Convert Simulated Taxon Data into a Cladogram
Convert ancestor-descendant relationships of taxa into an 'ideal' unscaled cladogram, where taxa that could share true synapomorphies are arranged into nested clades.
A five-column matrix of taxonomic data, as output by
Should cryptic species be dropped (except for the first)? Not dropped by default.
Should the result be plotted?
This function simulates an ideal cladistic process, where the relationships of a set of morphologically static taxa is resolved into a set of nested hierarchial 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 hierarcially-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
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 wouldn't recognize cryptic taxa as different OTUs). By
default, cryptic taxa are not dropped so that the same number of taxa as in
the simulated data is retained.
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
fossilRecord2fossilTaxa documentation for details.
David W. Bapst
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.
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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)