Electronic Supplementary Material
RSPB-2012-0857 – Reconstructing Past Species Assemblages Reveals the Changing Patterns and Drivers of Extinction Through Time
Lindell Bromham, Robert Lanfear, Phillip Cassey, Gillian Gibb, Marcel Cardillo
Table S3: Measures of phylogenetic clustering of extinct and currently threatened species. For each extinction period, we compared the
observed Mean Pairwise Distance (MPD) and Mean Nearest Taxon Distance (MNTD) value to a null distribution of 999 values, calculated by
randomizing the tip labels of the phylogeny of the assemblage for that time period. For each of these analyses, we generated the posterior
distribution of the test statistic (MPD and MNTD) from the sample of 1000 trees, by calculating the statistic on each tree in the sample using the
Picante package in R. We then asked whether the 95% Highest Posterior Density (95% HPD) of the posterior distribution of the each test statistic
was either entirely below 0.025 (indicating significant clustering) or entirely above 0.975 (indicating significant overdispersion). Results are given
for the set of 1000 trees from the Bayesian posterior, with two different treatments of branch lengths: phylograms have branch lengths estimated
from the molecular data, cladograms have unitary branch lengths. The Highest Posterior Density (HPD) rank of the MPD and MNTD is the
position of the observed value of in a list of 1000 values, generated by randomly shuffling labels at the tips. Figures in bold indicate significant
phylogenetic clustering, where the entire HPD is below 0.025. Where part of the distribution is below 0.025, this may suggest that some trees in the
Bayesian sample show significant clustering, but others do not, indicating that phylogenetic uncertainty precludes a clear statement on the degree of
clustering. Similarly, where part of the distribution spans 0.975, some but not all phylogenies in the sample show evidence of significant
overdispersion.
Phylogeny
Historical
period
Phylogram E1
E2
E3
E4
Cladogram E1
E2
E3
E4
MPD rank HPD
Lower
Upper
0.001
0.473
0.186
0.847
0.69
1
0.04
0.299
0.001
0.010
0.001
0.012
0.001
0.008
0.46
0.962
MNTD rank HPD
Lower
Upper
0.001
0.052
0.001
0.012
0.011
0.308
0.001
0.019
0.001
0.001
0.001
0.001
0.001
0.002
0.017
0.502