mapping” (Nielsen 2002; Huelsenbeck et al. 2003; Bollback 2006).”