Supplementary Information 5. Analyses of the relative role of phylogenetic signal and
phylogenetic depth on the accuracy of PTP in i) a simulated example and ii) an
empirical database
i)
We have 1) evolved 1000 binary traits with a range of phylogenetic signals
on a 100-species pure-birth tree, 2) calculated the phylogenetic depth at
which each trait was conserved following the consenTrait algorithm
developed by Martiny et al. (2013) and 3) applied the PTP algorithm to
reconstruct traits of 30% of removed species. The accuracy of the PTP
method (i.e., correlation between actual and reconstructed trait values)
increased with both the phylogenetic signals and depth, but the former
explained much variance than the latter. This result suggests that
phylogenetic signal is the most important factor determining the accuracy of
PTP but the method performs better for traits conserved deeper in the
phylogeny
(Intercept)
log(phylogenetic signal)
Phylogenetic depth
i)
Estimate Std.Error
0.393
0.04
0.204
0.02
0.285
0.09
t
9.59
12.1
3.1
Variance
p-value explained
<2.00E-16
<2.00E-16 13.0 %
0.9 %
0.002
To verify this conclusion in an empirical database, we have compared the
PTP accuracy for three pairs of traits with the same phylogenetic signal but
conserved at different depths in the Chai et al. (2014) database. To do it, we
have 1) calculated the phylogenetic depth at which the 741 traits are
conserved, 2) randomly pruned 30% of the 12404 species in the tree, and iii)
reconstructed the trait states of pruned species with the highest and the
lowest conservatism depth
Phylogenetic depth at which the trait is conserved
Shallow
Profound
PWY_4722; r=0.899[0.893-0.906] PWY_7206; r=0.943[0.939-0.947]
PWY_6511; r=0.683[0.665-0.699] PWY_7197; r=0.788[0.776-0.800]
PWY_6223; r=0.878[0.871-0.885] VALSYN; r=0.905[0.899-0.911]
In all three cases, trait prediction was significantly better for the trait more deeply
conserved, although the improvement was not very high, as expected for the low
percentage of variance explained by this variable.