Cophylogenetic signal (CS)
To test for a CS between Angiosperms and lemurs, we implemented a
Procrustean Approach to Cophylogeny (PACo; Balbuena et al. 2013). The
PACo approach assesses phylogenetic congruence by optimizing the
topological fit of two phylogenies using interaction graphs derived from
the matrix of interactions (see Suplementary Material S6 for further
details). It quantifies topological similarity by the extent to which
each internal node and branch-length in a phylogenetic tree maps to a
corresponding position in the other phylogenetic tree (Blasco-Costa et
al. 2021). When co-phylogenetic signal is high, diversification patterns
of associated organisms over evolutionary time tend to be dependent, and
congruence (i.e. topological similarity) between the phylogenies of
interacting clades is expected to occur.
We calculated one CS value for each interaction type in our dataset:
frugivory, folivory, florivory, nectarivory and granivory. PACo returns
a quantification of the global fit based on observed interactions as the
sum of squared residual distances (SS = ∑r 2) between phylogenetic-interaction graphs
(Balbuena et al. 2013). As in any regression analysis, the smaller the
residual distances (Procrustean residuals), the better the fit of the
two phylogenies, and the more support for a hypothesis of CS (Hutchinson
et al. 2017). CS values were considered to be significant whenever it
was smaller than 95% of the values obtained from 1000 randomizations of
each interaction matrix. The randomization approach implemented in PACo
(and other global-fit methods) maintains the topology of the phylogeny
of each group while shuffling the associations (i.e., interactions)
between species to generate random instances of the observed data
(Balbuena et al. 2013, Hutchinson et al. 2017). To ease interpretation
of results, CS was assessed as the Procrustes coefficient of
determination (R2 = 1 – SS ) (Legendre
& Legendre 2012), following Soares et al. (2023). Thus, congruence
expresses the extent to which each node in the phylogenetic tree of
lemurs corresponds to a position in the phylogenetic tree of plants. A
perfect congruence is obtained when R2 = 1
(i.e., SS = 0), and can be interpreted as a strong cospeciation
evidence, which may or may not result from coevolutionary mechanisms.