paleotree (version 1.8.2)

retiolitinae: Cladogram and Range Data for the Retiolitinae

Description

The majority rule consensus cladogram for 22 genera from the Retiolitinae, a clade of Silurian retiolitids, along with discrete time interval data, all taken from the same publication (Bates et al., 2005).

Usage

data(retiolitinae)

format

This dataset is composed of two objects, retioTree (an ape 'phylo' object containing the consensus cladogram) and retioRanges, a list containing two matrices. The first matrix describes the first and last interval times for 20 Silurian graptolite zones and the second matrix describes when the various genera on the cladogram first and last appear in those graptolite zones. (In other words, retioRanges has the 'timeList' format called by some paleotree functions).

source

Source for cladogram and zonal ranges for genera: Bates, D. E. B., A. Kozlowska, and A. C. Lenz. 2005. Silurian retiolitid graptolites: Morphology and evolution. Acta Palaeontologica Polonica 50(4):705-720. Source for interval dates for graptolite zones: Sadler, P. M., R. A. Cooper, and M. Melchin. 2009. High-resolution, early Paleozoic (Ordovician-Silurian) time scales. Geological Society of America Bulletin 121(5-6):887-906.

Details

Interval dates were taken from Sadler et al. (2009). These zones were not a 1-1 match to those in Bates et al., so it took some merging and splitting by the package author, so buyer beware.

Examples

#load data
data(retiolitinae)

#Can plot discrete time interval diversity curve with retioRanges
taxicDivDisc(retioRanges)

#Can plot the unscaled cladogram
plot(retioTree)

#Use basic time-scaling (terminal branches only go to FADs)
ttree<-bin_timePaleoPhy(tree=retioTree,timeList=retioRanges,type="basic",
	ntrees=1,plot=TRUE)

#Note that this function creates stochastic time-scaled trees...
	#A sample of 1 is not representative!

#phylogenetic diversity curve
phyloDiv(ttree)