taxa2cladogram: Convert Simulated Taxon Data into a Cladogram

In paleotree: Paleontological and Phylogenetic Analyses of Evolution

Convert Simulated Taxon Data into a Cladogram

Description

Convert ancestor-descendant relationships of taxa into an 'ideal' unscaled cladogram, where taxa that could share true synapomorphies are arranged into nested clades.

Usage

taxa2cladogram(taxaData, drop.cryptic = FALSE, plot = FALSE)

Arguments

taxaData	A five-column matrix of taxonomic data, as output by fossilRecord2fossilTaxa via simulations produced using simFossilRecord. Previously, this was the default output of the deprecated function simFossilTaxa.
drop.cryptic	Should cryptic species be dropped (except for the first; effectively merging the cryptic species complexes into a single apparent species)? drop.cryptic = FALSE by default, so cryptic species are not dropped by default.
plot	If TRUE result the output with ape::plot.phylo.

Details

This function simulates an ideal cladistic process, where the relationships of a set of morphologically static taxa is resolved into a set of nested hierarchical relationships (a standard cladogram), as much as would be expected given the input relationships among those taxa. taxa2cladogram uses information on the ancestor-descendant relationships of a bunch of taxa and constructs an unscaled cladogram of the hierarchically-nesting relationships among those taxa. There's no actual cladistics going on, this is just a simulation of that process. If there is any chance that a set of taxa could be resolved into a set of nested relationships given their ancestor-descendant relationships, they will be resolved so in the output of taxa2cladogram. No morphological characters are considered, we just assume that if there is a nesting relationship, then it could be resolved as such. This makes it the "ideal" cladogram of a simulated clade.

The result will probably not be fully resolved, as including both ancestor and descendant taxa will generally make it impossible to produce a fully nesting system of relationships. For example, consider a set of three morphologically-static taxa where the first is an ancestor (either direct or indirect, ala Foote, 1996) of both the second and third. If we imagine an ideal cladistic analysis of the morphological characters of those three taxa, this set of taxa will be unable to be broken up into bifurcating-nested relationships and thus result in a polytomy. Any set of ancestor-descendant relationships will have many of these, as some ancestors must have more than one descendant for the clade to diversify, as noted by Wagner and Erwin, 1995.

If there are cryptic taxa present in the output from simFossilRecord, these and any of their morphologically distinguishable descendants are collapsed into a polytomy to simulate the expected pattern of lack of phylogenetic resolution. In addition to this merging, cryptic taxa can be dropped via the argument drop.cryptic, such that only the first 'species' of each cryptic taxon assemblage is listed among the tip taxa (what we would actually expect to obtain, as we would not recognize cryptic taxa to be treated as different OTUs). By default, cryptic taxa are not dropped so that the same number of taxa as in the simulated data is retained.

Value

The resulting phylogeny without branch lengths is output as an object of class phylo.

The tip labels are the rownames from the simulation input; see documentation for simFossilRecord and fossilRecord2fossilTaxa documentation for details.

Author(s)

David W. Bapst

References

Foote, M. 1996 On the Probability of Ancestors in the Fossil Record. Paleobiology 22(2):141-151.

Wagner, P., and D. Erwin. 1995 Phylogenetic patterns as tests of speciation models. New approaches to speciation in the fossil record. Columbia University Press, New York:87-122.

See Also

simFossilRecord, taxa2phylo, fossilRecord2fossilTaxa

Examples

set.seed(444)
record <- simFossilRecord(p = 0.1, q = 0.1, nruns = 1,
	nTotalTaxa = c(30,40), nExtant = 0)
taxa <- fossilRecord2fossilTaxa(record)
#let's use taxa2cladogram to get the 'ideal' cladogram of the taxa
layout(1:2)
cladogram <- taxa2cladogram(taxa,plot = TRUE)
#compare the "real" time-scaled tree of taxon last occurrences (taxa2phylo) 
     #to the 'ideal' cladogram
tree <- taxa2phylo(taxa,plot = TRUE)

#testing with cryptic speciation
recordCrypt <- simFossilRecord(p = 0.1, q = 0.1, prop.cryptic = 0.5, nruns = 1,
	nTotalTaxa = c(30,40), nExtant = 0)
taxaCrypt <- fossilRecord2fossilTaxa(recordCrypt)
layout(1:2)
parOrig <- par(no.readonly = TRUE)
par(mar = c(0,0,0,0))
cladoCrypt1 <- taxa2cladogram(taxaCrypt,drop.cryptic = FALSE)
plot(cladoCrypt1)
cladoCrypt2 <- taxa2cladogram(taxaCrypt,drop.cryptic = TRUE)
plot(cladoCrypt2)

#reset plotting
par(parOrig)
layout(1) 

paleotree documentation built on Aug. 22, 2022, 9:09 a.m.