Exporting sampled ancestor trees

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:
##   t1_5, t6_8, t2_10, t4_13, t5_1, t3_1, ...
## 
## Rooted; includes branch length(s).

print(SAt$fossils)

##    sp edge      hmin      hmax         h tip.label
## 1   1    1 2.9081766 2.9081766 2.9081766      t1_2
## 2   1    1 2.8476941 2.8476941 2.8476941      t1_3
## 3   1    1 2.7765851 2.7765851 2.7765851      t1_4
## 5   2    2 0.4558356 0.4558356 0.4558356      t6_6
## 4   2    2 0.4128749 0.4128749 0.4128749      t6_7
## 6   3    3 0.6441739 0.6441739 0.6441739      t2_9
## 8   4    4 0.8311090 0.8311090 0.8311090     t4_11
## 7   4    4 0.7291585 0.7291585 0.7291585     t4_12
## 9   9    9 1.8797139 1.8797139 1.8797139     t9_14
## 10 10   10 1.5028183 1.5028183 1.5028183    t10_16
## ...
## Fossil record with 11 occurrences representing 7 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.