Cophylogenetic signal (CS)
To conduct a direct assessment of CS between Angiosperms and primates,
we implemented a Procrustean Approach to Cophylogeny (PACo; Balbuena et
al. 2013). The PACo approach addresses cophylogeny by optimizing the
phylogeny fit using interaction graphs of a given matrix. The
cophylogenetic signal of each individual interaction is given by the
squared residual distance, r, between the two corresponding points in
the phylogenetic trees. PACo thus returns a quantification of the global
fit of the phylogenetic objects based on observed interactions as the
sum of squared residual distances (R = ∑ r2) between
phylogenetic-interaction graphs (Balbuena et al. 2013). As in any
regression analysis, the smaller the residual distances, the better the
fit of the two phylogenies to each other and the more support for a
hypothesis of CS as reflected by the extant interactions (Hutchinson et
al. 2017).
A high CS illustrates a strong congruency of the phylogenies of the two
partner groups.
Procrustean
residuals measure the variation in interactions that is not explained by
the co-phylogenetic structure of the interaction matrix, so that
interactions with small Procrustean residuals contribute the most to CS,
while those deviating more from the expectation derived from the shared
phylogenetic history contribute the less to CS. CS was considered to be
significant when it was smaller than 95% of the values obtained from
1,000 randomizations of the aggregated interaction dataset. Further
details are available in Suplementary Material S5.
To ensure that the cophylogenetic pattern at the continental scale in
the whole Neotropics was not due to distinct geographical subsets of
primate species and plant genera coexisting in different regions, we
split our dataset into the following Neotropical biogeographic forests
(Morrone 2014): Atlantic forest, Amazon forest and Mesoamerican tropical
forest. We then filtered our dataset and obtained, for each region,
specific phylogenies of plants and primates, and their respective seed
dispersal interactions. We then measured the CS and tested for its
significance following the same statistical approach as for the
continent-wide assessment.