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Dataset summarizing 1000 posterior samples of BAMM for extant ponerine ants based on an old time-calibration for illustrative purposes

Source: R/datasets_doc.R
Ponerinae_BAMM_object_old_calib.Rd

An object of class "bammdata" containing information of diversification dynamics of extant ponerine ants (Ponerinae subfamily) modeled with BAMM based on an old time-calibration for illustrative purposes. For a BAMM based on the proper time-calibrated phylogeny of ponerine ants, see the Ponerinae_BAMM_object in deepSTRAPP.

Source: Doré, M., Borowiec, M. L., Branstetter, M. G., Camacho, G. P., Fisher, B. L., Longino, J. T., Ward, P. S., Blaimer, B. B. (2025). Evolutionary history of ponerine ants highlights how the timing of dispersal events shapes modern biodiversity. Nature Communications, 16, 8297. https://doi.org/10.1038/s41467-025-63709-3

Usage

data(Ponerinae_BAMM_object_old_calib)

Format

A list with 24 elements.

Details

An object of class "bammdata" containing information of diversification dynamics of extant ponerine ants (Ponerinae subfamily) modeled with BAMM based on an old time-calibration for illustrative purposes.

Phylogeny-related elements used to plot a phylogeny with ape::plot.phylo():

  • $edge Matrix of integers. Defines the tree topology by providing rootward and tipward node ID of each edge.

  • $Nnode Integer. Number of internal nodes.

  • $tip.label Vector of character strings. Labels of all tips.

  • $edge.length Vector of numerical. Length of edges/branches.

BAMM internal elements used for tree exploration:

  • $begin Vector of numerical. Absolute time since root of edge/branch start (rootward).

  • $end Vector of numerical. Absolute time since root of edge/branch end (tipward).

  • $downseq Vector of integers. Order of node visits when using a pre-order tree traversal.

  • $lastvisit ID of the last node visited when starting from the node in the corresponding position in $downseq.

BAMM elements summarizing diversification data:

  • $numberEvents Vector of integer. Number of events/macroevolutionary regimes (k+1) recorded in each posterior configuration. k = number of shifts.

  • $eventData List of data.frames. One per posterior sample. Records shift events and macroevolutionary regimes parameters. 1st line = Background root regime.

  • $eventVectors List of integer vectors. One per posterior sample. Record regime ID per branches.

  • $tipStates List of integer vectors. One per posterior sample. Record regime ID per tips.

  • $tipLambda List of numerical vectors. One per posterior sample. Record speciation rates per tips.

  • $tipMu List of numerical vectors. One per posterior sample. Record extinction rates per tips.

  • $eventBranchSegs List of matrix of numerical. One per posterior sample. Record regime ID per segments of branches.

  • $meanTipLambda Vector of numerical. Mean tip speciation rates across all posterior configurations of tips.

  • $meanTipMu Vector of numerical. Mean tip extinction rates across all posterior configurations of tips.

  • $type Character string. Set the type of data modeled with BAMM. Here, type = "diversification".

Additional elements providing key information for downstream analyses:

  • $expectedNumberOfShifts Integer. The expected number of regime shifts used to set the prior in BAMM.

  • $MSP_tree Object of class phylo. List of 4 elements duplicating information from the Phylogeny-related elements above, except $MSP_tree$edge.length is recording the Marginal Shift Probability of each branch (i.e., the probability of a regime shift to occur along each branch)

  • $MAP_indices Vector of integers. The indices of the Maximum A Posteriori probability (MAP) configurations among the posterior samples.

  • $MAP_BAMM_object. List of 18 elements of class `"bammdata" recording the mean rates and regime shift locations found across the Maximum A Posteriori probability (MAP) configurations. All BAMM elements summarizing diversification data holds a single entry describing this mean diversification history.

  • $MSC_indices Vector of integers. The indices of the Maximum Shift Credibility (MSC) configurations among the posterior samples.

  • $MSC_BAMM_object List of 18 elements of class `"bammdata" recording the mean rates and regime shift locations found across the Maximum Shift Credibility (MSC) configurations. All BAMM elements summarizing diversification data holds a single entry describing this mean diversification history.

References

Doré, M., Borowiec, M. L., Branstetter, M. G., Camacho, G. P., Fisher, B. L., Longino, J. T., Ward, P. S., Blaimer, B. B. (2025). Evolutionary history of ponerine ants highlights how the timing of dispersal events shapes modern biodiversity. Nature Communications, 16, 8297. https://doi.org/10.1038/s41467-025-63709-3

See also

BAMM software website: http://bamm-project.org/