paleotree (version 2.5)

makePBDBtaxonTree: Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database

Description

This function creates phylogeny-like object of type phylo from the taxonomic information recorded in a taxonomy download from the PBDB for a given group. Two different algorithms are provided, the default being based on parent-child taxon relationships, the other based on the nested Linnean hierarchy.

Usage

makePBDBtaxonTree(data, rank, method = "parentChild", solveMissing = NULL,
  tipSet = "nonParents", cleanTree = TRUE, APIversion = "1.1")

Arguments

data

A table of taxonomic data collected from the Paleobiology Database, using the taxa list option with show=phylo. Should work with versions 1.1-1.2 of the API, with either the 'pbdb' or 'com' vocab. However, as 'accepted_name' is not available in API v1.1

rank

The selected taxon rank; must be one of 'species', 'genus', 'family', 'order', 'class' or 'phylum'.

method

Controls which algorithm is used for calculating the taxon-tree: either method = "parentChild" (the default option) which converts the listed binary parent-child taxon relationships from the input PBDB data, or method = "

solveMissing

Under method = "parentChild", what should makePBDBtaxonTree do about multiple 'floating' parent taxa, listed without their own parent taxon information in the input dataset under data? Each of these i

tipSet

This argument only impacts analyses where the argument method = "parentChild" is also used. This tipSet controls which taxa are selected as tip taxa for the output tree. The default tipSet = "no

cleanTree

By default, the tree is run through a series of post-processing, including having singles collapsed, nodes reordered and being written out as a Newick string and read back in, to ensure functionality with ape functions and ape-derived functions. If FALS

APIversion

Version of the Paleobiology Database API used by makePBDBtaxonTree when solveMissing = "queryPBDB". The current default is "1.1", which is the only option available as of 05/05/2015. In the future, the improved API

Value

• A phylogeny of class 'phylo', where each tip is a taxon of the given 'rank'. See additional details regarding branch lengths can be found in the sub-algorithms used to create the taxon-tree by this function: parentChild2taxonTree and taxonTable2taxonTree. Depending on the method used, either the element $parentChild or $taxonTable is added to the list structure of the output phylogeny object, which was used as input for one of the two algorithms mentioned above. Please note that when applied to output from the taxa option of the API version 1.1, the taxon names returned are the original taxon names as 'accepted_name' is not available in API v1.1, while under API v1.2, the returned taxon names should be the most up-to-date formal names for those taxa. Similar issues also effect the identification of parent taxa, as the accepted name of the parent ID number is only provided in version 1.2 of the API.

Details

This function should not be taken too seriously. Many groups in the Paleobiology Database have out-of-date or very incomplete taxonomic information. This function is meant to help visualize what information is present, and by use of time-scaling functions, allow us to visualize the intersection of temporal and phylogenetic, mainly to look for incongruence due to either incorrect taxonomic placements, erroneous occurrence data or both. Note however that, contrary to common opinion among some paleontologists, taxon-trees may be just as useful for macroevolutionary studies as reconstructed phylogenies (Soul and Friedman, in press.).

References

Soul, L. C., and M. Friedman. In Press. Taxonomy and Phylogeny Can Yield Comparable Results in Comparative Palaeontological Analyses. Systematic Biology (http://sysbio.oxfordjournals.org/content/early/2015/03/23/sysbio.syv015.abstract{Link})

See Also

Two other functions in paleotree are used as sub-algorithms by makePBDBtaxonTree to create the taxon-tree within this function, and users should consult their manual pages for additional details: parentChild2taxonTree and taxonTable2taxonTree Other functions for manipulating PBDB data can be found at taxonSortPBDBocc, occData2timeList, and the example data at graptPBDB.

Examples

easyGetPBDBtaxa<-function(taxon,show=c("phylo","img","app")){
	#let's get some taxonomic data
	taxaData<-read.csv(paste0("http://paleobiodb.org/",
		"data1.1/taxa/list.txt?base_name=",taxon,
		"&rel=all_children&show=",
		paste0(show,collapse=","),"&status=senior"),
		stringsAsFactors=FALSE)
	return(taxaData)
	}

#graptolites
graptData<-easyGetPBDBtaxa("Graptolithina")
graptTree<-makePBDBtaxonTree(graptData,"genus",
	method="parentChild", solveMissing="queryPBDB")
#try Linnean
graptTree<-makePBDBtaxonTree(graptData,"genus",
	method="Linnean")
plot(graptTree,show.tip.label=FALSE,no.margin=TRUE,edge.width=0.35)
nodelabels(graptTree$node.label,adj=c(0,1/2))

#conodonts
conoData<-easyGetPBDBtaxa("Conodonta")
conoTree<-makePBDBtaxonTree(conoData,"genus",
	method="parentChild", solveMissing="queryPBDB")
plot(conoTree,show.tip.label=FALSE,no.margin=TRUE,edge.width=0.35)
nodelabels(conoTree$node.label,adj=c(0,1/2))

#asaphid trilobites
asaData<-easyGetPBDBtaxa("Asaphida")
asaTree<-makePBDBtaxonTree(asaData,"genus",
	method="parentChild", solveMissing="queryPBDB")
plot(asaTree,show.tip.label=FALSE,no.margin=TRUE,edge.width=0.35)
nodelabels(asaTree$node.label,adj=c(0,1/2))

#Ornithischia
ornithData<-easyGetPBDBtaxa("Ornithischia")
ornithTree<-makePBDBtaxonTree(ornithData,"genus",
	method="parentChild", solveMissing="queryPBDB")
#try Linnean
#need to drop repeated taxon first: Hylaeosaurus
ornithData<-ornithData[-(which(ornithData[,"taxon_name"]=="Hylaeosaurus")[1]),]
ornithTree<-makePBDBtaxonTree(ornithData,"genus",
	method="Linnean")
plot(ornithTree,show.tip.label=FALSE,no.margin=TRUE,edge.width=0.35)
nodelabels(ornithTree$node.label,adj=c(0,1/2))

#Rhynchonellida
rynchData<-easyGetPBDBtaxa("Rhynchonellida")
rynchTree<-makePBDBtaxonTree(rynchData,"genus",
	method="parentChild", solveMissing="queryPBDB")
plot(rynchTree,show.tip.label=FALSE,no.margin=TRUE,edge.width=0.35)
nodelabels(rynchTree$node.label,adj=c(0,1/2))

#some of these look pretty messy!

###################################
#let's try time-scaling the graptolite tree

#get some example occurrence and taxonomic data
data(graptPBDB)

#get the taxon tree: Linnean method
graptTree<-makePBDBtaxonTree(graptTaxaPBDB, "genus", method="Linnean")
plot(graptTree,cex=0.4)
nodelabels(graptTree$node.label,cex=0.5)

#get the taxon tree: parentChild method
graptTree<-makePBDBtaxonTree(graptTaxaPBDB, "genus", method="parentChild")
plot(graptTree,cex=0.4)
nodelabels(graptTree$node.label,cex=0.5)

#get time data from occurrences
graptOccGenus<-taxonSortPBDBocc(graptOccPBDB,rank="genus",onlyFormal=FALSE)
graptTimeGenus<-occData2timeList(occList=graptOccGenus)

#let's time-scale the parentChild tree with paleotree
		# use minimum branch length for visualization
		# and nonstoch.bin so we plot maximal ranges
timeTree<-bin_timePaleoPhy(graptTree,timeList=graptTimeGenus,
	nonstoch.bin=TRUE,type="mbl",vartime=3)

#drops a lot of taxa; some of this is due to mispellings, etc
#make pretty plot with library strap
library(strap)
geoscalePhylo(timeTree, ages=timeTree$ranges.used)
nodelabels(timeTree$node.label,cex=0.5)