paleotree (version 3.4.7)

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 taken from the same publication (Bates et al., 2005). Additional character state data are included for three major, binary-state morphological traits.

Format

This dataset is composed of three objects:

retioTree

The consensus cladogram, given as an object of class phylo.

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).

retioChar

A matrix containing binary presence-absence character states for these 22 Retiolitinae genera for three characters which they vary in: the presence of extrathecal threads (note only one taxon lacks this character state), the presence of determinant growth and the secondary loss of a nema via resorption. Note these character do not vary within these genera.

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.

Character data are from an in prep manuscript containing character data for certain major morphological innovations of graptoloids, coded for a large number of genera based on an extensive survey of the published descriptions. The character data presented here is a small subset of the full dataset.

See Also

For more example graptolite datasets, see graptDisparity

Examples

#load data
data(retiolitinae)

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

#Can plot the unscaled cladogram
plot(retioTree)
#Can plot the determinant growth character on the cladogram
tiplabels(pch = 16, col = (retioChar[,2]+1),adj = 0.25)

#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)