Description Usage Format Details Author(s) Source References Examples
This is the Carex dataset used in Hipp (2007). It is a list with three items: a tree of 53 taxa for which chromosome counts are known; a vector of log-transformed mean chromosome counts for all taxa; and a list of eight taxon vectors.
1 |
A list with four items:
ovales.tree
An ultrametric tree in phylo
format with 53 tips
ovales.data
A named numeric vector of log-transformed mean chromosome counts for all 53 taxa
ovales.nodes
A list of eight taxon vectors defining the eight nodes studied.
ovales.bayesTrees
A list of 100 ultrametric trees in phylo
format, subsampled from the MCMC analysis underlying
carex$ovales.bayesTrees
.
Phylogeny (ovales.tree
) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using
penalized likelihood in ape
, and then the tree was pruned down to only those taxa for which chromosome counts were
available. Chromosome counts (ovales.data
) were averaged by population, and the means log-transformed for
analysis. Nodes were selected for analysis based on clade support and number of taxa in the clade.
Andrew L. Hipp <ahipp@mortonarb.org>
Hipp, A.L. (2007) Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). Evolution 61:2175-2194.
Hipp, A.L., P.E. Rothrock, A.A. Reznicek, and J.A. Weber (2006) Phylogeny and classification of Carex section Ovales (Cyperaceae). International Journal of Plant Sciences 167:1029-1048.
Hipp, A.L. (2007) Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). Evolution 61:2175-2194.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | data(carex)
# tree comes in in phylo format, but we need an ouchtree object
trees <- lapply(carex$ovales.bayesTrees[1:2], ape2ouch)
contree <- ape2ouch(carex$ovales.tree)
# for expedience, only tests for changes at up to 2 of the first 4 nodes
# on 2 trees visited in the MCMC phylogenetic analysis:
trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4],
maxNodes = 2)
summary(trialBayesTrees) # summarizes results using summary.hansenBatch
# and displays the results using print.hansenSummary
# same analysis as above, but on a single tree
trialBayesConsensus <- runBatchHansen(contree, carex$ovales.data,
carex$ovales.nodes[1:4], maxNodes = 2)
# compares five different models of character change at node 2
multiModel(carex$ovales.tree, carex$ovales.data, carex$ovales.nodes[[2]])
# simulates the evolution of the chromosome number under the model-averaged values
trialSim <- ouSim(trialBayesConsensus, contree)
# plots the character simulation, with all branches black
plot(trialSim)
# plots the character simulation, with branch colors changing at all 8 nodes
plot(trialSim, colors = paintBranches(carex$ovales.nodes[1:4], contree))
# plots the character simulation, with branch colors changing only at node 2
plot(trialSim, colors = paintBranches(list(carex$ovales.nodes[[2]]), contree))
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