Zero-edge format

Many phylogenetic inference software packages, such as BEAST2 and RevBayes, can handle trees containing fossil samples. In the zero-edge format, tip samples are represented normally in the tree, but sampled ancestors, i.e fossil samples which have sampled descendants, are represented as tips at the end of edges with length 0.

This format is included in FossilSim as the SAtree objects.

Converting to SAtree

SAtree objects can be built from a fossils object and the associated tree. Tips (both extinct and extant) will be labelled with the species they were sampled from followed by an index: the oldest sample for a given species will get index 1 and all other samples will be ordered from oldest to youngest. The SAtree format also includes a field complete which indicates whether the tree should be considered as including all lineages of the process or only sampled lineages. Note that if the tree is complete, the youngest tip of a given extinct species represents the extinction event for this species and not a fossil sample.

t = ape::rtree(6)
f = sim.fossils.poisson(rate = 2, tree = t)

SAt = SAtree.from.fossils(tree = t, fossils = f)
print(SAt$tree)
## 
## Phylogenetic tree with 17 tips and 16 internal nodes.
## 
## Tip labels:
##   t3_1, t5_2, t1_1, t2_4, t4_1, t6_4, ...
## 
## Rooted; includes branch length(s).
print(SAt$fossils)
##    sp edge      hmin      hmax         h tip.label
## 1   2    2 0.8281425 0.8281425 0.8281425      t5_1
## 3   4    4 0.5519460 0.5519460 0.5519460      t2_1
## 2   4    4 0.3695546 0.3695546 0.3695546      t2_2
## 4   4    4 0.2994706 0.2994706 0.2994706      t2_3
## 6   6    6 0.9701078 0.9701078 0.9701078      t6_1
## 5   6    6 0.5516212 0.5516212 0.5516212      t6_2
## 7   6    6 0.4466096 0.4466096 0.4466096      t6_3
## 8   8    8 1.4940072 1.4940072 1.4940072      t8_1
## 10  9    9 0.9822055 0.9822055 0.9822055      t9_1
## 9   9    9 0.9214728 0.9214728 0.9214728      t9_2
## ...
## Fossil record with 11 occurrences representing 6 species
## Fossil record not simulated using taxonomy: all speciation events are assumed to be symmetric
print(SAt$tree$complete)
## [1] TRUE

Other useful functions

Other functions are present in FossilSim to modify trees. prune.fossils will remove all intermediate fossil samples and keep only the first and last occurrences of any species.

SAt_pruned = prune.fossils(tree = SAt$tree)
plot(SAt_pruned)

sampled.tree.from.combined removes all unsampled lineages from the tree, and can optionally apply a sampling probability to extant samples, or keep only a specified list of extant samples.

SAt_sampled = sampled.tree.from.combined(tree = SAt$tree)
plot(SAt_sampled)

These two functions can be applied to any object of type phylo, but are designed to work on trees which include fossil samples.