map_dollo_changes {Claddis}

Stochastic Character Map For Dollo Character

Description

Given a tree with binary tip states produces a stochastic Dollo character map.

Usage

map_dollo_changes(time_tree, tip_states)

Arguments

time_tree

A tree in phylo format with positive branch lengths and a value for $root.time.

tip_states

A named vector of tip states (must be 0 or 1), where the names match tree$tip.label.

Details

The non-ideal solution from Tarver et al. (2018) to the problem of generating a stochastic character map for a Dollo character (i.e., a single gain of the derived state, 1) with any number of losses (1 -> 0).

The function operates as follows:

1) Establishes the least inclusive clade exhibiting the derived state (1). 2) Assumes a single gain occurred with equal probability along the branch subtending this clade. 3) Prunes the inclusive clade to generate a subtree with a strong root prior of the derived state (1). 4) Calls make.simmap from the phytools package to generate a stochastic character map using a model where only losses are possible. 5) Outputs both the stochastic character map (time spent in each state on each branch) and a matrix of state changes.

NB: As the map is stochastic the answer will be different each time the function is run and multiple replicates are strongly advised in order to characterise this uncertainty.

Value

changes

A matrix of all changes (gains and losses).

stochastic_character_map

The stochastic character map.

Author(s)

Graeme T. Lloyd [e-mail]

References

Tarver, J. E., Taylor, R. S., Puttick, M. N., Lloyd, G. T., Pett, W., Fromm, B., Schirrmeister, B. E., Pisani, D., Peterson, K. J. and Donoghue, P. C. J., 2018. Well-annotated microRNAomes do not evidence pervasive miRNA loss. Genome Biology and Evolution, 6, 1457-1470.

Examples

# Build example ten-tip tree:
time_tree <- ape::read.tree(text = paste0("(A:1,(B:1,((C:1,(D:1,(E:1,F:1):1):1):1,",
  "((G:1,H:1):1,(I:1,J:1):1):1):1):1);"))

# Arbitrarily add a root.time value of 100 Ma:
time_tree$root.time <- 100

# Build example tip state values:
tip_states <- c(A = 0, B = 0, C = 1, D = 1, E = 0, F = 1, G = 1, H = 1, I = 0, J = 1)

# Run map_dollo_changes on data and store output:
out <- map_dollo_changes(time_tree, tip_states)

# View matrix of changes:
out$changes

# View stochastic character map (time spent in each state on each branch):
out$stochastic_character_map