Remove tips by non-random extinction — prune

Applies one extinction event to a tree and removes a fixed fraction of its tips. Tips are lost according to risk, which links extinction to a trait or to any other property of the species, or, without risk, according to a latent liability that evolves on the tree, so that signal sets how clustered the losses are: signal = 0 is random extinction, and with signal = 1 close relatives tend to be lost together, up to whole clades.

Usage

prune_tips(tree, fraction, risk = NULL, signal = 1)

Arguments

tree: A binary, rooted phylo object with branch lengths.
fraction: Fraction of the tips that are lost, a single number greater than 0 and less than 1. round(fraction * Ntip(tree)) tips are removed, and at least two must remain.
risk: NULL, or a numeric vector of non-negative weights named with the tip labels of tree. Tips are drawn without replacement with probability proportional to risk. To link extinction to a trait, use for instance exp(b * trait).
signal: Pagel's lambda of the latent liability, a single number from 0 to 1, used when risk is NULL. The tips with the highest liability are lost.

Value

The remaining tree, with the labels of the lost tips in attribute lost.

Details

Under a homogeneous birth-death process the shape of the reconstructed tree is the same as under pure birth (Gernhard 2008), so extinction changes the topology only if it differs among lineages. The event acts on the tree as it stands, at the present; it does not model extinction that differs among lineages throughout the history of the clade, for which speciation and extinction have to be simulated together (Maddison et al. 2007; Rabosky 2009; Verboom et al. 2020).

Random extinction removes relatively little evolutionary history (Nee & May 1997), but extinction risk is clumped on the tree (Purvis et al. 2000), and its effect depends on how risk relates to speciation rates (Heard & Mooers 2000) and on the shape of the tree (Veron et al. 2017). The same fraction with signal = 0 is therefore the natural control.

Unlike sampling_fraction in sim_tree_shape(), the tree is not rescaled and the tip labels are kept, so that traits stay aligned with the species that remain. If a whole daughter clade of the root is lost, the root of the remaining tree is younger. The separation between gamma and the Colless index holds before the event, not after it, and calibrate_shape() does not apply to the remaining tree.

References

Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253, 769–778. doi:10.1016/j.jtbi.2008.04.005

Heard, S. B., & Mooers, A. O. (2000). Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proceedings of the Royal Society B, 267, 613–620. doi:10.1098/rspb.2000.1046

Maddison, W. P., Midford, P. E., & Otto, S. P. (2007). Estimating a binary character's effect on speciation and extinction. Systematic Biology, 56, 701–710. doi:10.1080/10635150701607033

Nee, S., & May, R. M. (1997). Extinction and the loss of evolutionary history. Science, 278, 692–694. doi:10.1126/science.278.5338.692

Purvis, A., Agapow, P.-M., Gittleman, J. L., & Mace, G. M. (2000). Nonrandom extinction and the loss of evolutionary history. Science, 288, 328–330. doi:10.1126/science.288.5464.328

Rabosky, D. L. (2009). Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils. Systematic Biology, 58, 629–640. doi:10.1093/sysbio/syp069

Verboom, G. A., Boucher, F. C., Ackerly, D. D., Wootton, L. M., & Freyman, W. A. (2020). Species selection regime and phylogenetic tree shape. Systematic Biology, 69, 774–794. doi:10.1093/sysbio/syz076

Veron, S., Davies, T. J., Cadotte, M. W., Clergeau, P., & Pavoine, S. (2017). Predicting loss of evolutionary history: Where are we? Biological Reviews, 92, 271–291. doi:10.1111/brv.12228

Examples

set.seed(1)
tr <- sim_tree_shape(50, beta = -1)
clustered <- prune_tips(tr, 0.4, signal = 1)
random <- prune_tips(tr, 0.4, signal = 0)
attr(clustered, "lost")
#>  [1] "t35" "t28" "t6"  "t47" "t14" "t46" "t29" "t43" "t44" "t42" "t13" "t45"
#> [13] "t48" "t25" "t5"  "t27" "t49" "t24" "t26" "t16"
# extinction linked to a trait
body_size <- setNames(rnorm(50), tr$tip.label)
prune_tips(tr, 0.4, risk = exp(2 * body_size))
#> 
#> Phylogenetic tree with 30 tips and 29 internal nodes.
#> 
#> Tip labels:
#>   t2, t3, t4, t5, t6, t7, ...
#> 
#> Rooted; includes branch length(s).